diff --git a/.all-contributorsrc b/.all-contributorsrc deleted file mode 100644 index bc6a9103..00000000 --- a/.all-contributorsrc +++ /dev/null @@ -1,45 +0,0 @@ -{ - "files": [ - "README.md" - ], - "imageSize": 100, - "commit": false, - "contributorsPerLine": 7, - "projectName": "al-folio", - "projectOwner": "alshedivat", - "repoType": "github", - "repoHost": "https://github.com", - "badgeTemplate": "[core_contributors]: https://img.shields.io/badge/core_contributors-<%= contributors.length %>-orange.svg 'Number of core contributors'", - "contributorTemplate": "\">\" width=\"<%= options.imageSize %>px;\" alt=\"\"/>
<%= contributor.name %>", - "skipCi": true, - "contributors": [ - { - "login": "alshedivat", - "name": "Maruan", - "avatar_url": "https://avatars.githubusercontent.com/u/2126561?v=4", - "profile": "http://maruan.alshedivat.com", - "contributions": [ - "design", - "code" - ] - }, - { - "login": "rohandebsarkar", - "name": "Rohan Deb Sarkar", - "avatar_url": "https://avatars.githubusercontent.com/u/50144004?v=4", - "profile": "http://rohandebsarkar.github.io", - "contributions": [ - "code" - ] - }, - { - "login": "pourmand1376", - "name": "Amir Pourmand", - "avatar_url": "https://avatars.githubusercontent.com/u/32064808?v=4", - "profile": "https://amirpourmand.ir", - "contributions": [ - "code" - ] - } - ] -} diff --git a/.dockerignore b/.dockerignore deleted file mode 100644 index 1574b961..00000000 --- a/.dockerignore +++ /dev/null @@ -1,3 +0,0 @@ -_site/ -.git/ -assets/ \ No newline at end of file diff --git a/.editorconfig b/.editorconfig deleted file mode 100644 index 0b008c95..00000000 --- a/.editorconfig +++ /dev/null @@ -1,15 +0,0 @@ -# editorconfig.org - -root = true - -[*] -indent_style = space -indent_size = 2 -end_of_line = lf -charset = utf-8 -trim_trailing_whitespace = true -insert_final_newline = true - -[*.py] -indent_style = space -indent_size = 4 diff --git a/.github/FUNDING.yml b/.github/FUNDING.yml deleted file mode 100644 index c78502f4..00000000 --- a/.github/FUNDING.yml +++ /dev/null @@ -1,12 +0,0 @@ -# These are supported funding model platforms - -github: # Replace with up to 4 GitHub Sponsors-enabled usernames e.g., [user1, user2] -patreon: # Replace with a single Patreon username -open_collective: # Replace with a single Open Collective username -ko_fi: alshedivat -tidelift: # Replace with a single Tidelift platform-name/package-name e.g., npm/babel -community_bridge: # Replace with a single Community Bridge project-name e.g., cloud-foundry -liberapay: # Replace with a single Liberapay username -issuehunt: # Replace with a single IssueHunt username -otechie: # Replace with a single Otechie username -custom: # ['https://www.buymeacoffee.com/TkFxuKo'] diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md deleted file mode 100644 index 511f5851..00000000 --- a/.github/ISSUE_TEMPLATE/bug_report.md +++ /dev/null @@ -1,38 +0,0 @@ ---- -name: Bug report -about: Create a report to help us improve -title: '' -labels: bug -assignees: '' - ---- - -**Acknowledge the following** -- [ ] I carefully read and followed the [Getting Started](https://github.com/alshedivat/al-folio#getting-started) guide. -- [ ] I read through [FAQ](https://github.com/alshedivat/al-folio#faq) and searched through the [past issues](https://github.com/alshedivat/al-folio/issues), none of which addressed my issue. -- [ ] The issue I am raising is a potential bug in al-folio and not just a usage question.
[For usage questions, please post in the [Discussions](https://github.com/alshedivat/al-folio/discussions) instead of raising an issue.] - -**Describe the bug** -A clear and concise description of what the bug is. - -**To Reproduce** -Steps to reproduce the behavior: -1. Go to '...' -2. Click on '....' -3. Scroll down to '....' -4. See error - -**Expected behavior** -A clear and concise description of what you expected to happen. - -**Screenshots** -If applicable, add screenshots to help explain your problem. - -**System (please complete the following information):** - - OS: [e.g. iOS] - - Browser (and its version) [e.g. chrome, safari] - - Jekyll version [e.g. 3.8.7] -- Ruby version [e.g. 2.6.5] - -**Additional context** -Add any other context about the problem here. diff --git a/.github/ISSUE_TEMPLATE/feature_request.md b/.github/ISSUE_TEMPLATE/feature_request.md deleted file mode 100644 index 11fc491e..00000000 --- a/.github/ISSUE_TEMPLATE/feature_request.md +++ /dev/null @@ -1,20 +0,0 @@ ---- -name: Feature request -about: Suggest an idea for this project -title: '' -labels: enhancement -assignees: '' - ---- - -**Is your feature request related to a problem? Please describe.** -A clear and concise description of what the problem is. Ex. I'm always frustrated when [...] - -**Describe the solution you'd like** -A clear and concise description of what you want to happen. - -**Describe alternatives you've considered** -A clear and concise description of any alternative solutions or features you've considered. - -**Additional context** -Add any other context or screenshots about the feature request here. diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md deleted file mode 100644 index a5db9d85..00000000 --- a/.github/pull_request_template.md +++ /dev/null @@ -1,25 +0,0 @@ - - -## OpenReview Submission Thread - - - -## Checklist before requesting a review - - - -- [ ] I am opening a pull request against the `accepted` branch of the `staging` repo. -- [ ] I have de-anonymized my post, added author lists, etc. -- [ ] My post matches the formatting requirements - - [ ] I have a short 2-3 sentence abstract in the `description` field of my front-matter ([example](https://github.com/iclr-blogposts/staging/blob/aa15aa3797b572e7b7bb7c8881fd350d5f76fcbd/_posts/2022-12-01-distill-example.md?plain=1#L4-L5)) - - [ ] I have a table of contents, formatted using the `toc` field of my front-matter ([example](https://github.com/iclr-blogposts/staging/blob/aa15aa3797b572e7b7bb7c8881fd350d5f76fcbd/_posts/2022-12-01-distill-example.md?plain=1#L33-L42)) - - [ ] My bibliography is correctly formatted, using a `.bibtex` file as per the sample post - -## Changes implemented in response to reviewer feedback - -- [ ] Tick this box if you received a conditional accept -- [ ] I have implemented the necessary changes in response to reviewer feedback (if any) - - - -## Any other comments diff --git a/.github/stale.yml b/.github/stale.yml deleted file mode 100644 index 8ec2004d..00000000 --- a/.github/stale.yml +++ /dev/null @@ -1,18 +0,0 @@ -# Number of days of inactivity before an issue becomes stale -daysUntilStale: 60 -# Number of days of inactivity before a stale issue is closed -daysUntilClose: 7 -# Issues with these labels will never be considered stale -exemptLabels: - - pinned - - security - - enhancement -# Label to use when marking an issue as stale -staleLabel: wontfix -# Comment to post when marking an issue as stale. Set to `false` to disable -markComment: > - This issue has been automatically marked as stale because it has not had - recent activity. It will be closed if no further activity occurs. Thank you - for your contributions. -# Comment to post when closing a stale issue. Set to `false` to disable -closeComment: false diff --git a/.github/workflows/deploy-docker-tag.yml b/.github/workflows/deploy-docker-tag.yml deleted file mode 100644 index 3e6b6a3a..00000000 --- a/.github/workflows/deploy-docker-tag.yml +++ /dev/null @@ -1,40 +0,0 @@ -name: Docker Image CI (Upload Tag) - -on: - push: - tags: - - 'v*' - -jobs: - - build: - - runs-on: ubuntu-latest - - steps: - - name: Checkout - uses: actions/checkout@v2 - - name: Buildx - uses: docker/setup-buildx-action@v1 - - - - name: Docker meta - id: meta - uses: docker/metadata-action@v4 - with: - images: amirpourmand/al-folio - - - name: Login - uses: docker/login-action@v1 - with: - username: ${{ secrets.DOCKER_USERNAME }} - password: ${{ secrets.DOCKER_PASSWORD }} - - - name: Build and push - uses: docker/build-push-action@v3 - with: - context: . - push: ${{ github.event_name != 'pull_request' }} - tags: ${{ steps.meta.outputs.tags }} - labels: ${{ steps.meta.outputs.labels }} - diff --git a/.github/workflows/deploy-image.yml b/.github/workflows/deploy-image.yml deleted file mode 100644 index b747dfc1..00000000 --- a/.github/workflows/deploy-image.yml +++ /dev/null @@ -1,31 +0,0 @@ -name: Docker Image CI - -on: - push: - branches: [ master ] - -jobs: - - build: - - runs-on: ubuntu-latest - if: github.repository_owner == 'alshedivat' - - steps: - - name: Checkout - uses: actions/checkout@v2 - - name: Buildx - uses: docker/setup-buildx-action@v1 - - - name: Login - uses: docker/login-action@v1 - with: - username: ${{ secrets.DOCKER_USERNAME }} - password: ${{ secrets.DOCKER_PASSWORD }} - - - name: Build and push - uses: docker/build-push-action@v2 - with: - context: . - push: true - tags: amirpourmand/al-folio diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml deleted file mode 100644 index 0301f080..00000000 --- a/.github/workflows/deploy.yml +++ /dev/null @@ -1,42 +0,0 @@ -name: deploy - -on: - push: - branches: - - master - - main - pull_request: - branches: - - master - - main - -jobs: - deploy: - runs-on: ubuntu-latest - steps: - - name: Checkout code - uses: actions/checkout@v3 - - name: Setup Ruby - uses: ruby/setup-ruby@v1 - with: - ruby-version: '3.0.2' - bundler-cache: true - - name: Install deps - run: | - npm install -g mermaid.cli - - name: Setup deploy options - id: setup - run: | - git config --global user.name "GitHub Action" - git config --global user.email "41898282+github-actions[bot]@users.noreply.github.com" - if [[ ${GITHUB_REF} = refs/pull/*/merge ]]; then # pull request - echo "SRC_BRANCH=${GITHUB_HEAD_REF}" >> $GITHUB_OUTPUT - echo "NO_PUSH=--no-push" >> $GITHUB_OUTPUT - elif [[ ${GITHUB_REF} = refs/heads/* ]]; then # branch, e.g. master, source etc - echo "SRC_BRANCH=${GITHUB_REF#refs/heads/}" >> $GITHUB_OUTPUT - fi - echo "DEPLOY_BRANCH=gh-pages" >> $GITHUB_OUTPUT - - name: Deploy website - run: yes | bash bin/deploy --verbose ${{ steps.setup.outputs.NO_PUSH }} - --src ${{ steps.setup.outputs.SRC_BRANCH }} - --deploy ${{ steps.setup.outputs.DEPLOY_BRANCH }} diff --git a/.github/workflows/jekyll-gh-pages.yml b/.github/workflows/jekyll-gh-pages.yml deleted file mode 100644 index 559bddf5..00000000 --- a/.github/workflows/jekyll-gh-pages.yml +++ /dev/null @@ -1,51 +0,0 @@ -# Sample workflow for building and deploying a Jekyll site to GitHub Pages -name: Deploy Jekyll with GitHub Pages dependencies preinstalled - -on: - # Runs on pushes targeting the default branch - push: - branches: ["main"] - - # Allows you to run this workflow manually from the Actions tab - workflow_dispatch: - -# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages -permissions: - contents: read - pages: write - id-token: write - -# Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued. -# However, do NOT cancel in-progress runs as we want to allow these production deployments to complete. -concurrency: - group: "pages" - cancel-in-progress: false - -jobs: - # Build job - build: - runs-on: ubuntu-latest - steps: - - name: Checkout - uses: actions/checkout@v3 - - name: Setup Pages - uses: actions/configure-pages@v3 - - name: Build with Jekyll - uses: actions/jekyll-build-pages@v1 - with: - source: ./ - destination: ./_site - - name: Upload artifact - uses: actions/upload-pages-artifact@v2 - - # Deployment job - deploy: - environment: - name: github-pages - url: ${{ steps.deployment.outputs.page_url }} - runs-on: ubuntu-latest - needs: build - steps: - - name: Deploy to GitHub Pages - id: deployment - uses: actions/deploy-pages@v2 diff --git a/.nojekyll b/.nojekyll new file mode 100644 index 00000000..e69de29b diff --git a/404.html b/404.html index 1a27dcf9..32fe1264 100644 --- a/404.html +++ b/404.html @@ -1,12 +1 @@ ---- -layout: page -permalink: /404.html -title: "Page not found" -description: "Looks like there has been a mistake. Nothing exists here." -redirect: false ---- - -

This page does not exist. If you got here after having clicked on a link to review a blog post, it means the associated PR has not been merge yet. - It will be merged by the 19th of February 2023. - - Click here to be redirected to the home page.

+ 404: Page not found | 6.S898 Deep Learning Blogs 2023

404: Page not found

Sorry, we’ve misplaced that URL or it’s pointing to something that doesn’t exist. Head back home to try finding it again.

\ No newline at end of file diff --git a/404.md b/404.md deleted file mode 100644 index 8ca926cf..00000000 --- a/404.md +++ /dev/null @@ -1,8 +0,0 @@ ---- -layout: default -title: "404: Page not found" -permalink: 404.html ---- - -# 404: Page not found -Sorry, we've misplaced that URL or it's pointing to something that doesn't exist. [Head back home]({{ site.url }}) to try finding it again. diff --git a/Gemfile b/Gemfile deleted file mode 100644 index 498497f3..00000000 --- a/Gemfile +++ /dev/null @@ -1,25 +0,0 @@ -source 'https://rubygems.org' -group :jekyll_plugins do - gem 'jekyll' - gem 'jekyll-archives' - gem 'jekyll-diagrams' - gem 'jekyll-email-protect' - gem 'jekyll-feed' - gem 'jekyll-imagemagick' - gem 'jekyll-minifier' - gem 'jekyll-paginate-v2' - gem 'jekyll-scholar' - gem 'jekyll-sitemap' - # gem 'jekyll-target-blank' - # gem 'jekyll-twitter-plugin' - gem 'jekyll-redirect-from' - # gem 'jemoji' - # gem 'mini_racer' - # gem 'mini_racer', '>=0.2.1' - gem 'unicode_utils' - gem 'webrick' -end -group :other_plugins do - gem 'httparty' - gem 'feedjira' -end diff --git a/_bibliography/papers.bib b/_bibliography/papers.bib deleted file mode 100644 index 1c707bc5..00000000 --- a/_bibliography/papers.bib +++ /dev/null @@ -1,82 +0,0 @@ ---- ---- - -@string{aps = {American Physical Society,}} - -@book{einstein1956investigations, - bibtex_show={true}, - title={Investigations on the Theory of the Brownian Movement}, - author={Einstein, Albert}, - year={1956}, - publisher={Courier Corporation,}, - preview={brownian-motion.gif} -} - -@article{einstein1950meaning, - abbr={AJP}, - bibtex_show={true}, - title={The meaning of relativity}, - author={Einstein, Albert and Taub, AH}, - journal={American Journal of Physics,}, - volume={18}, - number={6}, - pages={403--404}, - year={1950}, - publisher={American Association of Physics Teachers,} -} - -@article{PhysRev.47.777, - abbr={PhysRev}, - title={Can Quantum-Mechanical Description of Physical Reality Be Considered Complete?}, - author={Einstein, A. and Podolsky, B. and Rosen, N.}, - abstract={In a complete theory there is an element corresponding to each element of reality. A sufficient condition for the reality of a physical quantity is the possibility of predicting it with certainty, without disturbing the system. In quantum mechanics in the case of two physical quantities described by non-commuting operators, the knowledge of one precludes the knowledge of the other. Then either (1) the description of reality given by the wave function in quantum mechanics is not complete or (2) these two quantities cannot have simultaneous reality. Consideration of the problem of making predictions concerning a system on the basis of measurements made on another system that had previously interacted with it leads to the result that if (1) is false then (2) is also false. One is thus led to conclude that the description of reality as given by a wave function is not complete.}, - journal={Phys. Rev.,}, - volume={47}, - issue={10}, - pages={777--780}, - numpages={0}, - year={1935}, - month={May}, - publisher=aps, - doi={10.1103/PhysRev.47.777}, - url={http://link.aps.org/doi/10.1103/PhysRev.47.777}, - html={https://journals.aps.org/pr/abstract/10.1103/PhysRev.47.777}, - pdf={example_pdf.pdf}, - selected={true} -} - -@article{einstein1905molekularkinetischen, - title={{\"U}ber die von der molekularkinetischen Theorie der W{\"a}rme geforderte Bewegung von in ruhenden Fl{\"u}ssigkeiten suspendierten Teilchen}, - author={Einstein, A.}, - journal={Annalen der physik,}, - volume={322}, - number={8}, - pages={549--560}, - year={1905}, - publisher={Wiley Online Library} -} - -@article{einstein1905movement, - abbr={Ann. Phys.}, - title={Un the movement of small particles suspended in statiunary liquids required by the molecular-kinetic theory 0f heat}, - author={Einstein, A.}, - journal={Ann. Phys.,}, - volume={17}, - pages={549--560}, - year={1905} -} - -@article{einstein1905electrodynamics, - title={On the electrodynamics of moving bodies}, - author={Einstein, A.}, - year={1905} -} - -@book{przibram1967letters, - bibtex_show={true}, - title={Letters on wave mechanics}, - author={Einstein, Albert and Schrödinger, Erwin and Planck, Max and Lorentz, Hendrik Antoon and Przibram, Karl}, - year={1967}, - publisher={Vision}, - preview={wave-mechanics.gif} -} diff --git a/_config.yml b/_config.yml deleted file mode 100644 index 1653424d..00000000 --- a/_config.yml +++ /dev/null @@ -1,342 +0,0 @@ -# ----------------------------------------------------------------------------- -# Site settings -# ----------------------------------------------------------------------------- - -title: 6.S898 Deep Learning Blogs 2023 # the website title (if blank, full name will be used instead) -first_name: abc -middle_name: b -last_name: c -email: charlie.gauthier@umontreal.ca -description: > # the ">" symbol means to ignore newlines until "footer_text:" - Staging website for the 2023 ICLR Blogposts track -footer_text: > - Powered by Jekyll with al-folio theme. - Hosted by GitHub Pages. - Photos from Unsplash. -keywords: machine-learning, ml, deep-learning, reinforcement-learning, iclr # add your own keywords or leave empty - -lang: en # the language of your site (for example: en, fr, cn, ru, etc.) -icon: iclr_favicon.ico # the emoji used as the favicon (alternatively, provide image name in /assets/img/) -url: https://deep-learning-mit.github.io # the base hostname & protocol for your site -baseurl: /staging # the subpath of your site, e.g. /blog/ - - -# url: https://iclr-blogposts.github.io # the base hostname & protocol for your site -# baseurl: /staging # the subpath of your site, e.g. /blog/ -last_updated: false # set to true if you want to display last updated in the footer -impressum_path: # set to path to include impressum link in the footer, use the same path as permalink in a page, helps to conform with EU GDPR - -# ----------------------------------------------------------------------------- -# Theme -# ----------------------------------------------------------------------------- - -# code highlighter theme -highlight_theme_light: github # https://github.com/jwarby/jekyll-pygments-themes -highlight_theme_dark: native # https://github.com/jwarby/jekyll-pygments-themes - -# repo color theme -repo_theme_light: default # https://github.com/anuraghazra/github-readme-stats/blob/master/themes/README.md -repo_theme_dark: dark # https://github.com/anuraghazra/github-readme-stats/blob/master/themes/README.md - -# ----------------------------------------------------------------------------- -# RSS Feed -# ----------------------------------------------------------------------------- -# will use title and url fields -# Take a look to https://github.com/jekyll/jekyll-feed for more customization - -rss_icon: true - -# ----------------------------------------------------------------------------- -# Layout -# ----------------------------------------------------------------------------- - -navbar_fixed: true -footer_fixed: true - -# Dimensions -max_width: 1000px - -# TODO: add layout settings (single page vs. multi-page) - -# ----------------------------------------------------------------------------- -# Open Graph & Schema.org -# ----------------------------------------------------------------------------- -# Display links to the page with a preview object on social media. -serve_og_meta: false # Include Open Graph meta tags in the HTML head -serve_schema_org: false # Include Schema.org in the HTML head -og_image: # The site-wide (default for all links) Open Graph preview image - -# ----------------------------------------------------------------------------- -# Social integration -# ----------------------------------------------------------------------------- - -github_username: # your GitHub user name -gitlab_username: # your GitLab user name -twitter_username: # your Twitter handle -linkedin_username: # your LinkedIn user name -scholar_userid: # your Google Scholar ID -semanticscholar_id: # your Semantic Scholar ID -orcid_id: # your ORCID ID -medium_username: # your Medium username -quora_username: # your Quora username -publons_id: # your ID on Publons -research_gate_profile: # your profile on ResearchGate -blogger_url: # your blogger URL -work_url: # work page URL -keybase_username: # your keybase user name -wikidata_id: # your wikidata id -dblp_url: # your DBLP profile url -stackoverflow_id: # your stackoverflow id -kaggle_id: # your kaggle id -lastfm_id: # your lastfm id -spotify_id: # your spotify id -pinterest_id: # your pinterest id -unsplash_id: # your unsplash id -instagram_id: # your instagram id -facebook_id: # your facebook id -discord_id: # your discord id (18-digit unique numerical identifier) - -contact_note: - -# ----------------------------------------------------------------------------- -# Analytics and search engine verification -# ----------------------------------------------------------------------------- - -google_analytics: # your Goole Analytics measurement ID (format: G-XXXXXXXXXX) -panelbear_analytics: # panelbear analytics site ID (format: XXXXXXXXX) - -google_site_verification: # your google-site-verification ID (Google Search Console) -bing_site_verification: # out your bing-site-verification ID (Bing Webmaster) - -# ----------------------------------------------------------------------------- -# Blog -# ----------------------------------------------------------------------------- - -blog_name: 6.S898 Deep Learning Blogs # blog_name will be displayed in your blog page -blog_nav_title: blog # your blog must have a title for it to be displayed in the nav bar -blog_description: Fall 2023 -permalink: /blog/:year/:title/ - -# Pagination -pagination: - enabled: true - -# Comments -disqus_shortname: # put your disqus shortname -# https://help.disqus.com/en/articles/1717111-what-s-a-shortname - -# External sources. -# If you have blog posts published on medium.com or other exteranl sources, -# you can display them in your blog by adding a link to the RSS feed. -external_sources: - -# ----------------------------------------------------------------------------- -# Collections -# ----------------------------------------------------------------------------- - -collections: - news: - defaults: - layout: post - output: true - permalink: /news/:path/ - projects: - output: false - permalink: /projects/:path/ - -news_scrollable: true # adds a vertical scroll bar if there are more than 3 news items -news_limit: 5 # leave blank to include all the news in the `_news` folder - -# ----------------------------------------------------------------------------- -# Jekyll settings -# ----------------------------------------------------------------------------- - -# Markdown and syntax highlight -markdown: kramdown -highlighter: rouge -kramdown: - input: GFM - syntax_highlighter_opts: - css_class: 'highlight' - span: - line_numbers: false - block: - line_numbers: false - start_line: 1 - -# Includes & excludes -include: ['_pages'] -exclude: - - bin - - Gemfile - - Gemfile.lock - - vendor -keep_files: - - CNAME - - .nojekyll - - .git - -# Plug-ins -plugins: - - jekyll-archives - - jekyll-diagrams - - jekyll-email-protect - - jekyll-feed - - jekyll-imagemagick - - jekyll-minifier - - jekyll-paginate-v2 - - jekyll/scholar - - jekyll-sitemap - # - jekyll-target-blank - # - jekyll-twitter-plugin - # - jemoji - -# Sitemap settings -defaults: - - scope: - path: "assets/**/*.*" - values: - sitemap: false - -# ----------------------------------------------------------------------------- -# Jekyll Minifier -# ----------------------------------------------------------------------------- - -jekyll-minifier: - exclude: ['robots.txt'] - uglifier_args: - harmony: true - -# ----------------------------------------------------------------------------- -# Jekyll Archives -# ----------------------------------------------------------------------------- - -jekyll-archives: - enabled: [year, tags, categories] # enables year, tag and category archives (remove if you need to disable one of them). - layouts: - year: archive-year - tag: archive-tag - category: archive-category - permalinks: - year: '/blog/:year/' - tag: '/blog/tag/:name/' - category: '/blog/category/:name/' - - -# ----------------------------------------------------------------------------- -# Jekyll Scholar -# ----------------------------------------------------------------------------- - -scholar: - - last_name: - first_name: - - style: apa - locale: en - - source: /_bibliography/ - bibliography: papers.bib - bibliography_template: bib - # Note: if you have latex math in your bibtex, the latex filter - # preprocessing may conflict with MathJAX if the latter is enabled. - # See https://github.com/alshedivat/al-folio/issues/357. - bibtex_filters: [latex, smallcaps, superscript] - - replace_strings: true - join_strings: true - - details_dir: bibliography - details_layout: bibtex.html - details_link: Details - - query: "@*" - -# Filter out certain bibtex entry keywords used internally from the bib output -filtered_bibtex_keywords: [abbr, abstract, arxiv, bibtex_show, html, pdf, selected, supp, blog, code, poster, slides, website, preview] - -# Maximum number of authors to be shown for each publication (more authors are visible on click) -max_author_limit: 3 # leave blank to always show all authors -more_authors_animation_delay: 10 # more authors are revealed on click using animation; smaller delay means faster animation - - -# ----------------------------------------------------------------------------- -# Responsive WebP Images -# ----------------------------------------------------------------------------- - -imagemagick: - enabled: true # enables responsive images for your site (recomended, see https://github.com/alshedivat/al-folio/issues/537) - widths: - - 480 - - 800 - - 1400 - input_directories: - - assets/img/ - input_formats: - - ".jpg" - - ".jpeg" - - ".png" - - ".tiff" - output_formats: - webp: "-resize 800x" - -# ----------------------------------------------------------------------------- -# Jekyll Diagrams -# ----------------------------------------------------------------------------- - -jekyll-diagrams: - # configuration, see https://github.com/zhustec/jekyll-diagrams. - # feel free to comment out this section if not using jekyll diagrams. - - -# ----------------------------------------------------------------------------- -# Optional Features -# ----------------------------------------------------------------------------- - -enable_google_analytics: false # enables google analytics -enable_panelbear_analytics: false # enables panelbear analytics -enable_google_verification: false # enables google site verification -enable_bing_verification: false # enables bing site verification -enable_masonry: true # enables automatic project cards arangement -enable_math: true # enables math typesetting (uses MathJax) -enable_tooltips: false # enables automatic tooltip links generated - # for each section titles on pages and posts -enable_darkmode: true # enables switching between light/dark modes -enable_navbar_social: false # enables displaying social links in the - # navbar on the about page -enable_project_categories: true # enables categorization of projects into - # multiple categories -enable_medium_zoom: true # enables image zoom feature (as on medium.com) - - -# ----------------------------------------------------------------------------- -# Library versions -# ----------------------------------------------------------------------------- - -academicons: - version: "1.9.1" - integrity: "sha256-i1+4qU2G2860dGGIOJscdC30s9beBXjFfzjWLjBRsBg=" -bootstrap: - version: "4.6.1" - integrity: - css: "sha256-DF7Zhf293AJxJNTmh5zhoYYIMs2oXitRfBjY+9L//AY=" - js: "sha256-fgLAgv7fyCGopR/gBNq2iW3ZKIdqIcyshnUULC4vex8=" -fontawesome: - version: "5.15.4" - integrity: "sha256-mUZM63G8m73Mcidfrv5E+Y61y7a12O5mW4ezU3bxqW4=" -jquery: - version: "3.6.0" - integrity: "sha256-/xUj+3OJU5yExlq6GSYGSHk7tPXikynS7ogEvDej/m4=" -mathjax: - version: "3.2.0" -masonry: - version: "4.2.2" - integrity: "sha256-Nn1q/fx0H7SNLZMQ5Hw5JLaTRZp0yILA/FRexe19VdI=" -mdb: - version: "4.20.0" - integrity: - css: "sha256-jpjYvU3G3N6nrrBwXJoVEYI/0zw8htfFnhT9ljN3JJw=" - js: "sha256-NdbiivsvWt7VYCt6hYNT3h/th9vSTL4EDWeGs5SN3DA=" -medium_zoom: - version: "1.0.6" - integrity: "sha256-EdPgYcPk/IIrw7FYeuJQexva49pVRZNmt3LculEr7zM=" diff --git a/_data/coauthors.yml b/_data/coauthors.yml deleted file mode 100644 index 8ed52124..00000000 --- a/_data/coauthors.yml +++ /dev/null @@ -1,34 +0,0 @@ -"Adams": - - firstname: ["Edwin", "E.", "E. P.", "Edwin Plimpton"] - url: https://en.wikipedia.org/wiki/Edwin_Plimpton_Adams - -"Podolsky": - - firstname: ["Boris", "B.", "B. Y.", "Boris Yakovlevich"] - url: https://en.wikipedia.org/wiki/Boris_Podolsky - -"Rosen": - - firstname: ["Nathan", "N."] - url: https://en.wikipedia.org/wiki/Nathan_Rosen - -"Bach": - - firstname: ["Johann Sebastian", "J. S."] - url: https://en.wikipedia.org/wiki/Johann_Sebastian_Bach - - - firstname: ["Carl Philipp Emanuel", "C. P. E."] - url: https://en.wikipedia.org/wiki/Carl_Philipp_Emanuel_Bach - -"Przibram": - - firstname: ["Karl"] - url: https://link.springer.com/article/10.1007/s00016-019-00242-z - -"Schrödinger": - - firstname: ["Erwin"] - url: https://en.wikipedia.org/wiki/Erwin_Schr%C3%B6dinger - -"Lorentz": - - firstname: ["Hendrik Antoon"] - url: https://en.wikipedia.org/wiki/Hendrik_Lorentz - -"Planck": - - firstname: ["Max"] - url: https://en.wikipedia.org/wiki/Max_Planck diff --git a/_data/cv.yml b/_data/cv.yml deleted file mode 100644 index 5b115724..00000000 --- a/_data/cv.yml +++ /dev/null @@ -1,97 +0,0 @@ -- title: General Information - type: map - contents: - - name: Full Name - value: Albert Einstein - - name: Date of Birth - value: 14th March 1879 - - name: Languages - value: English, German - -- title: Education - type: time_table - contents: - - title: PhD - institution: University of Zurich, Zurich, Switzerland - year: 1905 - description: - - Description 1. - - Description 2. - - title: Description 3. - contents: - - Sub-description 1. - - Sub-description 2. - - title: Federal teaching diploma - institution: Eidgenössische Technische Hochschule, Zurich, Switzerland - year: 1900 - description: - - Description 1. - - Description 2. - -- title: Experience - type: time_table - contents: - - title: Professor of Theoretical Physics - institution: Institute for Advanced Study, Princeton University - year: 1933 - 1955 - description: - - Description 1. - - Description 2. - - title: Description 3. - contents: - - Sub-description 1. - - Sub-description 2. - - title: Visiting Professor - institution: California Institute of Technology, Pasadena, California, US - year: 1933 - description: - - Description 1. - - Description 2. - - - title: Director - institution: Kaiser Wilhelm Institute for Physics, Berlin, Germany. - year: 1917-1933 - - - title: Professor of Theoretical Physics - institution: Karl-Ferdinand University, Prague, Czechoslovakia - year: 1911 - 1917 - description: - - - title: Associate Professor of Theoretical Physics - institution: University of Zurich, Zurich, Switzerland - year: 1909 - 1911 - -- title: Open Source Projects - type: time_table - contents: - - title: al-folio - year: 2015-now - description: A beautiful, simple, clean, and responsive Jekyll theme for academics. - -- title: Honors and Awards - type: time_table - contents: - - year: 1921 - items: - - Nobel Prize in Physics - - Matteucci Medal - - year: 2029 - items: - - Max Planck Medal - -- title: Academic Interests - type: nested_list - contents: - - title: Topic 1. - items: - - Description 1. - - Description 2. - - title: Topic 2. - items: - - Description 1. - - Description 2. - -- title: Other Interests - type: list - contents: - - Hobbies: Hobby 1, Hobby 2, etc. diff --git a/_data/repositories.yml b/_data/repositories.yml deleted file mode 100644 index 5205c9f6..00000000 --- a/_data/repositories.yml +++ /dev/null @@ -1,12 +0,0 @@ -github_users: - - torvalds - - alshedivat - -github_repos: - - alshedivat/al-folio - - twbs/bootstrap - - jekyll/jekyll - - jquery/jquery - - FortAwesome/Font-Awesome - - jpswalsh/academicons - - mathjax/MathJax diff --git a/_data/venues.yml b/_data/venues.yml deleted file mode 100644 index 6c16ad5d..00000000 --- a/_data/venues.yml +++ /dev/null @@ -1,6 +0,0 @@ -"AJP": - url: https://aapt.scitation.org/journal/ajp - color: "#00369f" - -"PhysRev": - url: https://journals.aps.org/ diff --git a/_includes/cv/list.html b/_includes/cv/list.html deleted file mode 100644 index 75625859..00000000 --- a/_includes/cv/list.html +++ /dev/null @@ -1,5 +0,0 @@ - \ No newline at end of file diff --git a/_includes/cv/map.html b/_includes/cv/map.html deleted file mode 100644 index e0d1983e..00000000 --- a/_includes/cv/map.html +++ /dev/null @@ -1,8 +0,0 @@ - - {% for content in entry.contents %} - - - - - {% endfor %} -
{{ content.name }}{{ content.value }}
\ No newline at end of file diff --git a/_includes/cv/nested_list.html b/_includes/cv/nested_list.html deleted file mode 100644 index 4778aca0..00000000 --- a/_includes/cv/nested_list.html +++ /dev/null @@ -1,14 +0,0 @@ - \ No newline at end of file diff --git a/_includes/cv/time_table.html b/_includes/cv/time_table.html deleted file mode 100644 index 123b9d09..00000000 --- a/_includes/cv/time_table.html +++ /dev/null @@ -1,59 +0,0 @@ - \ No newline at end of file diff --git a/_includes/figure.html b/_includes/figure.html deleted file mode 100644 index e67e8043..00000000 --- a/_includes/figure.html +++ /dev/null @@ -1,36 +0,0 @@ -{%- assign img_path = include.path | remove: ".jpg" | remove: ".jpeg" | remove: ".png" | remove: ".tiff" -%} - -
- - - {% if site.imagemagick.enabled %} - {% for i in site.imagemagick.widths -%} - - {% endfor -%} - {% endif %} - - - - - - - {%- if include.caption -%}
{{ include.caption }}
{%- endif %} - -
diff --git a/_includes/footer.html b/_includes/footer.html deleted file mode 100644 index acc4688f..00000000 --- a/_includes/footer.html +++ /dev/null @@ -1,25 +0,0 @@ - {% if site.footer_fixed %} - - {%- else -%} - - {%- endif %} \ No newline at end of file diff --git a/_includes/head.html b/_includes/head.html deleted file mode 100644 index 3796eb38..00000000 --- a/_includes/head.html +++ /dev/null @@ -1,31 +0,0 @@ - - {% include metadata.html %} - - - - - - - - - - - - - - - {% if site.icon.size < 3 %} - - {% elsif site.icon != blank %} - - {% endif %} - - - - - {% if site.enable_darkmode %} - - - - - {% endif %} diff --git a/_includes/header.html b/_includes/header.html deleted file mode 100644 index f72668e5..00000000 --- a/_includes/header.html +++ /dev/null @@ -1,137 +0,0 @@ - -
- - - -
\ No newline at end of file diff --git a/_includes/metadata.html b/_includes/metadata.html deleted file mode 100644 index af3813a8..00000000 --- a/_includes/metadata.html +++ /dev/null @@ -1,196 +0,0 @@ -{% if site.enable_google_verification or site.enable_bing_verification %} - - {% if site.enable_google_verification -%} - - {%- endif -%} - {% if site.enable_bing_verification -%} - - {%- endif -%} -{%- endif %} - - - - - - - {%- if site.title == "blank" -%} - {%- capture title -%}{{ site.first_name }} {{ site.middle_name }} {{ site.last_name }}{%- endcapture -%} - {%- else -%} - {%- capture title -%}{{ site.title }}{%- endcapture -%} - {%- endif -%} - {% if page.url == '/blog/index.html' %} - {{ site.blog_nav_title }} | {{ title }} - {%- elsif page.title != "blank" and page.url != "/" -%} - {%- if page.title == nil or page.title == "" -%} - {{ page.date | date: "%Y" }} | {{ title }} - {%- else -%} - {{ page.title }} | {{ title }} - {%- endif -%} - {%- else -%} - {{ title }} - {%- endif -%} - - - -{%- if page.keywords or site.keywords %} - -{%- endif %} - -{%- if site.serve_og_meta %} - - - - - - - - {% if page.og_image or site.og_image -%} - - {%- endif %} - - - - - - - {% if page.og_image or site.og_image -%} - - {%- endif %} - {% if site.twitter_username -%} - - - {%- endif %} -{%- endif %} - -{%- if site.serve_schema_org %} - - - {%- comment -%} Social links generator for "sameAs schema" {%- endcomment %} - {% assign sameaslinks = "" | split: "," %} - {%- if site.orcid_id -%} - {%- capture link -%}https://orcid.org/{{ site.orcid_id }}{%- endcapture -%} - {%- assign sameaslinks = sameaslinks | push: link -%} - {%- endif -%} - {%- if site.scholar_userid -%} - {%- capture link -%}https://scholar.google.com/citations?user={{ site.scholar_userid }}{%- endcapture -%} - {%- assign sameaslinks = sameaslinks | push: link -%} - {%- endif -%} - {%- if site.semanticscholar_id -%} - {%- capture link -%}https://www.semanticscholar.org/author/{{ site.semanticscholar_id }}{%- endcapture -%} - {%- assign sameaslinks = sameaslinks | push: link -%} - {%- endif -%} - {%- if site.publons_id -%} - {%- capture link -%}https://publons.com/a/{{ site.publons_id }}/{%- endcapture -%} - {%- assign sameaslinks = sameaslinks | push: link -%} - {%- endif -%} - {%- if site.research_gate_profile -%} - {%- capture link -%}https://www.researchgate.net/profile/{{site.research_gate_profile}}{%- endcapture -%} - {%- assign sameaslinks = sameaslinks | push: link -%} - {%- endif -%} - {%- if site.github_username -%} - {%- capture link -%}https://github.com/{{ site.github_username }}{%- endcapture -%} - {%- assign sameaslinks = sameaslinks | push: link -%} - {%- endif -%} - {%- if site.linkedin_username -%} - {%- capture link -%}https://www.linkedin.com/in/{{ site.linkedin_username }}{%- endcapture -%} - {%- assign sameaslinks = sameaslinks | push: link -%} - {%- endif -%} - {%- if site.twitter_username -%} - {%- capture link -%}https://twitter.com/{{ site.twitter_username }}{%- endcapture -%} - {%- assign sameaslinks = sameaslinks | push: link -%} - {%- endif -%} - {%- if site.medium_username -%} - {%- capture link -%}https://medium.com/@{{ site.medium_username }}{%- endcapture -%} - {%- assign sameaslinks = sameaslinks | push: link -%} - {%- endif -%} - {%- if site.quora_username -%} - {%- capture link -%}https://www.quora.com/profile/{{ site.quora_username }}{%- endcapture -%} - {%- assign sameaslinks = sameaslinks | push: link -%} - {%- endif -%} - {%- if site.blogger_url -%} - {%- capture link -%}{{ site.blogger_url }}{%- endcapture -%} - {%- assign sameaslinks = sameaslinks | push: link -%} - {%- endif -%} - {%- if site.work_url -%} - {%- capture link -%}{{ site.work_url }}{%- endcapture -%} - {%- assign sameaslinks = sameaslinks | push: link -%} - {%- endif -%} - {%- if site.wikidata_id -%} - {%- capture link -%}https://www.wikidata.org/wiki/{{ site.wikidata_id }}{%- endcapture -%} - {%- assign sameaslinks = sameaslinks | push: link -%} - {%- endif -%} - {%- if site.strava_userid -%} - {%- capture link -%}https://www.strava.com/athletes/{{ site.strava_userid }}{%- endcapture -%} - {%- assign sameaslinks = sameaslinks | push: link -%} - {%- endif -%} - {%- if site.keybase_username -%} - {%- capture link -%}https://keybase.io/{{ site.keybase_username }}{%- endcapture -%} - {%- assign sameaslinks = sameaslinks | push: link -%} - {%- endif -%} - {%- if site.gitlab_username -%} - {%- capture link -%}https://gitlab.com/{{ site.gitlab_username }}{%- endcapture -%} - {%- assign sameaslinks = sameaslinks | push: link -%} - {%- endif -%} - {%- if site.dblp_url -%} - {%- capture link -%}{{ site.dblp_url }}{%- endcapture -%} - {%- assign sameaslinks = sameaslinks | push: link -%} - {%- endif -%} - {%- if site.stackoverflow_id -%} - {%- capture link -%}https://stackoverflow.com/users/{{ site.stackoverflow_id }}{%- endcapture -%} - {%- assign sameaslinks = sameaslinks | push: link -%} - {%- endif -%} - {%- if site.kaggle_id -%} - {%- capture link -%}https://www.kaggle.com/{{ site.kaggle_id }}{%- endcapture -%} - {%- assign sameaslinks = sameaslinks | push: link -%} - {%- endif -%} - {%- if site.lastfm_id -%} - {%- capture link -%}https://www.last.fm/user/{{ site.lastfm_id }}{%- endcapture -%} - {%- assign sameaslinks = sameaslinks | push: link -%} - {%- endif -%} - {%- if site.spotify_id -%} - {%- capture link -%}https://open.spotify.com/user/{{ site.spotify_id }}{%- endcapture -%} - {%- assign sameaslinks = sameaslinks | push: link -%} - {%- endif -%} - {%- if site.pinterest_id -%} - {%- capture link -%}https://www.pinterest.com/{{ site.pinterest_id }}{%- endcapture -%} - {%- assign sameaslinks = sameaslinks | push: link -%} - {%- endif -%} - {%- if site.unsplash_id -%} - {%- capture link -%}https://unsplash.com/@{{ site.unsplash_id }}{%- endcapture -%} - {%- assign sameaslinks = sameaslinks | push: link -%} - {%- endif -%} - {%- if site.instagram_id -%} - {%- capture link -%}https://instagram.com/{{ site.instagram_id }}{%- endcapture -%} - {%- assign sameaslinks = sameaslinks | push: link -%} - {%- endif -%} - {%- if site.facebook_id -%} - {%- capture link -%}https://facebook.com/{{ site.facebook_id }}{%- endcapture -%} - {%- assign sameaslinks = sameaslinks | push: link -%} - {%- endif -%} - {%- if site.discord_id -%} - {%- capture link -%}https://discord.com/users/{{ site.discord_id }}{%- endcapture -%} - {%- assign sameaslinks = sameaslinks | push: link -%} - {%- endif -%} - {%- if sameaslinks != blank -%} - {%- assign sameaslinks = sameaslinks | split: "" -%} - {%- endif -%} - - -{%- endif %} diff --git a/_includes/news.html b/_includes/news.html deleted file mode 100644 index 307e532d..00000000 --- a/_includes/news.html +++ /dev/null @@ -1,31 +0,0 @@ - -
-

news

- {% if site.news != blank -%} - {%- assign news_size = site.news | size -%} -
3 %}style="max-height: 10vw"{% endif %}> - - {%- assign news = site.news | reverse -%} - {% if site.news_limit %} - {% assign news_limit = site.news_limit %} - {% else %} - {% assign news_limit = news_size %} - {% endif %} - {% for item in news limit: news_limit %} - - - - - {%- endfor %} -
{{ item.date | date: "%b %-d, %Y" }} - {% if item.inline -%} - {{ item.content | remove: '

' | remove: '

' | emojify }} - {%- else -%} - {{ item.title }} - {%- endif %} -
-
- {%- else -%} -

No news so far...

- {%- endif %} -
diff --git a/_includes/pagination.html b/_includes/pagination.html deleted file mode 100644 index 4b8d27e3..00000000 --- a/_includes/pagination.html +++ /dev/null @@ -1,17 +0,0 @@ -{%- if paginator.total_pages > 1 -%} - -{%- endif -%} diff --git a/_includes/people.html b/_includes/people.html deleted file mode 100644 index b5a79f1f..00000000 --- a/_includes/people.html +++ /dev/null @@ -1,16 +0,0 @@ - -
-
- -
- {%- include figure.html - path=include.img - alt=include.name - -%} -
-
{{- include.name -}}
-

{{- include.affiliation -}}

-
-
- -
diff --git a/_includes/people_horizontal.html b/_includes/people_horizontal.html deleted file mode 100644 index 957bc768..00000000 --- a/_includes/people_horizontal.html +++ /dev/null @@ -1,17 +0,0 @@ -
- -
-
-
- {% include figure.html path=include.img alt=include.name %} -
-
-
-
{{ include.name }}
-

{{ include.affiliation }}

-
-
-
-
- -
diff --git a/_includes/projects.html b/_includes/projects.html deleted file mode 100644 index 503146e2..00000000 --- a/_includes/projects.html +++ /dev/null @@ -1,36 +0,0 @@ - -
-
- {% if project.redirect -%} - - {%- else -%} - - {%- endif %} -
- {%- if project.img %} - {%- include figure.html - path=project.img - alt="project thumbnail" -%} - {%- endif %} -
-

{{ project.title }}

-

{{ project.description }}

-
- {%- if project.github -%} -
-
- -
- {%- if project.github_stars -%} - - - - - {%- endif %} -
- {%- endif %} -
-
-
- -
\ No newline at end of file diff --git a/_includes/projects_horizontal.html b/_includes/projects_horizontal.html deleted file mode 100644 index ddf74058..00000000 --- a/_includes/projects_horizontal.html +++ /dev/null @@ -1,40 +0,0 @@ -
- {%- if project.redirect -%} - - {%- else -%} - - {%- endif -%} -
-
- {%- if project.img -%} -
- {% include figure.html path=project.img alt="project thumbnail" %} -
-
- {%- else -%} -
- {%- endif -%} -
-

{{ project.title }}

-

{{ project.description }}

-
- {%- if project.github -%} -
-
- -
- {%- if project.github_stars -%} - - - - - {%- endif -%} -
- {%- endif -%} -
-
-
-
-
- -
diff --git a/_includes/repository/repo.html b/_includes/repository/repo.html deleted file mode 100644 index 6344b860..00000000 --- a/_includes/repository/repo.html +++ /dev/null @@ -1,14 +0,0 @@ -{% assign repo_url = include.repository | split: '/' %} - -{% if site.data.repositories.github_users contains repo_url.first %} - {% assign show_owner = false %} -{% else %} - {% assign show_owner = true %} -{% endif %} - -
- - {{ include.repository }} - {{ include.repository }} - -
diff --git a/_includes/repository/repo_user.html b/_includes/repository/repo_user.html deleted file mode 100644 index ae06a058..00000000 --- a/_includes/repository/repo_user.html +++ /dev/null @@ -1,6 +0,0 @@ -
- - {{ include.username }} - {{ include.username }} - -
diff --git a/_includes/scripts/analytics.html b/_includes/scripts/analytics.html deleted file mode 100644 index db2aeef9..00000000 --- a/_includes/scripts/analytics.html +++ /dev/null @@ -1,18 +0,0 @@ -{%- if site.enable_google_analytics -%} - - - -{%- endif -%} -{%- if site.enable_panelbear_analytics -%} - - - -{%- endif -%} diff --git a/_includes/scripts/bootstrap.html b/_includes/scripts/bootstrap.html deleted file mode 100644 index 1c213650..00000000 --- a/_includes/scripts/bootstrap.html +++ /dev/null @@ -1,3 +0,0 @@ - - - diff --git a/_includes/scripts/jquery.html b/_includes/scripts/jquery.html deleted file mode 100644 index f84a2f22..00000000 --- a/_includes/scripts/jquery.html +++ /dev/null @@ -1,2 +0,0 @@ - - diff --git a/_includes/scripts/masonry.html b/_includes/scripts/masonry.html deleted file mode 100644 index 804389d3..00000000 --- a/_includes/scripts/masonry.html +++ /dev/null @@ -1,6 +0,0 @@ - {%- if site.enable_masonry -%} - - - - - {%- endif -%} diff --git a/_includes/scripts/mathjax.html b/_includes/scripts/mathjax.html deleted file mode 100644 index c55ec056..00000000 --- a/_includes/scripts/mathjax.html +++ /dev/null @@ -1,12 +0,0 @@ - {%- if site.enable_math -%} - - - - - {%- endif %} diff --git a/_includes/scripts/misc.html b/_includes/scripts/misc.html deleted file mode 100644 index 08ba49f0..00000000 --- a/_includes/scripts/misc.html +++ /dev/null @@ -1,14 +0,0 @@ -{% if site.enable_tooltips %} - - -{%- endif %} -{%- if site.enable_medium_zoom %} - - - -{%- endif -%} - - - diff --git a/_includes/selected_papers.html b/_includes/selected_papers.html deleted file mode 100644 index 61457dbc..00000000 --- a/_includes/selected_papers.html +++ /dev/null @@ -1,5 +0,0 @@ - -
-

selected publications

- {% bibliography -f papers -q @*[selected=true]* %} -
diff --git a/_includes/social.html b/_includes/social.html deleted file mode 100644 index 8c7a079c..00000000 --- a/_includes/social.html +++ /dev/null @@ -1,84 +0,0 @@ - {%- if site.email -%} - - {% endif %} - {%- if site.orcid_id -%} - - {% endif %} - {%- if site.scholar_userid -%} - - {% endif %} - {%- if site.semanticscholar_id -%} - - {% endif %} - {%- if site.publons_id -%} - - {% endif %} - {%- if site.research_gate_profile -%} - - {% endif %} - {%- if site.github_username -%} - - {% endif %} - {%- if site.linkedin_username -%} - - {% endif %} - {%- if site.twitter_username -%} - - {% endif %} - {%- if site.medium_username -%} - - {% endif %} - {%- if site.quora_username -%} - - {% endif %} - {%- if site.blogger_url -%} - - {% endif %} - {%- if site.work_url -%} - - {% endif %} - {%- if site.wikidata_id -%} - - {% endif %} - {%- if site.strava_userid -%} - - {% endif %} - {%- if site.keybase_username -%} - - {% endif %} - {%- if site.gitlab_username -%} - - {% endif %} - {%- if site.dblp_url -%} - - {% endif %} - {%- if site.stackoverflow_id -%} - - {% endif %} - {%- if site.kaggle_id -%} - - {% endif %} - {%- if site.lastfm_id -%} - - {% endif %} - {%- if site.spotify_id -%} - - {% endif %} - {%- if site.pinterest_id -%} - - {% endif %} - {%- if site.unsplash_id -%} - - {% endif %} - {%- if site.instagram_id -%} - - {% endif %} - {%- if site.facebook_id -%} - - {% endif %} - {%- if site.discord_id -%} - - {% endif %} - {%- if site.rss_icon -%} - - {% endif %} diff --git a/_layouts/about.html b/_layouts/about.html deleted file mode 100644 index d3628377..00000000 --- a/_layouts/about.html +++ /dev/null @@ -1,66 +0,0 @@ ---- -layout: default ---- - - -
-
- -

{{ page.subtitle }}

-
- -
- {% if page.profile -%} -
- {%- if page.profile.image %} - {%- assign profile_image_path = page.profile.image | prepend: 'assets/img/' -%} - - {% if page.profile.image_circular %} - {%- assign profile_image_class = "img-fluid z-depth-1 rounded-circle" -%} - {% else %} - {%- assign profile_image_class = "img-fluid z-depth-1 rounded" -%} - {% endif %} - - {% include figure.html - path=profile_image_path - class=profile_image_class - alt=page.profile.image -%} - {% endif -%} - {%- if page.profile.address %} -
- {{ page.profile.address }} -
- {%- endif %} -
- {%- endif %} - -
- {{ content }} -
- - {% if page.news -%} - - {%- include news.html %} - {%- endif %} - {% if page.selected_papers -%} - - {%- include selected_papers.html %} - {%- endif %} - {%- if page.social %} - - - {%- endif %} -
- -
diff --git a/_layouts/archive-category.html b/_layouts/archive-category.html deleted file mode 100644 index 79aad74f..00000000 --- a/_layouts/archive-category.html +++ /dev/null @@ -1,27 +0,0 @@ ---- -layout: default ---- - -
- -
-

{{ page.title }}

-

an archive of posts in this category

-
- -
-
- - {% for post in page.posts %} - - - - - {% endfor %} -
{{ post.date | date: "%b %-d, %Y" }} - {{ post.title }} -
-
-
- -
diff --git a/_layouts/archive-tag.html b/_layouts/archive-tag.html deleted file mode 100644 index 66abaebb..00000000 --- a/_layouts/archive-tag.html +++ /dev/null @@ -1,27 +0,0 @@ ---- -layout: default ---- - -
- -
-

{{ page.title }}

-

an archive of posts with this tag

-
- -
-
- - {% for post in page.posts %} - - - - - {% endfor %} -
{{ post.date | date: "%b %-d, %Y" }} - {{ post.title }} -
-
-
- -
diff --git a/_layouts/archive-year.html b/_layouts/archive-year.html deleted file mode 100644 index 8af1d29b..00000000 --- a/_layouts/archive-year.html +++ /dev/null @@ -1,27 +0,0 @@ ---- -layout: default ---- - -
- -
-

{{ page.date | date: "%Y" }}

-

an archive of posts from this year

-
- -
-
- - {% for post in page.posts %} - - - - - {% endfor %} -
{{ post.date | date: "%b %-d, %Y" }} - {{ post.title }} -
-
-
- -
diff --git a/_layouts/bib.html b/_layouts/bib.html deleted file mode 100644 index eb6520a2..00000000 --- a/_layouts/bib.html +++ /dev/null @@ -1,196 +0,0 @@ ---- ---- - -
-
- {%- if entry.preview -%} - {% if entry.preview contains '://' -%} - - {%- else -%} - - {%- endif -%} - {%- elsif entry.abbr -%} - {%- if site.data.venues[entry.abbr] -%} - {%- assign venue_style = nil -%} - {%- if site.data.venues[entry.abbr].color != blank -%} - {%- assign venue_style = site.data.venues[entry.abbr].color | prepend: 'style="background-color:' | append: '"' -%} - {%- endif -%} - {{entry.abbr}} - {%- else -%} - {{entry.abbr}} - {%- endif -%} - {%- endif -%} -
- - -
- {% if entry.type == "thesis" -%} - {{reference}} - {%- else %} - -
{{entry.title}}
- -
- {% assign author_array_size = entry.author_array | size %} - - {% assign author_array_limit = author_array_size %} - {%- if site.max_author_limit and author_array_size > site.max_author_limit %} - {% assign author_array_limit = site.max_author_limit %} - {% endif %} - - {%- for author in entry.author_array limit: author_array_limit -%} - {%- assign author_is_self = false -%} - {%- assign author_last_name = author.last | remove: "¶" | remove: "&" | remove: "*" | remove: "†" | remove: "^" -%} - {%- if site.scholar.last_name contains author_last_name -%} - {%- if site.scholar.first_name contains author.first -%} - {%- assign author_is_self = true -%} - {%- endif -%} - {%- endif -%} - {%- assign coauthor_url = nil -%} - {%- if site.data.coauthors[author_last_name] -%} - {%- for coauthor in site.data.coauthors[author_last_name] -%} - {%- if coauthor.firstname contains author.first -%} - {%- assign coauthor_url = coauthor.url -%} - {%- break -%} - {%- endif -%} - {%- endfor -%} - {%- endif -%} - - {%- if forloop.length > 1 -%} - {%- if forloop.first == false -%}, {%- endif -%} - {%- if forloop.last and author_array_limit == author_array_size -%}and {%- endif -%} - {%- endif -%} - {%- if author_is_self -%} - {{author.first}} {{author.last}} - {%- else -%} - {%- if coauthor_url -%} - {{author.first}} {{author.last}} - {%- else -%} - {{author.first}} {{author.last}} - {%- endif -%} - {%- endif -%} - {%- endfor -%} - {%- assign more_authors = author_array_size | minus: author_array_limit -%} - - {%- assign more_authors_hide = more_authors | append: " more author" -%} - {%- if more_authors > 0 -%} - {%- if more_authors > 1 -%} - {%- assign more_authors_hide = more_authors_hide | append: "s" -%} - {%- endif -%} - {%- assign more_authors_show = '' -%} - {%- for author in entry.author_array offset: author_array_limit -%} - {%- assign more_authors_show = more_authors_show | append: author.first | append: " " | append: author.last -%} - {%- unless forloop.last -%} - {%- assign more_authors_show = more_authors_show | append: ", " -%} - {%- endunless -%} - {%- endfor -%} - , and - {{more_authors_hide}} - {%- endif -%} - -
- - - {% assign proceedings = "inproceedings, incollection" | split: ','%} - {% if entry.type == "article" -%} - {%- capture entrytype -%}{{entry.journal}}{%- endcapture -%} - {%- elsif proceedings contains entry.type -%} - {%- capture entrytype -%}In {{entry.booktitle}} {%- endcapture -%} - {%- else -%} - {%- capture entrytype -%}{%- endcapture -%} - {%- endif -%} - {%- if entry.month -%} - {%- capture entrymonth -%}{{ " " }}{{ entry.month | capitalize }}{%- endcapture -%} - {%- endif -%} - {%- if entry.year -%} - {%- capture entryyear -%}{{ " " }}{{entry.year}}{%- endcapture -%} - {%- endif -%} - {%- capture periodical -%}{{ entrytype }}{{ entrymonth }}{{ entryyear }}{%- endcapture -%} -
- {{ periodical | strip }} -
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- {%- if entry.abstract %} - Abs - {%- endif %} - {%- if entry.arxiv %} - arXiv - {%- endif %} - {%- if entry.bibtex_show %} - Bib - {%- endif %} - {%- if entry.html %} - HTML - {%- endif %} - {%- if entry.pdf %} - {% if entry.pdf contains '://' -%} - PDF - {%- else -%} - PDF - {%- endif %} - {%- endif %} - {%- if entry.supp %} - {% if entry.supp contains '://' -%} - Supp - {%- else -%} - Supp - {%- endif %} - {%- endif %} - {%- if entry.blog %} - Blog - {%- endif %} - {%- if entry.code %} - Code - {%- endif %} - {%- if entry.poster %} - {% if entry.poster contains '://' -%} - Poster - {%- else -%} - Poster - {%- endif %} - {%- endif %} - {%- if entry.slides %} - {% if entry.slides contains '://' -%} - Slides - {%- else -%} - Slides - {%- endif %} - {%- endif %} - {%- if entry.website %} - Website - {%- endif %} -
- - {% if entry.abstract -%} - - - {%- endif -%} - - {% if entry.bibtex_show -%} - - - {%- endif %} -
-
diff --git a/_layouts/cv.html b/_layouts/cv.html deleted file mode 100644 index bb3d85af..00000000 --- a/_layouts/cv.html +++ /dev/null @@ -1,35 +0,0 @@ ---- -layout: default ---- - -
- -
-

{{ page.title }} {% if page.cv_pdf %}{% endif %}

-

{{ page.description }}

-
- -
-
- {% for entry in site.data.cv %} -
-

{{ entry.title }}

-
- {% if entry.type == "list" %} - {% include cv/list.html %} - {% elsif entry.type == "map" %} - {% include cv/map.html %} - {% elsif entry.type == "nested_list" %} - {% include cv/nested_list.html %} - {% elsif entry.type == "time_table" %} - {% include cv/time_table.html %} - {% else %} - {{ entry.contents }} - {% endif %} -
-
- {% endfor %} -
-
- -
diff --git a/_layouts/default.html b/_layouts/default.html deleted file mode 100644 index 1001a5b5..00000000 --- a/_layouts/default.html +++ /dev/null @@ -1,36 +0,0 @@ - - - - - - {%- if page.redirect -%} - - {%- endif -%} - {% include head.html %} - - - - - - - {%- include header.html %} - -
- - -
- {{ content }} -
- - - - - - {% include scripts/jquery.html %} - {% include scripts/bootstrap.html %} - {% include scripts/masonry.html %} - {% include scripts/misc.html %} - {% include scripts/mathjax.html %} - {% include scripts/analytics.html %} - - diff --git a/_layouts/distill.html b/_layouts/distill.html deleted file mode 100644 index c3a8d48c..00000000 --- a/_layouts/distill.html +++ /dev/null @@ -1,114 +0,0 @@ - - - - - {%- include head.html %} - - {% include scripts/jquery.html %} - {% include scripts/mathjax.html %} - - - - - {% if page._styles %} - - - {%- endif %} - - - - - - - - - - {%- include header.html %} - - -
- - -

{{ page.title }}

-

{{ page.description }}

- - - - - - {% if page.toc -%} - - - - {%- endif %} - - {{ content }} - - - - - - - -
- - - - - - {% include scripts/bootstrap.html %} - {% include scripts/analytics.html %} - - diff --git a/_layouts/none.html b/_layouts/none.html deleted file mode 100644 index b92f6522..00000000 --- a/_layouts/none.html +++ /dev/null @@ -1 +0,0 @@ -{{content}} diff --git a/_layouts/page.html b/_layouts/page.html deleted file mode 100644 index 5a0c4080..00000000 --- a/_layouts/page.html +++ /dev/null @@ -1,16 +0,0 @@ ---- -layout: default ---- - -
- - - -
- {{ content }} -
- -
diff --git a/_layouts/post.html b/_layouts/post.html deleted file mode 100644 index 8061c407..00000000 --- a/_layouts/post.html +++ /dev/null @@ -1,71 +0,0 @@ ---- -layout: default ---- - -{%- assign year = page.date | date: "%Y" -%} -{%- assign tags = page.tags | join: "" -%} -{%- assign categories = page.categories | join: "" -%} - -{% if page._styles %} - - -{% endif %} - -
- -
-

{{ page.title }}

-

{{ page.date | date: "%B %-d, %Y" }}{%- if page.author -%} • {{ page.author }}{%- endif -%}{%- if page.meta -%} • {{ page.meta }}{%- endif -%}

-

- {{ year }} - {%- if tags != "" %} -   ·   - {% for tag in page.tags -%} - - {{ tag }}   - {% endfor -%} - {% endif %} - - {%- if categories != "" %} -   ·   - {% for category in page.categories -%} - - {{ category }}   - {% endfor -%} - {% endif %} - -

-
- -
- {{ content }} -
- - {%- if site.disqus_shortname and page.comments -%} -
- - - {%- endif %} - - - -
diff --git a/_news/announcement_1.md b/_news/announcement_1.md deleted file mode 100644 index 98e5af5c..00000000 --- a/_news/announcement_1.md +++ /dev/null @@ -1,7 +0,0 @@ ---- -layout: post -date: 2015-10-22 15:59:00-0400 -inline: true ---- - -A simple inline announcement. diff --git a/_news/announcement_2.md b/_news/announcement_2.md deleted file mode 100644 index dbd4b4d4..00000000 --- a/_news/announcement_2.md +++ /dev/null @@ -1,31 +0,0 @@ ---- -layout: post -title: A long announcement with details -date: 2015-11-07 16:11:00-0400 -inline: false ---- - -Announcements and news can be much longer than just quick inline posts. In fact, they can have all the features available for the standard blog posts. See below. - -*** - -Jean shorts raw denim Vice normcore, art party High Life PBR skateboard stumptown vinyl kitsch. Four loko meh 8-bit, tousled banh mi tilde forage Schlitz dreamcatcher twee 3 wolf moon. Chambray asymmetrical paleo salvia, sartorial umami four loko master cleanse drinking vinegar brunch. Pinterest DIY authentic Schlitz, hoodie Intelligentsia butcher trust fund brunch shabby chic Kickstarter forage flexitarian. Direct trade cold-pressed meggings stumptown plaid, pop-up taxidermy. Hoodie XOXO fingerstache scenester Echo Park. Plaid ugh Wes Anderson, freegan pug selvage fanny pack leggings pickled food truck DIY irony Banksy. - -#### Hipster list - - -Hoodie Thundercats retro, tote bag 8-bit Godard craft beer gastropub. Truffaut Tumblr taxidermy, raw denim Kickstarter sartorial dreamcatcher. Quinoa chambray slow-carb salvia readymade, bicycle rights 90's yr typewriter selfies letterpress cardigan vegan. - -*** - -Pug heirloom High Life vinyl swag, single-origin coffee four dollar toast taxidermy reprehenderit fap distillery master cleanse locavore. Est anim sapiente leggings Brooklyn ea. Thundercats locavore excepteur veniam eiusmod. Raw denim Truffaut Schlitz, migas sapiente Portland VHS twee Bushwick Marfa typewriter retro id keytar. - -> We do not grow absolutely, chronologically. We grow sometimes in one dimension, and not in another, unevenly. We grow partially. We are relative. We are mature in one realm, childish in another. -> —Anais Nin - -Fap aliqua qui, scenester pug Echo Park polaroid irony shabby chic ex cardigan church-key Odd Future accusamus. Blog stumptown sartorial squid, gastropub duis aesthetic Truffaut vero. Pinterest tilde twee, odio mumblecore jean shorts lumbersexual. diff --git a/_news/announcement_3.md b/_news/announcement_3.md deleted file mode 100644 index d9072191..00000000 --- a/_news/announcement_3.md +++ /dev/null @@ -1,7 +0,0 @@ ---- -layout: post -date: 2016-01-15 07:59:00-0400 -inline: true ---- - -A simple inline announcement with Markdown emoji! :sparkles: :smile: diff --git a/_pages/dropdown.md b/_pages/dropdown.md deleted file mode 100644 index a5c07b2d..00000000 --- a/_pages/dropdown.md +++ /dev/null @@ -1,13 +0,0 @@ ---- -layout: page -title: past iterations -nav: true -nav_order: 99 -dropdown: true -children: - # - title: 2023 - # permalink: /about/ - # - title: divider - - title: 2022 - permalink: https://iclr-blog-track.github.io/home/ ---- \ No newline at end of file diff --git a/_pages/dropdown/index.html b/_pages/dropdown/index.html new file mode 100644 index 00000000..7136bcc4 --- /dev/null +++ b/_pages/dropdown/index.html @@ -0,0 +1 @@ + past iterations | 6.S898 Deep Learning Blogs 2023
\ No newline at end of file diff --git a/_plugins/external-posts.rb b/_plugins/external-posts.rb deleted file mode 100644 index e4fd5eb6..00000000 --- a/_plugins/external-posts.rb +++ /dev/null @@ -1,36 +0,0 @@ -require 'feedjira' -require 'httparty' -require 'jekyll' - -module ExternalPosts - class ExternalPostsGenerator < Jekyll::Generator - safe true - priority :high - - def generate(site) - if site.config['external_sources'] != nil - site.config['external_sources'].each do |src| - p "Fetching external posts from #{src['name']}:" - xml = HTTParty.get(src['rss_url']).body - feed = Feedjira.parse(xml) - feed.entries.each do |e| - p "...fetching #{e.url}" - slug = e.title.downcase.strip.gsub(' ', '-').gsub(/[^\w-]/, '') - path = site.in_source_dir("_posts/#{slug}.md") - doc = Jekyll::Document.new( - path, { :site => site, :collection => site.collections['posts'] } - ) - doc.data['external_source'] = src['name']; - doc.data['feed_content'] = e.content; - doc.data['title'] = "#{e.title}"; - doc.data['description'] = e.summary; - doc.data['date'] = e.published; - doc.data['redirect'] = e.url; - site.collections['posts'].docs << doc - end - end - end - end - end - -end diff --git a/_plugins/hideCustomBibtex.rb b/_plugins/hideCustomBibtex.rb deleted file mode 100644 index 4a852fde..00000000 --- a/_plugins/hideCustomBibtex.rb +++ /dev/null @@ -1,15 +0,0 @@ - module Jekyll - module HideCustomBibtex - def hideCustomBibtex(input) - keywords = @context.registers[:site].config['filtered_bibtex_keywords'] - - keywords.each do |keyword| - input = input.gsub(/^.*#{keyword}.*$\n/, '') - end - - return input - end - end -end - -Liquid::Template.register_filter(Jekyll::HideCustomBibtex) diff --git a/_posts/2022-12-01-diffusion-is-all-you-need.md b/_posts/2022-12-01-diffusion-is-all-you-need.md deleted file mode 100644 index e93531ab..00000000 --- a/_posts/2022-12-01-diffusion-is-all-you-need.md +++ /dev/null @@ -1,243 +0,0 @@ ---- -layout: distill -title: A Match Made in Drug Discovery - Marrying Geometric and Diffusion Models -description: The chemical space of molecular candidates is vast, and within this space, interesting and powerful drugs are waiting to be found. The use of machine learning has shown to be an effective method to speed up the process of discovering novel compounds, especially the use of (deep) generative models. The recent surge in graph generative models have opened up new avenues for exploring the chemical space of molecular candidates, enabling a more efficient and systematic exploration of the chemical space, increasing the chances of finding novel and potent molecules. One of the recent breakthroughs includes the use of diffusion models, which have proven to yield superior performance in molecular conformation tasks, among others. In this blog post, we aim to highlight one of them, which is the 'GeoDiff - A Geometric Diffusion Model for Molecular Conformation Generation' paper by Xu et al. (2022). We aim to distill the paper in semi-layman terms, to provide researchers and practitioners with a deeper understanding of the (i) methodology and results and (ii) (societal) implications of this breakthrough in the field of drug discovery and (iii) discuss future applications in the field of (bio)medicine. -date: 2023-02-17 -htmlwidgets: true - -# Anonymize when submitting -# authors: -# - name: Anonymous - -authors: - - name: Anonymous - -# must be the exact same name as your blogpost -bibliography: 2022-12-01-diffusion-is-all-you-need.bib - -# Add a table of contents to your post. -# - make sure that TOC names match the actual section names -# for hyperlinks within the post to work correctly. -toc: - - name: Introduction - - name: Motivation - - name: Formulating the conformation generation problem - subsections: - - name: Roto-translation equivariance - - name: Decomposing GeoDiff - subsections: - - name: A primer on Diffusion Models - - name: Forward process - - name: Reverse process - - name: Making the reverse process roto-translation equivariant - - name: Improved Training Objective - - name: Sampling - - name: But why generative models? - - name: Future work ---- - -# A Match Made in Drug Discovery: Marrying Geometric and Diffusion Models - -## Introduction -With the initial breakthrough of the Denoising Diffusion , diffusion models have evolved into a powerful tool for a wide range of applications in machine learning, including image generation and text generation. The rise and the recent release of Stable Diffusion in August 2022 has shown superior performance in a wide range of practical applications - from artistic and creative projects to scientific and industrial ones and has recently paved its way into the natural sciences, which includes the field of drug discovery . - -Data-driven applications have increasingly been shown to accelerate solving diverse problems in the drug discovery pipeline -- from the use of predictive analytical methods for target identification and lead optimization, to the analysis of large-scale biological data for drug repurposing and personalized medicine. To limit the scope of the blog post, we will only focus on the use of generative methods in **molecular conformation generation**. - -## Motivation -Generating molecular conformations is a task fundamental to cheminformatics and drug discovery. The conformation of a molecule refers to the three-dimensional (3D) coordinates of all the atoms in a molecule in a 3D Euclidean space, which can be interconverted by rotations about formally single bonds . It allows for the prediction of the physical and chemical properties and interactions of molecules based on their possible 3D conformations, as well as their biological activity. In drug discovery, it is integral to obtain all the possible conformations of molecules for various tasks, such as three-dimensional quantitative structure-activity relationships (3D-QSAR), pharmacophore searching, molecular docking and thermodynamic calculations. Deep generative modelling, which aims to learn complex data distributions, is a recent promising approach to tackle the conformation generation problem . -When studying molecules it is important to understand them as three-dimensional structures formed by atoms bonded to each other. To encode the chemical properties, molecules could be represented as graphs where atoms (nodes) are connected by bonds (edges). Representing molecules as 3D molecular graphs captures the spatial arrangement of a molecule, which in turn determines its chemical property. A molecule could take up any conformation based on all possible permutations and combinations of spatial arrangements of atoms. However, some conformations may not occur physically, due to e.g steric hindrance, which arises when the spatial arrangement of atoms leads to unfavourable interactions/repulsive forces, leading to a higher energy state and less stable conformation. - -Therefore, we are only interested in conformations that fall in stable low-energy minima, as these low-energy conformations are the ones that the molecule will most likely adopt under natural conditions and play a crucial role in determining the molecule’s behaviour and properties. By identifying and characterizing the low-energy conformations, researchers gain insights into their stability, reactivity and interactions with other molecules. - - -## Formulating the conformation generation problem - -{% include figure.html path="assets/img/2022-12-01-diffusion-is-all-you-need/formulation.png" class="img-fluid" %} -A formulation of the conformation generation problem, adapted from - -We can formulate the problem of conformation generation as a conditional generative problem where we aim to generate stable conformations $$C$$ from a molecule’s graph $$G$$. For each $$G$$ given its conformations $$C$$ as i.i.d samples from an underlying Boltzmann distribution , our goal is to learn a generative model $$p_\theta(C|G)$$ to draw possible conformations from. - - - -### Roto-translation equivariance - -{% include figure.html path="assets/img/2022-12-01-diffusion-is-all-you-need/roto-trans.png" class="img-fluid" %} -A visualisation of roto-translation equivariance, adapted from - -To generate stable molecular conformations, we need an algorithm that preserves roto-translation equivariance of the conformations that previous work has not focused on. To explain this property, let us delve into what equivariance is. A representation $$φ$$ is equivariant with a transformation $$g$$ of the input if the transformation can be transferred to the representation output. Invariance is a special case of equivariance obtained when the transformation is the identity map . - - -In the context of molecular conformations, we have to achieve the special case of equivariance in terms of rotation and translation, namely, roto-translation equivariance of the conformations which ensures that however the molecule is rotated or translated, the estimated (conditional) likelihood should be unaffected. GeoDiff considers the SE(3) Lie group which can be used to represent rotation and translation in 3D space . - - -## Decomposing GeoDiff - -{% include figure.html path="assets/img/2022-12-01-diffusion-is-all-you-need/geodiff_main.png" class="img-fluid" %} -The diffusion model of GeoDiff, adapted from - - - **Legend**: -- $$C^{0}$$ denotes the ground truth conformations -- $$C^{t}$$, where $$t = 1,···, T$$ is the index for diffusion steps and $$C^{t}$$, is the sequence of latent variables with the same dimension -- $$q(C^{t} \mid C^{t-1})$$ is the fixed posterior distribution -- $$p_\theta(C^{t-1} \mid G, C^{t})$$ are the Markov kernels through which the conformations are refined - -### A primer on Diffusion Models -A diffusion probabilistic model can be described as a latent variable model with two processes: the forward and the reverse generative processes. Intuitively, the diffusion process progressively injects small noises into $$C^{0}$$, while the generative process learns to revert the diffusion process by gradually eliminating the noise to recover the ground truth. Diffusion models are trained by adding noise to the input, which the model then learns how to remove. - - -In this blog post, we use the GeoDiff implementation of diffusion models to explain how the diffusion model works and how it is being used for the geometric representation of molecules. The implementation of the diffusion model in GeoDiff is inspired by the DDPM paper . To give a quick overview, the forward process $$q$$ transforms the original input into complete noise over a certain number of timesteps and follows a normal distribution; the $$p_0$$ involves denoising complete noise to the actual input using a neural network. - - -### Forward process -Let $$q(\mathbf{C}^0)$$ be the real data distribution of molecular conformation. We can sample from this distribution to get a conformation, $$\mathbf{C}^0 \sim q(\mathbf{C}^0)$$. We define the forward diffusion process which adds Gaussian noise at each time step $$t$$, according to a known variance schedule \beta_t which can be linear, quadratic, cosine, etc. as follows: - -$$ -\begin{align}\tag{1} -q\left(\mathcal{C}^{1: T} \mid \mathcal{C}^0\right)=\prod_{t=1}^T q\left(\mathcal{C}^t \mid \mathcal{C}^{t-1}\right) -\end{align} -$$ - -where $$\quad q\left(\mathcal{C}^t \mid \mathcal{C}^{t-1}\right)=\mathcal{N}\left(\mathcal{C}^t ; \sqrt{1-\beta_t} \mathcal{C}^{t-1}, \beta_t I\right)$$ - -Instead of having to compute $$q\left(\mathcal{C}^t \mid \mathcal{C}^{t-1}\right)$$ at every timestep $$t$$, we could compute at an arbitrary timestep in closed form: - -$$ -\begin{equation}\tag{2} -q\left(\mathcal{C}^t \mid \mathcal{C}^0\right)=\mathcal{N}\left(\mathcal{C}^t ; \sqrt{\bar{\alpha}_t} \mathcal{C}^0,\left(1-\bar{\alpha}_t\right) I\right) -\end{equation} -$$ - -where $$\alpha_t=1-\beta_t$$ and $$\bar{\alpha}_t=\prod_{s=1}^t \alpha_s$$ - -Thus with a sufficiently large number of timesteps, the forward process could convert $$\mathcal{C}^0$$ to whitened isotropic Gaussian and so we could set $$p\left(\mathcal{C}^T\right)$$ as a standard Gaussian distribution. - - -### Reverse Process -The reverse process involved recovering the original conformation $$\mathcal{C}^0$$ from the white noise $$\mathcal{C}^T$$ . We need the conditional distribution $$p_\theta\left(\mathcal{C}^{t-1} \mid \mathcal{G}, \mathcal{C}^t\right)$$ to sample some random Gaussian noise $$\mathcal{C}^t$$, and "denoise" gradually to end up with a sample from the real distribution $$\mathcal{C}^0$$. - -However, the conditional distribution of $$p_\theta\left(\mathcal{C}^{t-1} \mid \mathcal{G}, \mathcal{C}^t\right)$$ is intractable as it requires knowing the distribution of all possible conformations in order to calculate this conditional probability. Hence, a neural network could be used to learn this conditional probability distribution, let's call it $$p_\theta$$, with $$\theta$$ being the parameters of the neural network, updated by gradient descent. Thus, we formulate the reverse process as a conditional Markov chain with learnable transitions: - -$$ -\begin{align*}\tag{3} -p_\theta\left(\mathcal{C}^{0: T-1} \mid \mathcal{G}, \mathcal{C}^T\right)=\prod_{t=1}^T p_\theta\left(\mathcal{C}^{t-1} \mid \mathcal{G}, \mathcal{C}^t\right) -\end{align*} -$$ - -where $$\quad p_\theta\left(\mathcal{C}^{t-1} \mid \mathcal{G}, \mathcal{C}^t\right)=\mathcal{N}\left(\mathcal{C}^{t-1} ; \mu_\theta\left(\mathcal{G}, \mathcal{C}^t, t\right), \sigma_t^2 I\right)$$ - - - - - -Hence, the neural network in the reverse process needs to learn/represent the mean and variance. However, just like the DDPM paper, GeoDiff also lets the variance be user-defined and fixed, and $$\mu_\theta$$ is the neural network that estimates means. - -GeoDiff uses a parametrisation trick inspired by the diffusion model implementation from the DDPM paper such that this parametrisation resembles Langevin dynamics and simplifies the diffusion model's variational bound to an objective that resembles denoising score matching. Moreover, in the context of molecular conformation generation, this parametrisation trick is analogous to the physical force fields , which also gradually push particles towards convergence around the equilibrium states, and is defined by the following equation: - -$$ -\begin{align*}\tag{4} -\mu_\theta\left(\mathcal{C}^t, t\right)=\frac{1}{\sqrt{\alpha_t}}\left(\mathcal{C}^t-\frac{\beta_t}{\sqrt{1-\bar{\alpha}_t}} \epsilon_\theta\left(\mathcal{G}, \mathcal{C}^t, t\right)\right) -\end{align*} -$$ - -where $$\epsilon_\theta$$ are neural networks with trainable parameters $$\theta$$. - -Now, we need to make $$\epsilon_\theta$$ roto-translational equivariant which we elaborate on in the next section. - -### Making the reverse process roto-translation equivariant - -Firstly, we need to assume the prior distribution of the conformations and the intermediary conformations generated during the forward process are systems with zero centre of mass (CoM) or CoM-free systems . By considering CoM-free systems, moving the particles to zero CoM can always ensure translational invariance in the Markov kernels. - -GeoDiff employs the use of an equivariant convolutional layer, named graph field network (GFN) inspired by . In the $$l$$-th layer, GFN takes node embeddings $$h_l \in \mathbb{R}^{n \times b}$$ ($$b$$ denotes the feature dimension) and corresponding coordinate embeddings $$x_l \in \mathbb{R}^{n \times 3}$$ as inputs, and outputs $$h_{l+1}$$ and $$x_{l+1}$$ as follows: - -$$ -\begin{align} \tag{5} -& \mathbf{m}_{i j}=\Phi_m\left(\mathbf{h}_i^l, \mathbf{h}_j^l,\left\|\mathbf{x}_i^l-\mathbf{x}_j^l\right\|^2, e_{i j} ; \theta_m\right) \\ \tag{6} -& \mathbf{h}_i^{l+1}=\Phi_h\left(\mathbf{h}_i^l, \sum_{j \in \mathcal{N}(i)} \mathbf{m}_{i j} ; \theta_h\right) \\ -& \mathbf{x}_i^{l+1}=\sum_{j \in \mathcal{N}(i)} \frac{1}{d_{i j}}\left(\mathbf{c}_i-\mathbf{c}_j\right) \Phi_x\left(\mathbf{m}_{i j} ; \theta_x\right) \tag{7} -\end{align} -$$ - - - -where -- $$\Phi$$ are feed-forward networks -- $$d_{ij}$$ are interatomic distances -- $$\mathcal{N}(i)$$ is the neighbourhood of the $$i$$-th node, which consists of both connected atoms and other ones within a radius threshold $$\tau$$. - - -By introducing the neighbourhood function, we enable the model to accurately represent distant interactions between atoms, as well as the ability to handle partially disconnected molecular graphs. Initial embeddings $$h_0$$ are combinations of atom and timestep embeddings, and $$x_0$$ are atomic coordinates. A key change in GFN compared to a vanilla GNN is $$x$$ being updated as a combination of radial directions weighted by $$\Phi_x$$: $$\mathbb{R}^b \rightarrow \mathbb{R}$$ as seen in equation $$(7)$$. This allows the roto-translation equivariance property to be induced in the reverse process. - - - -### Improved Training Objective - -Now, we need to set the training objective having considered the reverse process dynamics. We cannot compute the exact log-likelihood of the generative process, as it involves computing the likelihood of the observed molecular conformation given the parameters of the model. However, this likelihood is difficult to compute, as it would require integrating over all possible intermediate conformations, giving us a high-dimensional integral that cannot be solved analytically. Therefore, the authors have opted to maximize the variational lower bound (ELBO), as defined below: - - -$$\begin{aligned} \mathbb{E}\left[\log p_\theta\left(\mathcal{C}^0 \mid \mathcal{G}\right)\right] & =\mathbb{E}\left[\log \mathbb{E}_{q\left(\mathcal{C}^{1: T} \mid \mathcal{C}^0\right)} \frac{p_\theta\left(\mathcal{C}^{0: T} \mid \mathcal{G}\right)}{q\left(\mathcal{C}^{1: T} \mid \mathcal{C}^0\right)}\right] \\ & \geq-\mathbb{E}_q\left[\sum_{t=1}^T D_{\mathrm{KL}}\left(q\left(\mathcal{C}^{t-1} \mid \mathcal{C}^t, \mathcal{C}^0\right) \| p_\theta\left(\mathcal{C}^{t-1} \mid \mathcal{C}^t, \mathcal{G}\right)\right)\right]:=-\mathcal{L}_{\mathrm{ELBO}}\end{aligned}$$ - -where $$q\left(\mathcal{C}^{t-1} \mid \mathcal{C}^t, \mathcal{C}^0\right)$$ is analytically tractable as $$\mathcal{N}\left(\frac{\sqrt{\bar{\alpha}_{t-1}} \beta_t}{1-\bar{\alpha}_t} \mathcal{C}^0+\frac{\sqrt{\alpha_t}\left(1-\bar{\alpha}_{t-1}\right)}{1-\bar{\alpha}_t} \mathcal{C}^t, \frac{1-\bar{\alpha}_{t-1}}{1-\bar{\alpha}_t} \beta_t\right)$$. - - -Using the parametrisation trick in the reverse process as seen in equation $$(4)$$, the ELBO could be simplified by taking the KL divergences between Gaussians as weighted $$\mathcal{L}_2$$ distances between the means $$\epsilon_\theta$$ and $$\epsilon^3$$ as follows: -$$ -\mathcal{L}_{\mathrm{ELBO}}=\sum_{t=1}^T \gamma_t \mathbb{E}_{\left\{\mathcal{C}^0, \mathcal{G}\right\} \sim q\left(\mathcal{C}^0, \mathcal{G}\right), \epsilon \sim \mathcal{N}(0, I)}\left[\left\|\epsilon-\epsilon_\theta\left(\mathcal{G}, \mathcal{C}^t, t\right)\right\|_2^2\right] -$$ -where $$\mathcal{C}^t=\sqrt{\bar{\alpha}_t} \mathcal{C}^0+\sqrt{1-\bar{\alpha}_t} \epsilon$$. - -The idea behind this objective is to independently sample chaotic conformations of different timesteps from $$q\left(C^{t-1} \mid C^t, C^0\right)$$, and use $$\epsilon_\theta$$ to approximate the noise vector $$\epsilon$$. - - - -### Sampling - -Now, we can generate stable molecular conformations via sampling. Given a graph $$\mathcal{G}$$, its geometry $$\mathcal{C}^0$$ is generated by first sampling chaotic particles $$\mathcal{C}^T \sim p\left(\mathcal{C}^T\right)$$. For each timestep in the reverse process $$t=T, T-$$ $$1, \cdots, 1$$, we first shift the CoM of the conformation to zero, compute the transition means, $$\mu_\theta\left(\mathcal{G}, \mathcal{C}^t, t\right)$$, using equation $$(4)$$ and sample $$\mathcal{C}^{t-1} \sim$$ $$p_\theta\left(\mathcal{C}^{t-1} \mid \mathcal{G}, \mathcal{C}^t\right)$$. The sampling algorithm is given in pseudo-code below: - - - -| Algorithm 1 Sampling Algorithm of GEODIFF | -|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------| -| Input: the molecular graph $$\mathcal{G}$$, the learned reverse model $$\epsilon_\theta$$. | -| Output: the molecular conformation $$\mathcal{C}$$. | -| 1: Sample $$\mathcal{C}^T \sim p\left(\mathcal{C}^T\right)=\mathcal{N}(0, I)$$ | -| 2: for $$s=T, T-1, \cdots, 1$$ do | -| 3: $$\quad$$ Shift $$\mathcal{C}^s$$ to zero CoM | -| 4: $$\quad$$ Compute $$\mu_\theta\left(\mathcal{C}^s, \mathcal{G}, s\right)$$ from $$\epsilon_\theta\left(\mathcal{C}^s, \mathcal{G}, s\right)$$ using equation 4 | -| 5: $$\quad$$ Sample $$\mathcal{C}^{s-1} \sim \mathcal{N}\left(\mathcal{C}^{s-1} ; \mu_\theta\left(\mathcal{C}^{\mathcal{s}}, \mathcal{G}, s\right), \sigma_t^2 I\right)$$ | -| 6: end for | -| 7: return $$\mathcal{C}^0$$ as $\mathcal{C}$$ | - - - -## But why generative models? -The purpose of prediciting molecular conformations is to enable human experts to analyse the properties of the molecules and understand how these properties affect the viability of a molecule as a drug candidate. Therefore, it is important that the molecular conformations generated are diverse to capture the different possible conformations that could occur in nature but the conformations generated should not deviate significantly such that the analysis is affected. To set a threshold for the different possible conformations, the standard metric used has been selecting conformations that are within a certain root-mean-square deviation (RMSD), say a few ångströms, of the true structure. - -However, the objective of maximizing the proportion of predictions with RMSD within some tolerance $$\epsilon$$ is not differentiable and thus, cannot be used for training with stochastic gradient descent. Instead, maximizing the expected proportion of predictions with RMSD < $$\epsilon$$ corresponds to maximizing the likelihood of the true structure under the model’s output distribution, in the limit as $$\epsilon$$ goes to 0. This concept inspires the development of a generative model, whose objective is to minimize an upper bound on the negative log-likelihood of observed molecular structures under the distribution of the model. As a result, the problem of molecular docking is treated as a task of learning a distribution over possible positions of a ligand molecule conditioned on the protein structure and a diffusion generative model is developed to represent this space. Therefore, this observation has motivated several works on the use of generative models for molecular conformation generation, such as GeoDiff. - - -## Future work - -While diffusion models have shown promising results over the past months, there is still a need for further research and development to address some of the limitations and drawbacks of the use of diffusion models in conformer generation. As explained in our blog post, generative models are well-suited for molecular conformation generation. However, there are other kinds of established generative models, such as autoencoders that have been used for the same task . For instance, comparing diffusion models and autoencoders, diffusion models can handle all noise levels with a single set of parameters, without any bottlenecks, which an autoencoder would have . Thus, it is essential to study the advantages and disadvantages of different types and variants of generative models for conformation generation and understand what changes could be done to them to make them more suitable for molecular conformation. - -It must be noted that the experiments described in the study are done on benchmark geometric datasets, GEOM-QM9 and GEOM-Drugs , rather than industrial data, with a relatively small number of samples/drug/molecular compounds. Industry data may exhibit greater variability than standard geometric datasets, as they may be more diverse, complex and subject to greater fluctuations than these geometric datasets, which tend to be more standardized and more predictable. - - -GeoDiff as a framework sets a precedent for future work that could marry the concepts of geometric deep learning and diffusion models across various domains. In the context of drug discovery, it would be interesting to extend this framework to more challenging structures, such as proteins, which may enable more accurate prediction of protein folding, protein-protein interactions and protein-ligand binding positions which would facilitate the design of new drugs and treatments. Additionally, this framework could potentially be applied to other complex systems beyond proteins, such as RNA molecules, to enable more efficient and accurate prediction of their behaviour and properties. Continued research in this area has the potential to revolutionize drug discovery and development, as well as advance our understanding of the fundamental principles governing the behaviour of complex biological systems. - - -Research on the application of diffusion models in the life and natural sciences is still in its infancy, with great potential for improvement in terms of both theory as well as empirical testing. The GeoDiff model could be improved in terms of more efficient sampling and improved likelihood maximization methods. Traditionally, generating samples from diffusion models demand iterative approaches that involve a large number of evaluation steps. Recent work, such as the paper on Torsional Diffusion was able to speed up the sampling process, while also enhancing the quality of the resulting samples. Experimentally, Torsional Diffusion only takes 5 to 20 steps in comparison to GeoDiff which takes around 5000 steps . - -Looking ahead, GeoDiff has set a clear example for the use of diffusion models on geometric representations which could be extended to several problems, especially in the field of drug discovery. The novel contributions made by - are motivated by the physical characteristics of the molecular conformation generation problem, which has resulted in a strong candidate method for conformation generation that could act as a springboard for even more effective and efficient methods that would eventually benefit the field of drug discovery as a whole. - - - - - - - - - - - diff --git a/_posts/2022-12-01-distill-example.md b/_posts/2022-12-01-distill-example.md deleted file mode 100644 index 2d133452..00000000 --- a/_posts/2022-12-01-distill-example.md +++ /dev/null @@ -1,431 +0,0 @@ ---- -layout: distill -title: Sample Blog Post -description: Your blog post's abstract. - This is an example of a distill-style blog post and the main elements it supports. -date: 2022-12-01 -htmlwidgets: true - -# Anonymize when submitting -# authors: -# - name: Anonymous - -authors: - - name: Albert Einstein - url: "https://en.wikipedia.org/wiki/Albert_Einstein" - affiliations: - name: IAS, Princeton - - name: Boris Podolsky - url: "https://en.wikipedia.org/wiki/Boris_Podolsky" - affiliations: - name: IAS, Princeton - - name: Nathan Rosen - url: "https://en.wikipedia.org/wiki/Nathan_Rosen" - affiliations: - name: IAS, Princeton - -# must be the exact same name as your blogpost -bibliography: 2022-12-01-distill-example.bib - -# Add a table of contents to your post. -# - make sure that TOC names match the actual section names -# for hyperlinks within the post to work correctly. -toc: - - name: Equations - - name: Images and Figures - subsections: - - name: Interactive Figures - - name: Citations - - name: Footnotes - - name: Code Blocks - - name: Layouts - - name: Other Typography? - -# Below is an example of injecting additional post-specific styles. -# This is used in the 'Layouts' section of this post. -# If you use this post as a template, delete this _styles block. -_styles: > - .fake-img { - background: #bbb; - border: 1px solid rgba(0, 0, 0, 0.1); - box-shadow: 0 0px 4px rgba(0, 0, 0, 0.1); - margin-bottom: 12px; - } - .fake-img p { - font-family: monospace; - color: white; - text-align: left; - margin: 12px 0; - text-align: center; - font-size: 16px; - } ---- - -## Equations - -This theme supports rendering beautiful math in inline and display modes using [MathJax 3](https://www.mathjax.org/) engine. -You just need to surround your math expression with `$$`, like `$$ E = mc^2 $$`. -If you leave it inside a paragraph, it will produce an inline expression, just like $$ E = mc^2 $$. - -To use display mode, again surround your expression with `$$` and place it as a separate paragraph. -Here is an example: - -$$ -\left( \sum_{k=1}^n a_k b_k \right)^2 \leq \left( \sum_{k=1}^n a_k^2 \right) \left( \sum_{k=1}^n b_k^2 \right) -$$ - -Note that MathJax 3 is [a major re-write of MathJax](https://docs.mathjax.org/en/latest/upgrading/whats-new-3.0.html) that brought a significant improvement to the loading and rendering speed, which is now [on par with KaTeX](http://www.intmath.com/cg5/katex-mathjax-comparison.php). - - -## Images and Figures - -Its generally a better idea to avoid linking to images hosted elsewhere - links can break and you -might face losing important information in your blog post. -To include images in your submission in this way, you must do something like the following: - -```markdown -{% raw %}{% include figure.html path="assets/img/2022-12-01-distill-example/iclr.png" class="img-fluid" %}{% endraw %} -``` - -which results in the following image: - -{% include figure.html path="assets/img/2022-12-01-distill-example/iclr.png" class="img-fluid" %} - -To ensure that there are no namespace conflicts, you must save your asset to your unique directory -`/assets/img/2023-05-01-[SUBMISSION NAME]` within your submission. - -Please avoid using the direct markdown method of embedding images; they may not be properly resized. -Some more complex ways to load images (note the different styles of the shapes/shadows): - -
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- {% include figure.html path="assets/img/2022-12-01-distill-example/9.jpg" class="img-fluid rounded z-depth-1" %} -
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- {% include figure.html path="assets/img/2022-12-01-distill-example/7.jpg" class="img-fluid rounded z-depth-1" %} -
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- A simple, elegant caption looks good between image rows, after each row, or doesn't have to be there at all. -
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- {% include figure.html path="assets/img/2022-12-01-distill-example/8.jpg" class="img-fluid z-depth-2" %} -
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- -### Interactive Figures - -Here's how you could embed interactive figures that have been exported as HTML files. -Note that we will be using plotly for this demo, but anything built off of HTML should work -(**no extra javascript is allowed!**). -All that's required is for you to export your figure into HTML format, and make sure that the file -exists in the `assets/html/[SUBMISSION NAME]/` directory in this repository's root directory. -To embed it into any page, simply insert the following code anywhere into your page. - -```markdown -{% raw %}{% include [FIGURE_NAME].html %}{% endraw %} -``` - -For example, the following code can be used to generate the figure underneath it. - -```python -import pandas as pd -import plotly.express as px - -df = pd.read_csv('https://raw.githubusercontent.com/plotly/datasets/master/earthquakes-23k.csv') - -fig = px.density_mapbox( - df, lat='Latitude', lon='Longitude', z='Magnitude', radius=10, - center=dict(lat=0, lon=180), zoom=0, mapbox_style="stamen-terrain") -fig.show() - -fig.write_html('./assets/html/2022-12-01-distill-example/plotly_demo_1.html') -``` - -And then include it with the following: - -```html -{% raw %}
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{% endraw %} -``` - -Voila! - -
- -
- -## Citations - -Citations are then used in the article body with the `` tag. -The key attribute is a reference to the id provided in the bibliography. -The key attribute can take multiple ids, separated by commas. - -The citation is presented inline like this: (a number that displays more information on hover). -If you have an appendix, a bibliography is automatically created and populated in it. - -Distill chose a numerical inline citation style to improve readability of citation dense articles and because many of the benefits of longer citations are obviated by displaying more information on hover. -However, we consider it good style to mention author last names if you discuss something at length and it fits into the flow well — the authors are human and it’s nice for them to have the community associate them with their work. - -*** - -## Footnotes - -Just wrap the text you would like to show up in a footnote in a `` tag. -The number of the footnote will be automatically generated.This will become a hoverable footnote. - -*** - -## Code Blocks - -This theme implements a built-in Jekyll feature, the use of Rouge, for syntax highlighting. -It supports more than 100 languages. -This example is in C++. -All you have to do is wrap your code in a liquid tag: - -{% raw %} -{% highlight c++ linenos %}
code code code
{% endhighlight %} -{% endraw %} - -The keyword `linenos` triggers display of line numbers. You can try toggling it on or off yourself below: - -{% highlight c++ %} - -int main(int argc, char const \*argv[]) -{ -string myString; - - cout << "input a string: "; - getline(cin, myString); - int length = myString.length(); - - char charArray = new char * [length]; - - charArray = myString; - for(int i = 0; i < length; ++i){ - cout << charArray[i] << " "; - } - - return 0; -} - -{% endhighlight %} - -*** - -## Diagrams - -This theme supports generating various diagrams from a text description using [jekyll-diagrams](https://github.com/zhustec/jekyll-diagrams){:target="\_blank"} plugin. -Below, we generate a few examples of such diagrams using languages such as [mermaid](https://mermaid-js.github.io/mermaid/){:target="\_blank"}, [plantuml](https://plantuml.com/){:target="\_blank"}, [vega-lite](https://vega.github.io/vega-lite/){:target="\_blank"}, etc. - -**Note:** different diagram-generation packages require external dependencies to be installed on your machine. -Also, be mindful of that because of diagram generation the fist time you build your Jekyll website after adding new diagrams will be SLOW. -For any other details, please refer to [jekyll-diagrams](https://github.com/zhustec/jekyll-diagrams){:target="\_blank"} README. - -**Note:** This is not supported for local rendering! - -The diagram below was generated by the following code: - -{% raw %} -``` -{% mermaid %} -sequenceDiagram - participant John - participant Alice - Alice->>John: Hello John, how are you? - John-->>Alice: Great! -{% endmermaid %} -``` -{% endraw %} - -{% mermaid %} -sequenceDiagram -participant John -participant Alice -Alice->>John: Hello John, how are you? -John-->>Alice: Great! -{% endmermaid %} - -*** - -## Blockquotes - -
- We do not grow absolutely, chronologically. We grow sometimes in one dimension, and not in another, unevenly. We grow partially. We are relative. We are mature in one realm, childish in another. - —Anais Nin -
- -*** - - -## Layouts - -The main text column is referred to as the body. -It is the assumed layout of any direct descendants of the `d-article` element. - -
-

.l-body

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- -For images you want to display a little larger, try `.l-page`: - -
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.l-page

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- -All of these have an outset variant if you want to poke out from the body text a little bit. -For instance: - -
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.l-body-outset

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.l-page-outset

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- -Occasionally you’ll want to use the full browser width. -For this, use `.l-screen`. -You can also inset the element a little from the edge of the browser by using the inset variant. - -
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.l-screen

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.l-screen-inset

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- -The final layout is for marginalia, asides, and footnotes. -It does not interrupt the normal flow of `.l-body` sized text except on mobile screen sizes. - -
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.l-gutter

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- -*** - -## Other Typography? - -Emphasis, aka italics, with *asterisks* (`*asterisks*`) or _underscores_ (`_underscores_`). - -Strong emphasis, aka bold, with **asterisks** or __underscores__. - -Combined emphasis with **asterisks and _underscores_**. - -Strikethrough uses two tildes. ~~Scratch this.~~ - -1. First ordered list item -2. Another item -⋅⋅* Unordered sub-list. -1. Actual numbers don't matter, just that it's a number -⋅⋅1. Ordered sub-list -4. And another item. - -⋅⋅⋅You can have properly indented paragraphs within list items. Notice the blank line above, and the leading spaces (at least one, but we'll use three here to also align the raw Markdown). - -⋅⋅⋅To have a line break without a paragraph, you will need to use two trailing spaces.⋅⋅ -⋅⋅⋅Note that this line is separate, but within the same paragraph.⋅⋅ -⋅⋅⋅(This is contrary to the typical GFM line break behaviour, where trailing spaces are not required.) - -* Unordered list can use asterisks -- Or minuses -+ Or pluses - -[I'm an inline-style link](https://www.google.com) - -[I'm an inline-style link with title](https://www.google.com "Google's Homepage") - -[I'm a reference-style link][Arbitrary case-insensitive reference text] - -[I'm a relative reference to a repository file](../blob/master/LICENSE) - -[You can use numbers for reference-style link definitions][1] - -Or leave it empty and use the [link text itself]. - -URLs and URLs in angle brackets will automatically get turned into links. -http://www.example.com or and sometimes -example.com (but not on Github, for example). - -Some text to show that the reference links can follow later. - -[arbitrary case-insensitive reference text]: https://www.mozilla.org -[1]: http://slashdot.org -[link text itself]: http://www.reddit.com - -Here's our logo (hover to see the title text): - -Inline-style: -![alt text](https://github.com/adam-p/markdown-here/raw/master/src/common/images/icon48.png "Logo Title Text 1") - -Reference-style: -![alt text][logo] - -[logo]: https://github.com/adam-p/markdown-here/raw/master/src/common/images/icon48.png "Logo Title Text 2" - -Inline `code` has `back-ticks around` it. - -```javascript -var s = "JavaScript syntax highlighting"; -alert(s); -``` - -```python -s = "Python syntax highlighting" -print s -``` - -``` -No language indicated, so no syntax highlighting. -But let's throw in a tag. -``` - -Colons can be used to align columns. - -| Tables | Are | Cool | -| ------------- |:-------------:| -----:| -| col 3 is | right-aligned | $1600 | -| col 2 is | centered | $12 | -| zebra stripes | are neat | $1 | - -There must be at least 3 dashes separating each header cell. -The outer pipes (|) are optional, and you don't need to make the -raw Markdown line up prettily. You can also use inline Markdown. - -Markdown | Less | Pretty ---- | --- | --- -*Still* | `renders` | **nicely** -1 | 2 | 3 - -> Blockquotes are very handy in email to emulate reply text. -> This line is part of the same quote. - -Quote break. - -> This is a very long line that will still be quoted properly when it wraps. Oh boy let's keep writing to make sure this is long enough to actually wrap for everyone. Oh, you can *put* **Markdown** into a blockquote. - - -Here's a line for us to start with. - -This line is separated from the one above by two newlines, so it will be a *separate paragraph*. - -This line is also a separate paragraph, but... -This line is only separated by a single newline, so it's a separate line in the *same paragraph*. diff --git a/_posts/2022-12-02-test.md b/_posts/2022-12-02-test.md deleted file mode 100644 index c2497bdb..00000000 --- a/_posts/2022-12-02-test.md +++ /dev/null @@ -1,243 +0,0 @@ ---- -layout: distill -title: A Match Made in Drug Discovery - Marrying Geometric and Diffusion Models -description: The chemical space of molecular candidates is vast, and within this space, interesting and powerful drugs are waiting to be found. The use of machine learning has shown to be an effective method to speed up the process of discovering novel compounds, especially the use of (deep) generative models. The recent surge in graph generative models have opened up new avenues for exploring the chemical space of molecular candidates, enabling a more efficient and systematic exploration of the chemical space, increasing the chances of finding novel and potent molecules. One of the recent breakthroughs includes the use of diffusion models, which have proven to yield superior performance in molecular conformation tasks, among others. In this blog post, we aim to highlight one of them, which is the 'GeoDiff - A Geometric Diffusion Model for Molecular Conformation Generation' paper by Xu et al. (2022). We aim to distill the paper in semi-layman terms, to provide researchers and practitioners with a deeper understanding of the (i) methodology and results and (ii) (societal) implications of this breakthrough in the field of drug discovery and (iii) discuss future applications in the field of (bio)medicine. -date: 2023-02-17 -htmlwidgets: true - -# Anonymize when submitting -# authors: -# - name: Anonymous - -authors: - - name: Anonymous - -# must be the exact same name as your blogpost -bibliography: 2022-12-01-test.bib - -# Add a table of contents to your post. -# - make sure that TOC names match the actual section names -# for hyperlinks within the post to work correctly. -toc: - - name: Introduction - - name: Motivation - - name: Formulating the conformation generation problem - subsections: - - name: Roto-translation equivariance - - name: Decomposing GeoDiff - subsections: - - name: A primer on Diffusion Models - - name: Forward process - - name: Reverse process - - name: Making the reverse process roto-translation equivariant - - name: Improved Training Objective - - name: Sampling - - name: But why generative models? - - name: Future work ---- - -# A Match Made in Drug Discovery: Marrying Geometric and Diffusion Models - -## Introduction -With the initial breakthrough of the Denoising Diffusion , diffusion models have evolved into a powerful tool for a wide range of applications in machine learning, including image generation and text generation. The rise and the recent release of Stable Diffusion in August 2022 has shown superior performance in a wide range of practical applications - from artistic and creative projects to scientific and industrial ones and has recently paved its way into the natural sciences, which includes the field of drug discovery . - -Data-driven applications have increasingly been shown to accelerate solving diverse problems in the drug discovery pipeline -- from the use of predictive analytical methods for target identification and lead optimization, to the analysis of large-scale biological data for drug repurposing and personalized medicine. To limit the scope of the blog post, we will only focus on the use of generative methods in **molecular conformation generation**. - -## Motivation -Generating molecular conformations is a task fundamental to cheminformatics and drug discovery. The conformation of a molecule refers to the three-dimensional (3D) coordinates of all the atoms in a molecule in a 3D Euclidean space, which can be interconverted by rotations about formally single bonds . It allows for the prediction of the physical and chemical properties and interactions of molecules based on their possible 3D conformations, as well as their biological activity. In drug discovery, it is integral to obtain all the possible conformations of molecules for various tasks, such as three-dimensional quantitative structure-activity relationships (3D-QSAR), pharmacophore searching, molecular docking and thermodynamic calculations. Deep generative modelling, which aims to learn complex data distributions, is a recent promising approach to tackle the conformation generation problem . -When studying molecules it is important to understand them as three-dimensional structures formed by atoms bonded to each other. To encode the chemical properties, molecules could be represented as graphs where atoms (nodes) are connected by bonds (edges). Representing molecules as 3D molecular graphs captures the spatial arrangement of a molecule, which in turn determines its chemical property. A molecule could take up any conformation based on all possible permutations and combinations of spatial arrangements of atoms. However, some conformations may not occur physically, due to e.g steric hindrance, which arises when the spatial arrangement of atoms leads to unfavourable interactions/repulsive forces, leading to a higher energy state and less stable conformation. - -Therefore, we are only interested in conformations that fall in stable low-energy minima, as these low-energy conformations are the ones that the molecule will most likely adopt under natural conditions and play a crucial role in determining the molecule’s behaviour and properties. By identifying and characterizing the low-energy conformations, researchers gain insights into their stability, reactivity and interactions with other molecules. - - -## Formulating the conformation generation problem - -{% include figure.html path="assets/img/2022-12-01-test/formulation.png" class="img-fluid" %} -A formulation of the conformation generation problem, adapted from - -We can formulate the problem of conformation generation as a conditional generative problem where we aim to generate stable conformations $$C$$ from a molecule’s graph $$G$$. For each $$G$$ given its conformations $$C$$ as i.i.d samples from an underlying Boltzmann distribution , our goal is to learn a generative model $$p_\theta(C|G)$$ to draw possible conformations from. - - - -### Roto-translation equivariance - -{% include figure.html path="assets/img/2022-12-01-test/roto-trans.png" class="img-fluid" %} -A visualisation of roto-translation equivariance, adapted from - -To generate stable molecular conformations, we need an algorithm that preserves roto-translation equivariance of the conformations that previous work has not focused on. To explain this property, let us delve into what equivariance is. A representation $$φ$$ is equivariant with a transformation $$g$$ of the input if the transformation can be transferred to the representation output. Invariance is a special case of equivariance obtained when the transformation is the identity map . - - -In the context of molecular conformations, we have to achieve the special case of equivariance in terms of rotation and translation, namely, roto-translation equivariance of the conformations which ensures that however the molecule is rotated or translated, the estimated (conditional) likelihood should be unaffected. GeoDiff considers the SE(3) Lie group which can be used to represent rotation and translation in 3D space . - - -## Decomposing GeoDiff - -{% include figure.html path="assets/img/2022-12-01-test/geodiff_main.png" class="img-fluid" %} -The diffusion model of GeoDiff, adapted from - - - **Legend**: -- $$C^{0}$$ denotes the ground truth conformations -- $$C^{t}$$, where $$t = 1,···, T$$ is the index for diffusion steps and $$C^{t}$$, is the sequence of latent variables with the same dimension -- $$q(C^{t} \mid C^{t-1})$$ is the fixed posterior distribution -- $$p_\theta(C^{t-1} \mid G, C^{t})$$ are the Markov kernels through which the conformations are refined - -### A primer on Diffusion Models -A diffusion probabilistic model can be described as a latent variable model with two processes: the forward and the reverse generative processes. Intuitively, the diffusion process progressively injects small noises into $$C^{0}$$, while the generative process learns to revert the diffusion process by gradually eliminating the noise to recover the ground truth. Diffusion models are trained by adding noise to the input, which the model then learns how to remove. - - -In this blog post, we use the GeoDiff implementation of diffusion models to explain how the diffusion model works and how it is being used for the geometric representation of molecules. The implementation of the diffusion model in GeoDiff is inspired by the DDPM paper . To give a quick overview, the forward process $$q$$ transforms the original input into complete noise over a certain number of timesteps and follows a normal distribution; the $$p_0$$ involves denoising complete noise to the actual input using a neural network. - - -### Forward process -Let $$q(\mathbf{C}^0)$$ be the real data distribution of molecular conformation. We can sample from this distribution to get a conformation, $$\mathbf{C}^0 \sim q(\mathbf{C}^0)$$. We define the forward diffusion process which adds Gaussian noise at each time step $$t$$, according to a known variance schedule \beta_t which can be linear, quadratic, cosine, etc. as follows: - -$$ -\begin{align}\tag{1} -q\left(\mathcal{C}^{1: T} \mid \mathcal{C}^0\right)=\prod_{t=1}^T q\left(\mathcal{C}^t \mid \mathcal{C}^{t-1}\right) -\end{align} -$$ - -where $$\quad q\left(\mathcal{C}^t \mid \mathcal{C}^{t-1}\right)=\mathcal{N}\left(\mathcal{C}^t ; \sqrt{1-\beta_t} \mathcal{C}^{t-1}, \beta_t I\right)$$ - -Instead of having to compute $$q\left(\mathcal{C}^t \mid \mathcal{C}^{t-1}\right)$$ at every timestep $$t$$, we could compute at an arbitrary timestep in closed form: - -$$ -\begin{equation}\tag{2} -q\left(\mathcal{C}^t \mid \mathcal{C}^0\right)=\mathcal{N}\left(\mathcal{C}^t ; \sqrt{\bar{\alpha}_t} \mathcal{C}^0,\left(1-\bar{\alpha}_t\right) I\right) -\end{equation} -$$ - -where $$\alpha_t=1-\beta_t$$ and $$\bar{\alpha}_t=\prod_{s=1}^t \alpha_s$$ - -Thus with a sufficiently large number of timesteps, the forward process could convert $$\mathcal{C}^0$$ to whitened isotropic Gaussian and so we could set $$p\left(\mathcal{C}^T\right)$$ as a standard Gaussian distribution. - - -### Reverse Process -The reverse process involved recovering the original conformation $$\mathcal{C}^0$$ from the white noise $$\mathcal{C}^T$$ . We need the conditional distribution $$p_\theta\left(\mathcal{C}^{t-1} \mid \mathcal{G}, \mathcal{C}^t\right)$$ to sample some random Gaussian noise $$\mathcal{C}^t$$, and "denoise" gradually to end up with a sample from the real distribution $$\mathcal{C}^0$$. - -However, the conditional distribution of $$p_\theta\left(\mathcal{C}^{t-1} \mid \mathcal{G}, \mathcal{C}^t\right)$$ is intractable as it requires knowing the distribution of all possible conformations in order to calculate this conditional probability. Hence, a neural network could be used to learn this conditional probability distribution, let's call it $$p_\theta$$, with $$\theta$$ being the parameters of the neural network, updated by gradient descent. Thus, we formulate the reverse process as a conditional Markov chain with learnable transitions: - -$$ -\begin{align*}\tag{3} -p_\theta\left(\mathcal{C}^{0: T-1} \mid \mathcal{G}, \mathcal{C}^T\right)=\prod_{t=1}^T p_\theta\left(\mathcal{C}^{t-1} \mid \mathcal{G}, \mathcal{C}^t\right) -\end{align*} -$$ - -where $$\quad p_\theta\left(\mathcal{C}^{t-1} \mid \mathcal{G}, \mathcal{C}^t\right)=\mathcal{N}\left(\mathcal{C}^{t-1} ; \mu_\theta\left(\mathcal{G}, \mathcal{C}^t, t\right), \sigma_t^2 I\right)$$ - - - - - -Hence, the neural network in the reverse process needs to learn/represent the mean and variance. However, just like the DDPM paper, GeoDiff also lets the variance be user-defined and fixed, and $$\mu_\theta$$ is the neural network that estimates means. - -GeoDiff uses a parametrisation trick inspired by the diffusion model implementation from the DDPM paper such that this parametrisation resembles Langevin dynamics and simplifies the diffusion model's variational bound to an objective that resembles denoising score matching. Moreover, in the context of molecular conformation generation, this parametrisation trick is analogous to the physical force fields , which also gradually push particles towards convergence around the equilibrium states, and is defined by the following equation: - -$$ -\begin{align*}\tag{4} -\mu_\theta\left(\mathcal{C}^t, t\right)=\frac{1}{\sqrt{\alpha_t}}\left(\mathcal{C}^t-\frac{\beta_t}{\sqrt{1-\bar{\alpha}_t}} \epsilon_\theta\left(\mathcal{G}, \mathcal{C}^t, t\right)\right) -\end{align*} -$$ - -where $$\epsilon_\theta$$ are neural networks with trainable parameters $$\theta$$. - -Now, we need to make $$\epsilon_\theta$$ roto-translational equivariant which we elaborate on in the next section. - -### Making the reverse process roto-translation equivariant - -Firstly, we need to assume the prior distribution of the conformations and the intermediary conformations generated during the forward process are systems with zero centre of mass (CoM) or CoM-free systems . By considering CoM-free systems, moving the particles to zero CoM can always ensure translational invariance in the Markov kernels. - -GeoDiff employs the use of an equivariant convolutional layer, named graph field network (GFN) inspired by . In the $$l$$-th layer, GFN takes node embeddings $$h_l \in \mathbb{R}^{n \times b}$$ ($$b$$ denotes the feature dimension) and corresponding coordinate embeddings $$x_l \in \mathbb{R}^{n \times 3}$$ as inputs, and outputs $$h_{l+1}$$ and $$x_{l+1}$$ as follows: - -$$ -\begin{align} \tag{5} -& \mathbf{m}_{i j}=\Phi_m\left(\mathbf{h}_i^l, \mathbf{h}_j^l,\left\|\mathbf{x}_i^l-\mathbf{x}_j^l\right\|^2, e_{i j} ; \theta_m\right) \\ \tag{6} -& \mathbf{h}_i^{l+1}=\Phi_h\left(\mathbf{h}_i^l, \sum_{j \in \mathcal{N}(i)} \mathbf{m}_{i j} ; \theta_h\right) \\ -& \mathbf{x}_i^{l+1}=\sum_{j \in \mathcal{N}(i)} \frac{1}{d_{i j}}\left(\mathbf{c}_i-\mathbf{c}_j\right) \Phi_x\left(\mathbf{m}_{i j} ; \theta_x\right) \tag{7} -\end{align} -$$ - - - -where -- $$\Phi$$ are feed-forward networks -- $$d_{ij}$$ are interatomic distances -- $$\mathcal{N}(i)$$ is the neighbourhood of the $$i$$-th node, which consists of both connected atoms and other ones within a radius threshold $$\tau$$. - - -By introducing the neighbourhood function, we enable the model to accurately represent distant interactions between atoms, as well as the ability to handle partially disconnected molecular graphs. Initial embeddings $$h_0$$ are combinations of atom and timestep embeddings, and $$x_0$$ are atomic coordinates. A key change in GFN compared to a vanilla GNN is $$x$$ being updated as a combination of radial directions weighted by $$\Phi_x$$: $$\mathbb{R}^b \rightarrow \mathbb{R}$$ as seen in equation $$(7)$$. This allows the roto-translation equivariance property to be induced in the reverse process. - - - -### Improved Training Objective - -Now, we need to set the training objective having considered the reverse process dynamics. We cannot compute the exact log-likelihood of the generative process, as it involves computing the likelihood of the observed molecular conformation given the parameters of the model. However, this likelihood is difficult to compute, as it would require integrating over all possible intermediate conformations, giving us a high-dimensional integral that cannot be solved analytically. Therefore, the authors have opted to maximize the variational lower bound (ELBO), as defined below: - - -$$\begin{aligned} \mathbb{E}\left[\log p_\theta\left(\mathcal{C}^0 \mid \mathcal{G}\right)\right] & =\mathbb{E}\left[\log \mathbb{E}_{q\left(\mathcal{C}^{1: T} \mid \mathcal{C}^0\right)} \frac{p_\theta\left(\mathcal{C}^{0: T} \mid \mathcal{G}\right)}{q\left(\mathcal{C}^{1: T} \mid \mathcal{C}^0\right)}\right] \\ & \geq-\mathbb{E}_q\left[\sum_{t=1}^T D_{\mathrm{KL}}\left(q\left(\mathcal{C}^{t-1} \mid \mathcal{C}^t, \mathcal{C}^0\right) \| p_\theta\left(\mathcal{C}^{t-1} \mid \mathcal{C}^t, \mathcal{G}\right)\right)\right]:=-\mathcal{L}_{\mathrm{ELBO}}\end{aligned}$$ - -where $$q\left(\mathcal{C}^{t-1} \mid \mathcal{C}^t, \mathcal{C}^0\right)$$ is analytically tractable as $$\mathcal{N}\left(\frac{\sqrt{\bar{\alpha}_{t-1}} \beta_t}{1-\bar{\alpha}_t} \mathcal{C}^0+\frac{\sqrt{\alpha_t}\left(1-\bar{\alpha}_{t-1}\right)}{1-\bar{\alpha}_t} \mathcal{C}^t, \frac{1-\bar{\alpha}_{t-1}}{1-\bar{\alpha}_t} \beta_t\right)$$. - - -Using the parametrisation trick in the reverse process as seen in equation $$(4)$$, the ELBO could be simplified by taking the KL divergences between Gaussians as weighted $$\mathcal{L}_2$$ distances between the means $$\epsilon_\theta$$ and $$\epsilon^3$$ as follows: -$$ -\mathcal{L}_{\mathrm{ELBO}}=\sum_{t=1}^T \gamma_t \mathbb{E}_{\left\{\mathcal{C}^0, \mathcal{G}\right\} \sim q\left(\mathcal{C}^0, \mathcal{G}\right), \epsilon \sim \mathcal{N}(0, I)}\left[\left\|\epsilon-\epsilon_\theta\left(\mathcal{G}, \mathcal{C}^t, t\right)\right\|_2^2\right] -$$ -where $$\mathcal{C}^t=\sqrt{\bar{\alpha}_t} \mathcal{C}^0+\sqrt{1-\bar{\alpha}_t} \epsilon$$. - -The idea behind this objective is to independently sample chaotic conformations of different timesteps from $$q\left(C^{t-1} \mid C^t, C^0\right)$$, and use $$\epsilon_\theta$$ to approximate the noise vector $$\epsilon$$. - - - -### Sampling - -Now, we can generate stable molecular conformations via sampling. Given a graph $$\mathcal{G}$$, its geometry $$\mathcal{C}^0$$ is generated by first sampling chaotic particles $$\mathcal{C}^T \sim p\left(\mathcal{C}^T\right)$$. For each timestep in the reverse process $$t=T, T-$$ $$1, \cdots, 1$$, we first shift the CoM of the conformation to zero, compute the transition means, $$\mu_\theta\left(\mathcal{G}, \mathcal{C}^t, t\right)$$, using equation $$(4)$$ and sample $$\mathcal{C}^{t-1} \sim$$ $$p_\theta\left(\mathcal{C}^{t-1} \mid \mathcal{G}, \mathcal{C}^t\right)$$. The sampling algorithm is given in pseudo-code below: - - - -| Algorithm 1 Sampling Algorithm of GEODIFF | -|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------| -| Input: the molecular graph $$\mathcal{G}$$, the learned reverse model $$\epsilon_\theta$$. | -| Output: the molecular conformation $$\mathcal{C}$$. | -| 1: Sample $$\mathcal{C}^T \sim p\left(\mathcal{C}^T\right)=\mathcal{N}(0, I)$$ | -| 2: for $$s=T, T-1, \cdots, 1$$ do | -| 3: $$\quad$$ Shift $$\mathcal{C}^s$$ to zero CoM | -| 4: $$\quad$$ Compute $$\mu_\theta\left(\mathcal{C}^s, \mathcal{G}, s\right)$$ from $$\epsilon_\theta\left(\mathcal{C}^s, \mathcal{G}, s\right)$$ using equation 4 | -| 5: $$\quad$$ Sample $$\mathcal{C}^{s-1} \sim \mathcal{N}\left(\mathcal{C}^{s-1} ; \mu_\theta\left(\mathcal{C}^{\mathcal{s}}, \mathcal{G}, s\right), \sigma_t^2 I\right)$$ | -| 6: end for | -| 7: return $$\mathcal{C}^0$$ as $\mathcal{C}$$ | - - - -## But why generative models? -The purpose of prediciting molecular conformations is to enable human experts to analyse the properties of the molecules and understand how these properties affect the viability of a molecule as a drug candidate. Therefore, it is important that the molecular conformations generated are diverse to capture the different possible conformations that could occur in nature but the conformations generated should not deviate significantly such that the analysis is affected. To set a threshold for the different possible conformations, the standard metric used has been selecting conformations that are within a certain root-mean-square deviation (RMSD), say a few ångströms, of the true structure. - -However, the objective of maximizing the proportion of predictions with RMSD within some tolerance $$\epsilon$$ is not differentiable and thus, cannot be used for training with stochastic gradient descent. Instead, maximizing the expected proportion of predictions with RMSD < $$\epsilon$$ corresponds to maximizing the likelihood of the true structure under the model’s output distribution, in the limit as $$\epsilon$$ goes to 0. This concept inspires the development of a generative model, whose objective is to minimize an upper bound on the negative log-likelihood of observed molecular structures under the distribution of the model. As a result, the problem of molecular docking is treated as a task of learning a distribution over possible positions of a ligand molecule conditioned on the protein structure and a diffusion generative model is developed to represent this space. Therefore, this observation has motivated several works on the use of generative models for molecular conformation generation, such as GeoDiff. - - -## Future work - -While diffusion models have shown promising results over the past months, there is still a need for further research and development to address some of the limitations and drawbacks of the use of diffusion models in conformer generation. As explained in our blog post, generative models are well-suited for molecular conformation generation. However, there are other kinds of established generative models, such as autoencoders that have been used for the same task . For instance, comparing diffusion models and autoencoders, diffusion models can handle all noise levels with a single set of parameters, without any bottlenecks, which an autoencoder would have . Thus, it is essential to study the advantages and disadvantages of different types and variants of generative models for conformation generation and understand what changes could be done to them to make them more suitable for molecular conformation. - -It must be noted that the experiments described in the study are done on benchmark geometric datasets, GEOM-QM9 and GEOM-Drugs , rather than industrial data, with a relatively small number of samples/drug/molecular compounds. Industry data may exhibit greater variability than standard geometric datasets, as they may be more diverse, complex and subject to greater fluctuations than these geometric datasets, which tend to be more standardized and more predictable. - - -GeoDiff as a framework sets a precedent for future work that could marry the concepts of geometric deep learning and diffusion models across various domains. In the context of drug discovery, it would be interesting to extend this framework to more challenging structures, such as proteins, which may enable more accurate prediction of protein folding, protein-protein interactions and protein-ligand binding positions which would facilitate the design of new drugs and treatments. Additionally, this framework could potentially be applied to other complex systems beyond proteins, such as RNA molecules, to enable more efficient and accurate prediction of their behaviour and properties. Continued research in this area has the potential to revolutionize drug discovery and development, as well as advance our understanding of the fundamental principles governing the behaviour of complex biological systems. - - -Research on the application of diffusion models in the life and natural sciences is still in its infancy, with great potential for improvement in terms of both theory as well as empirical testing. The GeoDiff model could be improved in terms of more efficient sampling and improved likelihood maximization methods. Traditionally, generating samples from diffusion models demand iterative approaches that involve a large number of evaluation steps. Recent work, such as the paper on Torsional Diffusion was able to speed up the sampling process, while also enhancing the quality of the resulting samples. Experimentally, Torsional Diffusion only takes 5 to 20 steps in comparison to GeoDiff which takes around 5000 steps . - -Looking ahead, GeoDiff has set a clear example for the use of diffusion models on geometric representations which could be extended to several problems, especially in the field of drug discovery. The novel contributions made by - are motivated by the physical characteristics of the molecular conformation generation problem, which has resulted in a strong candidate method for conformation generation that could act as a springboard for even more effective and efficient methods that would eventually benefit the field of drug discovery as a whole. - - - - - - - - - - - diff --git a/_projects/1_project.md b/_projects/1_project.md deleted file mode 100644 index 3f7cf783..00000000 --- a/_projects/1_project.md +++ /dev/null @@ -1,80 +0,0 @@ ---- -layout: page -title: project 1 -description: a project with a background image -img: assets/img/12.jpg -importance: 1 -category: work ---- - -Every project has a beautiful feature showcase page. -It's easy to include images in a flexible 3-column grid format. -Make your photos 1/3, 2/3, or full width. - -To give your project a background in the portfolio page, just add the img tag to the front matter like so: - - --- - layout: page - title: project - description: a project with a background image - img: /assets/img/12.jpg - --- - -
-
- {% include figure.html path="assets/img/1.jpg" title="example image" class="img-fluid rounded z-depth-1" %} -
-
- {% include figure.html path="assets/img/3.jpg" title="example image" class="img-fluid rounded z-depth-1" %} -
-
- {% include figure.html path="assets/img/5.jpg" title="example image" class="img-fluid rounded z-depth-1" %} -
-
-
- Caption photos easily. On the left, a road goes through a tunnel. Middle, leaves artistically fall in a hipster photoshoot. Right, in another hipster photoshoot, a lumberjack grasps a handful of pine needles. -
-
-
- {% include figure.html path="assets/img/5.jpg" title="example image" class="img-fluid rounded z-depth-1" %} -
-
-
- This image can also have a caption. It's like magic. -
- -You can also put regular text between your rows of images. -Say you wanted to write a little bit about your project before you posted the rest of the images. -You describe how you toiled, sweated, *bled* for your project, and then... you reveal its glory in the next row of images. - - -
-
- {% include figure.html path="assets/img/6.jpg" title="example image" class="img-fluid rounded z-depth-1" %} -
-
- {% include figure.html path="assets/img/11.jpg" title="example image" class="img-fluid rounded z-depth-1" %} -
-
-
- You can also have artistically styled 2/3 + 1/3 images, like these. -
- - -The code is simple. -Just wrap your images with `
` and place them inside `
` (read more about the Bootstrap Grid system). -To make images responsive, add `img-fluid` class to each; for rounded corners and shadows use `rounded` and `z-depth-1` classes. -Here's the code for the last row of images above: - -{% raw %} -```html -
-
- {% include figure.html path="assets/img/6.jpg" title="example image" class="img-fluid rounded z-depth-1" %} -
-
- {% include figure.html path="assets/img/11.jpg" title="example image" class="img-fluid rounded z-depth-1" %} -
-
-``` -{% endraw %} diff --git a/_projects/2_project.md b/_projects/2_project.md deleted file mode 100644 index bebf7961..00000000 --- a/_projects/2_project.md +++ /dev/null @@ -1,80 +0,0 @@ ---- -layout: page -title: project 2 -description: a project with a background image -img: assets/img/3.jpg -importance: 2 -category: work ---- - -Every project has a beautiful feature showcase page. -It's easy to include images in a flexible 3-column grid format. -Make your photos 1/3, 2/3, or full width. - -To give your project a background in the portfolio page, just add the img tag to the front matter like so: - - --- - layout: page - title: project - description: a project with a background image - img: /assets/img/12.jpg - --- - -
-
- {% include figure.html path="assets/img/1.jpg" title="example image" class="img-fluid rounded z-depth-1" %} -
-
- {% include figure.html path="assets/img/3.jpg" title="example image" class="img-fluid rounded z-depth-1" %} -
-
- {% include figure.html path="assets/img/5.jpg" title="example image" class="img-fluid rounded z-depth-1" %} -
-
-
- Caption photos easily. On the left, a road goes through a tunnel. Middle, leaves artistically fall in a hipster photoshoot. Right, in another hipster photoshoot, a lumberjack grasps a handful of pine needles. -
-
-
- {% include figure.html path="assets/img/5.jpg" title="example image" class="img-fluid rounded z-depth-1" %} -
-
-
- This image can also have a caption. It's like magic. -
- -You can also put regular text between your rows of images. -Say you wanted to write a little bit about your project before you posted the rest of the images. -You describe how you toiled, sweated, *bled* for your project, and then... you reveal its glory in the next row of images. - - -
-
- {% include figure.html path="assets/img/6.jpg" title="example image" class="img-fluid rounded z-depth-1" %} -
-
- {% include figure.html path="assets/img/11.jpg" title="example image" class="img-fluid rounded z-depth-1" %} -
-
-
- You can also have artistically styled 2/3 + 1/3 images, like these. -
- - -The code is simple. -Just wrap your images with `
` and place them inside `
` (read more about the Bootstrap Grid system). -To make images responsive, add `img-fluid` class to each; for rounded corners and shadows use `rounded` and `z-depth-1` classes. -Here's the code for the last row of images above: - -{% raw %} -```html -
-
- {% include figure.html path="assets/img/6.jpg" title="example image" class="img-fluid rounded z-depth-1" %} -
-
- {% include figure.html path="assets/img/11.jpg" title="example image" class="img-fluid rounded z-depth-1" %} -
-
-``` -{% endraw %} diff --git a/_projects/3_project.md b/_projects/3_project.md deleted file mode 100644 index 3f3cbf70..00000000 --- a/_projects/3_project.md +++ /dev/null @@ -1,81 +0,0 @@ ---- -layout: page -title: project 3 -description: a project that redirects to another website -img: assets/img/7.jpg -redirect: https://unsplash.com -importance: 3 -category: work ---- - -Every project has a beautiful feature showcase page. -It's easy to include images in a flexible 3-column grid format. -Make your photos 1/3, 2/3, or full width. - -To give your project a background in the portfolio page, just add the img tag to the front matter like so: - - --- - layout: page - title: project - description: a project with a background image - img: /assets/img/12.jpg - --- - -
-
- {% include figure.html path="assets/img/1.jpg" title="example image" class="img-fluid rounded z-depth-1" %} -
-
- {% include figure.html path="assets/img/3.jpg" title="example image" class="img-fluid rounded z-depth-1" %} -
-
- {% include figure.html path="assets/img/5.jpg" title="example image" class="img-fluid rounded z-depth-1" %} -
-
-
- Caption photos easily. On the left, a road goes through a tunnel. Middle, leaves artistically fall in a hipster photoshoot. Right, in another hipster photoshoot, a lumberjack grasps a handful of pine needles. -
-
-
- {% include figure.html path="assets/img/5.jpg" title="example image" class="img-fluid rounded z-depth-1" %} -
-
-
- This image can also have a caption. It's like magic. -
- -You can also put regular text between your rows of images. -Say you wanted to write a little bit about your project before you posted the rest of the images. -You describe how you toiled, sweated, *bled* for your project, and then... you reveal its glory in the next row of images. - - -
-
- {% include figure.html path="assets/img/6.jpg" title="example image" class="img-fluid rounded z-depth-1" %} -
-
- {% include figure.html path="assets/img/11.jpg" title="example image" class="img-fluid rounded z-depth-1" %} -
-
-
- You can also have artistically styled 2/3 + 1/3 images, like these. -
- - -The code is simple. -Just wrap your images with `
` and place them inside `
` (read more about the Bootstrap Grid system). -To make images responsive, add `img-fluid` class to each; for rounded corners and shadows use `rounded` and `z-depth-1` classes. -Here's the code for the last row of images above: - -{% raw %} -```html -
-
- {% include figure.html path="assets/img/6.jpg" title="example image" class="img-fluid rounded z-depth-1" %} -
-
- {% include figure.html path="assets/img/11.jpg" title="example image" class="img-fluid rounded z-depth-1" %} -
-
-``` -{% endraw %} diff --git a/_projects/4_project.md b/_projects/4_project.md deleted file mode 100644 index edb5dd25..00000000 --- a/_projects/4_project.md +++ /dev/null @@ -1,80 +0,0 @@ ---- -layout: page -title: project 4 -description: another without an image -img: -importance: 3 -category: fun ---- - -Every project has a beautiful feature showcase page. -It's easy to include images in a flexible 3-column grid format. -Make your photos 1/3, 2/3, or full width. - -To give your project a background in the portfolio page, just add the img tag to the front matter like so: - - --- - layout: page - title: project - description: a project with a background image - img: /assets/img/12.jpg - --- - -
-
- {% include figure.html path="assets/img/1.jpg" title="example image" class="img-fluid rounded z-depth-1" %} -
-
- {% include figure.html path="assets/img/3.jpg" title="example image" class="img-fluid rounded z-depth-1" %} -
-
- {% include figure.html path="assets/img/5.jpg" title="example image" class="img-fluid rounded z-depth-1" %} -
-
-
- Caption photos easily. On the left, a road goes through a tunnel. Middle, leaves artistically fall in a hipster photoshoot. Right, in another hipster photoshoot, a lumberjack grasps a handful of pine needles. -
-
-
- {% include figure.html path="assets/img/5.jpg" title="example image" class="img-fluid rounded z-depth-1" %} -
-
-
- This image can also have a caption. It's like magic. -
- -You can also put regular text between your rows of images. -Say you wanted to write a little bit about your project before you posted the rest of the images. -You describe how you toiled, sweated, *bled* for your project, and then... you reveal its glory in the next row of images. - - -
-
- {% include figure.html path="assets/img/6.jpg" title="example image" class="img-fluid rounded z-depth-1" %} -
-
- {% include figure.html path="assets/img/11.jpg" title="example image" class="img-fluid rounded z-depth-1" %} -
-
-
- You can also have artistically styled 2/3 + 1/3 images, like these. -
- - -The code is simple. -Just wrap your images with `
` and place them inside `
` (read more about the Bootstrap Grid system). -To make images responsive, add `img-fluid` class to each; for rounded corners and shadows use `rounded` and `z-depth-1` classes. -Here's the code for the last row of images above: - -{% raw %} -```html -
-
- {% include figure.html path="assets/img/6.jpg" title="example image" class="img-fluid rounded z-depth-1" %} -
-
- {% include figure.html path="assets/img/11.jpg" title="example image" class="img-fluid rounded z-depth-1" %} -
-
-``` -{% endraw %} diff --git a/_projects/5_project.md b/_projects/5_project.md deleted file mode 100644 index efd9b6cf..00000000 --- a/_projects/5_project.md +++ /dev/null @@ -1,80 +0,0 @@ ---- -layout: page -title: project 5 -description: a project with a background image -img: assets/img/1.jpg -importance: 3 -category: fun ---- - -Every project has a beautiful feature showcase page. -It's easy to include images in a flexible 3-column grid format. -Make your photos 1/3, 2/3, or full width. - -To give your project a background in the portfolio page, just add the img tag to the front matter like so: - - --- - layout: page - title: project - description: a project with a background image - img: /assets/img/12.jpg - --- - -
-
- {% include figure.html path="assets/img/1.jpg" title="example image" class="img-fluid rounded z-depth-1" %} -
-
- {% include figure.html path="assets/img/3.jpg" title="example image" class="img-fluid rounded z-depth-1" %} -
-
- {% include figure.html path="assets/img/5.jpg" title="example image" class="img-fluid rounded z-depth-1" %} -
-
-
- Caption photos easily. On the left, a road goes through a tunnel. Middle, leaves artistically fall in a hipster photoshoot. Right, in another hipster photoshoot, a lumberjack grasps a handful of pine needles. -
-
-
- {% include figure.html path="assets/img/5.jpg" title="example image" class="img-fluid rounded z-depth-1" %} -
-
-
- This image can also have a caption. It's like magic. -
- -You can also put regular text between your rows of images. -Say you wanted to write a little bit about your project before you posted the rest of the images. -You describe how you toiled, sweated, *bled* for your project, and then... you reveal its glory in the next row of images. - - -
-
- {% include figure.html path="assets/img/6.jpg" title="example image" class="img-fluid rounded z-depth-1" %} -
-
- {% include figure.html path="assets/img/11.jpg" title="example image" class="img-fluid rounded z-depth-1" %} -
-
-
- You can also have artistically styled 2/3 + 1/3 images, like these. -
- - -The code is simple. -Just wrap your images with `
` and place them inside `
` (read more about the Bootstrap Grid system). -To make images responsive, add `img-fluid` class to each; for rounded corners and shadows use `rounded` and `z-depth-1` classes. -Here's the code for the last row of images above: - -{% raw %} -```html -
-
- {% include figure.html path="assets/img/6.jpg" title="example image" class="img-fluid rounded z-depth-1" %} -
-
- {% include figure.html path="assets/img/11.jpg" title="example image" class="img-fluid rounded z-depth-1" %} -
-
-``` -{% endraw %} diff --git a/_projects/6_project.md b/_projects/6_project.md deleted file mode 100644 index 9a95d6e8..00000000 --- a/_projects/6_project.md +++ /dev/null @@ -1,80 +0,0 @@ ---- -layout: page -title: project 6 -description: a project with no image -img: -importance: 4 -category: fun ---- - -Every project has a beautiful feature showcase page. -It's easy to include images in a flexible 3-column grid format. -Make your photos 1/3, 2/3, or full width. - -To give your project a background in the portfolio page, just add the img tag to the front matter like so: - - --- - layout: page - title: project - description: a project with a background image - img: /assets/img/12.jpg - --- - -
-
- {% include figure.html path="assets/img/1.jpg" title="example image" class="img-fluid rounded z-depth-1" %} -
-
- {% include figure.html path="assets/img/3.jpg" title="example image" class="img-fluid rounded z-depth-1" %} -
-
- {% include figure.html path="assets/img/5.jpg" title="example image" class="img-fluid rounded z-depth-1" %} -
-
-
- Caption photos easily. On the left, a road goes through a tunnel. Middle, leaves artistically fall in a hipster photoshoot. Right, in another hipster photoshoot, a lumberjack grasps a handful of pine needles. -
-
-
- {% include figure.html path="assets/img/5.jpg" title="example image" class="img-fluid rounded z-depth-1" %} -
-
-
- This image can also have a caption. It's like magic. -
- -You can also put regular text between your rows of images. -Say you wanted to write a little bit about your project before you posted the rest of the images. -You describe how you toiled, sweated, *bled* for your project, and then... you reveal its glory in the next row of images. - - -
-
- {% include figure.html path="assets/img/6.jpg" title="example image" class="img-fluid rounded z-depth-1" %} -
-
- {% include figure.html path="assets/img/11.jpg" title="example image" class="img-fluid rounded z-depth-1" %} -
-
-
- You can also have artistically styled 2/3 + 1/3 images, like these. -
- - -The code is simple. -Just wrap your images with `
` and place them inside `
` (read more about the Bootstrap Grid system). -To make images responsive, add `img-fluid` class to each; for rounded corners and shadows use `rounded` and `z-depth-1` classes. -Here's the code for the last row of images above: - -{% raw %} -```html -
-
- {% include figure.html path="assets/img/6.jpg" title="example image" class="img-fluid rounded z-depth-1" %} -
-
- {% include figure.html path="assets/img/11.jpg" title="example image" class="img-fluid rounded z-depth-1" %} -
-
-``` -{% endraw %} diff --git a/_sass/_base.scss b/_sass/_base.scss deleted file mode 100644 index 7b826527..00000000 --- a/_sass/_base.scss +++ /dev/null @@ -1,658 +0,0 @@ -/******************************************************************************* - * Styles for the base elements of the theme. - ******************************************************************************/ - -// Typography - -p, h1, h2, h3, h4, h5, h6, em, div, li, span, strong { - color: var(--global-text-color); -} - -hr { - border-top: 1px solid var(--global-divider-color); -} - -table { - td, th { - color: var(--global-text-color); - } - td { - font-size: 1rem; - } -} - -a, table.table a { - color: var(--global-theme-color); - &:hover { - color: var(--global-theme-color); - text-decoration: underline; - } - &:hover:after :not(.nav-item.dropdown) { - width: 100%; - } -} - -figure, img { - max-width: 90vw; -} - -blockquote { - background: var(--global-bg-color); - border-left: 2px solid var(--global-theme-color); - margin: 1.5em 10px; - padding: 0.5em 10px; - font-size: 1.1rem; -} - -// Math - -.equation { - margin-bottom: 1rem; - text-align: center; -} - -// Caption - -.caption { - font-size: 0.875rem; - margin-top: 0.75rem; - margin-bottom: 1.5rem; - text-align: center; -} - -// Card - -.card { - background-color: var(--global-card-bg-color); - - img { - width: 100%; - } - - .card-title { - color: var(--global-text-color); - } - - .card-item { - width: auto; - margin-bottom: 10px; - - .row { - display: flex; - align-items: center; - } - } -} - -// Citation - -.citation, .citation-number { - color: var(--global-theme-color); -} - -// Profile - -.profile { - width: 100%; - - .address { - margin-bottom: 5px; - margin-top: 5px; - font-family: monospace; - p { - display: inline-block; - margin: 0; - } - } -} -.profile.float-right{ - margin-left: 1rem; -} -.profile.float-left{ - margin-right: 1rem; -} - -@media (min-width: 576px) { - .profile { - width: 30%; - .address { - p { display: block; } - } - } -} - -.post-description { - margin-bottom: 2rem; - font-size: 0.875rem; - a { - color: inherit; - &:hover { - color: var(--global-theme-color); - text-decoration: none; - } - } -} - - -// Navbar customization - -.navbar { - box-shadow: none; - border-bottom: 1px solid var(--global-divider-color); - background-color: var(--global-bg-color); - opacity: 0.95; -} -.navbar .dropdown-menu { - background-color: var(--global-bg-color); - border: 1px solid var(--global-divider-color); - a:not(.active) { - color: var(--global-text-color); - } - a:hover { - color: var(--global-hover-color); - } - .dropdown-divider { - border-top: 1px solid var(--global-divider-color) !important; - } -} -.dropdown-item { - color: var(--global-text-color); - &:hover { - color: var(--global-hover-color); - background-color: var(--global-bg-color); - } -} -.navbar.navbar-light { - a { - &:hover { - text-decoration: none; - } - } - .navbar-brand { - color: var(--global-text-color); - } - .navbar-nav .nav-item .nav-link { - color: var(--global-text-color); - &:hover { - color: var(--global-hover-color); - } - } - .navbar-nav .nav-item.active>.nav-link { - background-color: inherit; - font-weight: bolder; - color: var(--global-theme-color); - &:hover { - color: var(--global-hover-color); - } - } - .navbar-brand.social { - padding-bottom: 0; - padding-top: 0; - font-size: 1.7rem; - a { - i::before { - color: var(--global-text-color); - transition-property: all 0.2s ease-in-out; - } - &:hover { - i::before { - color: var(--global-theme-color); - } - } - } - } -} - -.navbar-toggler { - .icon-bar { - display: block; - width: 22px; - height: 2px; - background-color: var(--global-text-color); - border-radius: 1px; - margin-bottom: 4px; - transition: all 0.2s; - } - .top-bar { - transform: rotate(45deg); - transform-origin: 10% 10%; - } - .middle-bar { - opacity: 0; - } - .bottom-bar { - transform: rotate(-45deg); - transform-origin: 10% 90%; - } -} - -.navbar-toggler.collapsed { - .top-bar { - transform: rotate(0); - } - .middle-bar { - opacity: 1; - } - .bottom-bar { - transform: rotate(0); - } -} - -#light-toggle { - padding: 0; - border: 0; - background-color: inherit; - color: var(--global-text-color); - &:hover { - color: var(--global-hover-color); - } -} - -// Social (bottom) - -.social { - text-align: center; - .contact-icons { - font-size: 4rem; - a { - i::before { - color: var(--global-text-color); - transition-property: all 0.2s ease-in-out; - } - &:hover { - i::before { - color: var(--global-theme-color); - } - } - } - } - .contact-note { - font-size: 0.8rem; - } -} - - -// Footer -footer.fixed-bottom { - background-color: var(--global-footer-bg-color); - font-size: 0.75rem; - .container { - color: var(--global-footer-text-color); - padding-top: 9px; - padding-bottom: 8px; - } - a { - color: var(--global-footer-link-color); - &:hover { - color: var(--global-theme-color); - text-decoration: none; - } - } -} - -footer.sticky-bottom { - border-top: 1px solid var(--global-divider-color); - padding-top: 40px; - padding-bottom: 40px; - font-size: 0.9rem; -} - -// CV - -.cv { - margin-bottom: 40px; - - .card { - background-color: var(--global-card-bg-color); - border: 1px solid var(--global-divider-color); - - .list-group-item { - background-color: inherit; - - .badge { - color: var(--global-card-bg-color) !important; - background-color: var(--global-theme-color) !important; - } - } - } -} - -// Repositories - -@media (min-width: 768px) { - .repo { - max-width: 50%; - } -} - -// Blog - -.header-bar { - border-bottom: 1px solid var(--global-divider-color); - text-align: center; - padding-top: 2rem; - padding-bottom: 3rem; - h1 { - color: var(--global-theme-color); - font-size: 5rem; - } -} - -.tag-list { - border-bottom: 1px solid var(--global-divider-color); - text-align: center; - padding-top: 1rem; - - ul { - justify-content: center; - display: flow-root; - - p, li { - list-style: none; - display: inline-block; - padding: 1rem 0.5rem; - color: var(--global-text-color-light); - } - } -} - -.post-list { - margin: 0; - margin-bottom: 40px; - padding: 0; - li { - border-bottom: 1px solid var(--global-divider-color); - list-style: none; - padding-top: 2rem; - padding-bottom: 2rem; - .post-meta { - color: var(--global-text-color-light); - font-size: 0.875rem; - margin-bottom: 0; - } - .post-tags { - color: var(--global-text-color-light); - font-size: 0.875rem; - padding-top: 0.25rem; - padding-bottom: 0; - } - a { - color: var(--global-text-color); - text-decoration: none; - &:hover { - color: var(--global-theme-color); - } - } - } -} - -.pagination { - .page-item { - .page-link { - color: var(--global-text-color); - &:hover { - color: $black-color; - } - } - &.active .page-link { - color: $white-color; - background-color: var(--global-theme-color); - &:hover { - background-color: var(--global-theme-color); - } - } - } -} - - -// Distill - -.distill { - a:hover { - border-bottom-color: var(--global-theme-color); - text-decoration: none; - } -} - - -// Projects - -.projects { - a { - text-decoration: none; - - &:hover { - .card-title { - color: var(--global-theme-color); - } - } - } - - .card { - img { - width: 100%; - } - } - - .card-item { - width: auto; - margin-bottom: 10px; - - .row { - display: flex; - align-items: center; - } - } - - .grid-sizer, .grid-item { - width: 250px; - margin-bottom: 10px; - } - - h2.category { - color: var(--global-divider-color); - border-bottom: 1px solid var(--global-divider-color); - padding-top: 0.5rem; - margin-top: 2rem; - margin-bottom: 1rem; - text-align: right; - } -} - - -// Publications - -.publications { - margin-top: 2rem; - h1 { - color: var(--global-theme-color); - font-size: 2rem; - text-align: center; - margin-top: 1em; - margin-bottom: 1em; - } - h2 { - margin-bottom: 1rem; - span { - font-size: 1.5rem; - } - } - h2.year { - color: var(--global-divider-color); - border-top: 1px solid var(--global-divider-color); - padding-top: 1rem; - margin-top: 2rem; - margin-bottom: -2rem; - text-align: right; - } - ol.bibliography { - list-style: none; - padding: 0; - margin-top: 0; - - li { - margin-bottom: 1rem; - .preview { - width: 100%; - min-width: 80px; - max-width: 200px; - } - .abbr { - height: 2rem; - margin-bottom: 0.5rem; - abbr { - display: inline-block; - background-color: var(--global-theme-color); - padding-left: 1rem; - padding-right: 1rem; - a { - color: white; - &:hover { - text-decoration: none; - } - } - } - .award { - color: var(--global-theme-color) !important; - border: 1px solid var(--global-theme-color); - } - } - .title { - font-weight: bolder; - } - .author { - a { - border-bottom: 1px dashed var(--global-theme-color); - &:hover { - border-bottom-style: solid; - text-decoration: none; - } - } - > em { - border-bottom: 1px solid; - font-style: normal; - } - > span.more-authors { - color: var(--global-text-color-light); - border-bottom: 1px dashed var(--global-text-color-light); - cursor: pointer; - &:hover { - color: var(--global-text-color); - border-bottom: 1px dashed var(--global-text-color); - } - } - } - .links { - a.btn { - color: var(--global-text-color); - border: 1px solid var(--global-text-color); - padding-left: 1rem; - padding-right: 1rem; - padding-top: 0.25rem; - padding-bottom: 0.25rem; - &:hover { - color: var(--global-theme-color); - border-color: var(--global-theme-color); - } - } - } - .hidden { - font-size: 0.875rem; - max-height: 0px; - overflow: hidden; - text-align: justify; - transition-property: 0.15s ease; - -moz-transition: 0.15s ease; - -ms-transition: 0.15s ease; - -o-transition: 0.15s ease; - transition: all 0.15s ease; - - p { - line-height: 1.4em; - margin: 10px; - } - pre { - font-size: 1em; - line-height: 1.4em; - padding: 10px; - } - } - .hidden.open { - max-height: 100em; - transition-property: 0.15s ease; - -moz-transition: 0.15s ease; - -ms-transition: 0.15s ease; - -o-transition: 0.15s ease; - transition: all 0.15s ease; - } - div.abstract.hidden { - border: dashed 1px var(--global-bg-color); - } - div.abstract.hidden.open { - border-color: var(--global-text-color); - } - } - } -} - -// Rouge Color Customization -figure.highlight { - margin: 0 0 1rem; -} - -pre { - color: var(--global-theme-color); - background-color: var(--global-code-bg-color); - border-radius: 6px; - padding: 6px 12px; - pre, code { - background-color: transparent; - border-radius: 0; - padding: 0; - } -} - -code { - color: var(--global-theme-color); - background-color: var(--global-code-bg-color); - border-radius: 3px; - padding: 3px 3px; -} - - -// Transitioning Themes -html.transition, -html.transition *, -html.transition *:before, -html.transition *:after { - transition: all 750ms !important; - transition-delay: 0 !important; -} - -// Extra Markdown style (post Customization) -.post{ - .post-meta{ - color: var(--global-text-color-light); - font-size: 0.875rem; - margin-bottom: 0; - } - .post-tags{ - color: var(--global-text-color-light); - font-size: 0.875rem; - padding-top: 0.25rem; - padding-bottom: 1rem; - a { - color: var(--global-text-color-light); - text-decoration: none; - &:hover { - color: var(--global-theme-color); - } - } - } - .post-content{ - blockquote { - border-left: 5px solid var(--global-theme-color); - padding: 8px; - } - } -} diff --git a/_sass/_distill.scss b/_sass/_distill.scss deleted file mode 100644 index d83fafd4..00000000 --- a/_sass/_distill.scss +++ /dev/null @@ -1,126 +0,0 @@ -/******************************************************************************* - * Style overrides for distill blog posts. - ******************************************************************************/ - -d-byline { - border-top-color: var(--global-divider-color) !important; -} - -d-byline h3 { - color: var(--global-text-color) !important; -} - -d-byline a, d-article d-byline a { - color: var(--global-text-color) !important; - &:hover { - color: var(--global-hover-color) !important; - } -} - -d-article { - border-top-color: var(--global-divider-color) !important; - a, p, h1, h2, h3, h4, h5, h6, li, table { - color: var(--global-text-color) !important; - } - a, h1, h2, hr, table, table th, table td { - border-bottom-color: var(--global-divider-color) !important; - } - a:hover { - border-bottom-color: var(--global-hover-color) !important; - } - b i { - display: inline; - } - - d-contents { - align-self: start; - grid-column: 1 / 4; - grid-row: auto / span 4; - justify-self: end; - margin-top: 0em; - padding-left: 2em; - padding-right: 3em; - border-right: 1px solid var(--global-divider-color); - width: calc(max(70%, 300px)); - margin-right: 0px; - margin-top: 0em; - display: grid; - grid-template-columns: - minmax(8px, 1fr) [toc] auto - minmax(8px, 1fr) [toc-line] 1px - minmax(32px, 2fr); - - nav { - grid-column: toc; - a { - border-bottom: none !important; - &:hover { - border-bottom: 1px solid var(--global-text-color) !important; - } - } - h3 { - margin-top: 0; - margin-bottom: 1em; - } - div { - display: block; - outline: none; - margin-bottom: 0.8em; - color: rgba(0, 0, 0, 0.8); - font-weight: bold; - } - ul { - padding-left: 1em; - margin-top: 0; - margin-bottom: 6px; - list-style-type: none; - li { - margin-bottom: 0.25em; - } - } - } - .figcaption { - line-height: 1.4em; - } - toc-line { - border-right: 1px solid var(--global-divider-color); - grid-column: toc-line; - } - } - - d-footnote { - scroll-margin-top: 66px; - } -} - -d-appendix { - border-top-color: var(--global-divider-color) !important; - color: var(--global-distill-app-color) !important; - h3, li, span { - color: var(--global-distill-app-color) !important; - } - a, a.footnote-backlink { - color: var(--global-distill-app-color) !important; - &:hover { - color: var(--global-hover-color) !important; - } - } -} - -@media (max-width: 1024px) { - d-article { - d-contents { - display: block; - grid-column-start: 2; - grid-column-end: -2; - padding-bottom: 0.5em; - margin-bottom: 1em; - padding-top: 0.5em; - width: 100%; - border: 1px solid var(--global-divider-color); - nav { - grid-column: none; - } - } - } -} diff --git a/_sass/_layout.scss b/_sass/_layout.scss deleted file mode 100644 index 9c10cac7..00000000 --- a/_sass/_layout.scss +++ /dev/null @@ -1,50 +0,0 @@ -/****************************************************************************** - * Content - ******************************************************************************/ - -body { - padding-bottom: 70px; - color: var(--global-text-color); - background-color: var(--global-bg-color); - - h1, h2, h3, h4, h5, h6 { - scroll-margin-top: 66px; - } -} - -body.fixed-top-nav { - // Add some padding for the nav-bar. - padding-top: 56px; -} - -body.sticky-bottom-footer { - // Remove padding below footer. - padding-bottom: 0; -} - -.container { - max-width: $max-content-width; -} - -// Profile -.profile { - img { - width: 100%; - } -} - -// TODO: redefine content layout. - - -/****************************************************************************** - * Publications - ******************************************************************************/ - -// TODO: redefine publications layout. - - -/***************************************************************************** -* Projects -*****************************************************************************/ - -// TODO: redefine projects layout. diff --git a/_sass/_themes.scss b/_sass/_themes.scss deleted file mode 100644 index e3fe03fd..00000000 --- a/_sass/_themes.scss +++ /dev/null @@ -1,100 +0,0 @@ -/******************************************************************************* - * Themes - ******************************************************************************/ - -:root { - --global-bg-color: #{$white-color}; - --global-code-bg-color: #{$code-bg-color-light}; - --global-text-color: #{$black-color}; - --global-text-color-light: #{$grey-color}; - --global-theme-color: #{$cyan-color}; - --global-hover-color: #{$cyan-color}; - --global-footer-bg-color: #{$grey-color-dark}; - --global-footer-text-color: #{$grey-color-light}; - --global-footer-link-color: #{$white-color}; - --global-distill-app-color: #{$grey-color}; - --global-divider-color: rgba(0,0,0,.1); - --global-card-bg-color: #{$white-color}; - - .fa-sun { - display : none; - } - .fa-moon { - padding-left: 10px; - padding-top: 12px; - display : block; - } - - .repo-img-light { - display: block; - } - .repo-img-dark { - display: none; - } -} - -.header-background .img { - // background-image: url("../img/ICLR-logo.png"); - background-repeat: no-repeat; - background-size: 400px; - background-position: center bottom; - height: 12em; - margin-bottom: 0em; - margin-top: -2.7em; -} - -html[data-theme='dark'] { - --global-bg-color: #{$grey-color-dark}; - --global-code-bg-color: #{$code-bg-color-dark}; - --global-text-color: #{$grey-color-light}; - --global-text-color-light: #{$grey-color-light}; - --global-theme-color: #{$cyan-color}; - --global-hover-color: #{$cyan-color}; - --global-footer-bg-color: #{$grey-color-light}; - --global-footer-text-color: #{$grey-color-dark}; - --global-footer-link-color: #{$black-color}; - --global-distill-app-color: #{$grey-color-light}; - --global-divider-color: #424246; - --global-card-bg-color: #{$grey-900}; - - .fa-sun { - padding-left: 10px; - padding-top: 12px; - display : block; - } - .fa-moon { - display : none; - } - - .repo-img-light { - display: none; - } - .repo-img-dark { - display: block; - } - -.header-background .img { - // background-image: url("../img/ICLR-logo-dark.png"); - background-repeat: no-repeat; - background-size: 400px; - background-position: center bottom; - height: 12em; - margin-bottom: 0em; - margin-top: -2.7em; - // filter: invert(89%); -} - - - - - // .header-background .img { - // background-image: url("../img/score_contour.jpg"); - // background-repeat: no-repeat; - // background-size: cover; - // background-position: center bottom; - // height: 15em; - // margin-bottom: 2em; - // margin-top: -2.7em; - // filter: invert(89%); - // } -} diff --git a/_sass/_variables.scss b/_sass/_variables.scss deleted file mode 100644 index b050aa6e..00000000 --- a/_sass/_variables.scss +++ /dev/null @@ -1,38 +0,0 @@ -/******************************************************************************* - * Variables used throughout the theme. - * To adjust anything, simply edit the variables below and rebuild the theme. - ******************************************************************************/ - - -// Colors -$red-color: #FF3636 !default; -$red-color-dark: #B71C1C !default; -$orange-color: #F29105 !default; -$blue-color: #0076df !default; -$blue-color-dark: #00369f !default; -$cyan-color: #2698BA !default; -$light-cyan-color: lighten($cyan-color, 25%); -$green-color: #00ab37 !default; -$green-color-lime: #B7D12A !default; -$green-color-dark: #009f06 !default; -$green-color-light: #ddffdd !default; -$green-color-bright: #11D68B !default; -$purple-color: #B509AC !default; -$light-purple-color: lighten($purple-color, 25%); -$pink-color: #f92080 !default; -$pink-color-light: #ffdddd !default; -$yellow-color: #efcc00 !default; - -$grey-color: #828282 !default; -$grey-color-light: lighten($grey-color, 40%); -$grey-color-dark: #1C1C1D; -$grey-900: #212529; - -$white-color: #ffffff !default; -$black-color: #000000 !default; - - -// Theme colors - -$code-bg-color-light: rgba($purple-color, 0.05); -$code-bg-color-dark: #2c3237 !default; diff --git a/assets/css/main.css b/assets/css/main.css new file mode 100644 index 00000000..8a7a1dc4 --- /dev/null +++ b/assets/css/main.css @@ -0,0 +1,3 @@ +:root{--global-bg-color:#fff;--global-code-bg-color:rgba(181,9,172,0.05);--global-text-color:#000;--global-text-color-light:#828282;--global-theme-color:#2698ba;--global-hover-color:#2698ba;--global-footer-bg-color:#1c1c1d;--global-footer-text-color:#e8e8e8;--global-footer-link-color:#fff;--global-distill-app-color:#828282;--global-divider-color:rgba(0,0,0,.1);--global-card-bg-color:#fff}:root .fa-sun{display:none}:root .fa-moon{padding-left:10px;padding-top:12px;display:block}:root .repo-img-light{display:block}:root .repo-img-dark{display:none}.header-background .img{background-repeat:no-repeat;background-size:400px;background-position:center bottom;height:12em;margin-bottom:0;margin-top:-2.7em}html[data-theme=dark]{--global-bg-color:#1c1c1d;--global-code-bg-color:#2c3237;--global-text-color:#e8e8e8;--global-text-color-light:#e8e8e8;--global-theme-color:#2698ba;--global-hover-color:#2698ba;--global-footer-bg-color:#e8e8e8;--global-footer-text-color:#1c1c1d;--global-footer-link-color:#000;--global-distill-app-color:#e8e8e8;--global-divider-color:#424246;--global-card-bg-color:#212529}html[data-theme=dark] .fa-sun{padding-left:10px;padding-top:12px;display:block}html[data-theme=dark] .fa-moon{display:none}html[data-theme=dark] .repo-img-light{display:none}html[data-theme=dark] .repo-img-dark{display:block}html[data-theme=dark] .header-background .img{background-repeat:no-repeat;background-size:400px;background-position:center bottom;height:12em;margin-bottom:0;margin-top:-2.7em}body{padding-bottom:70px;color:var(--global-text-color);background-color:var(--global-bg-color)}body h1,body h2,body h3,body h4,body h5,body h6{scroll-margin-top:66px}body.fixed-top-nav{padding-top:56px}body.sticky-bottom-footer{padding-bottom:0}.container{max-width:1000px}.profile img{width:100%}p,h1,h2,h3,h4,h5,h6,em,div,li,span,strong{color:var(--global-text-color)}hr{border-top:1px solid var(--global-divider-color)}table td,table th{color:var(--global-text-color)}table td{font-size:1rem}a,table.table a{color:var(--global-theme-color)}a:hover,table.table a:hover{color:var(--global-theme-color);text-decoration:underline}a:hover:after :not(.nav-item.dropdown),table.table a:hover:after :not(.nav-item.dropdown){width:100%}figure,img{max-width:90vw}blockquote{background:var(--global-bg-color);border-left:2px solid var(--global-theme-color);margin:1.5em 10px;padding:.5em 10px;font-size:1.1rem}.equation{margin-bottom:1rem;text-align:center}.caption{font-size:.875rem;margin-top:.75rem;margin-bottom:1.5rem;text-align:center}.card{background-color:var(--global-card-bg-color)}.card img{width:100%}.card .card-title{color:var(--global-text-color)}.card .card-item{width:auto;margin-bottom:10px}.card .card-item .row{display:flex;align-items:center}.citation,.citation-number{color:var(--global-theme-color)}.profile{width:100%}.profile .address{margin-bottom:5px;margin-top:5px;font-family:monospace}.profile .address p{display:inline-block;margin:0}.profile.float-right{margin-left:1rem}.profile.float-left{margin-right:1rem}@media(min-width:576px){.profile{width:30%}.profile .address p{display:block}}.post-description{margin-bottom:2rem;font-size:.875rem}.post-description a{color:inherit}.post-description a:hover{color:var(--global-theme-color);text-decoration:none}.navbar{box-shadow:none;border-bottom:1px solid var(--global-divider-color);background-color:var(--global-bg-color);opacity:.95}.navbar .dropdown-menu{background-color:var(--global-bg-color);border:1px solid var(--global-divider-color)}.navbar .dropdown-menu a:not(.active){color:var(--global-text-color)}.navbar .dropdown-menu a:hover{color:var(--global-hover-color)}.navbar .dropdown-menu .dropdown-divider{border-top:1px solid var(--global-divider-color)!important}.dropdown-item{color:var(--global-text-color)}.dropdown-item:hover{color:var(--global-hover-color);background-color:var(--global-bg-color)}.navbar.navbar-light a:hover{text-decoration:none}.navbar.navbar-light .navbar-brand{color:var(--global-text-color)}.navbar.navbar-light .navbar-nav .nav-item .nav-link{color:var(--global-text-color)}.navbar.navbar-light .navbar-nav .nav-item .nav-link:hover{color:var(--global-hover-color)}.navbar.navbar-light .navbar-nav .nav-item.active>.nav-link{background-color:inherit;font-weight:bolder;color:var(--global-theme-color)}.navbar.navbar-light .navbar-nav .nav-item.active>.nav-link:hover{color:var(--global-hover-color)}.navbar.navbar-light .navbar-brand.social{padding-bottom:0;padding-top:0;font-size:1.7rem}.navbar.navbar-light .navbar-brand.social a i::before{color:var(--global-text-color);transition-property:all .2s ease-in-out}.navbar.navbar-light .navbar-brand.social a:hover i::before{color:var(--global-theme-color)}.navbar-toggler .icon-bar{display:block;width:22px;height:2px;background-color:var(--global-text-color);border-radius:1px;margin-bottom:4px;transition:all .2s}.navbar-toggler .top-bar{transform:rotate(45deg);transform-origin:10% 10%}.navbar-toggler .middle-bar{opacity:0}.navbar-toggler .bottom-bar{transform:rotate(-45deg);transform-origin:10% 90%} +.navbar-toggler.collapsed .top-bar{transform:rotate(0)}.navbar-toggler.collapsed .middle-bar{opacity:1}.navbar-toggler.collapsed .bottom-bar{transform:rotate(0)}#light-toggle{padding:0;border:0;background-color:inherit;color:var(--global-text-color)}#light-toggle:hover{color:var(--global-hover-color)}.social{text-align:center}.social .contact-icons{font-size:4rem}.social .contact-icons a i::before{color:var(--global-text-color);transition-property:all .2s ease-in-out}.social .contact-icons a:hover i::before{color:var(--global-theme-color)}.social .contact-note{font-size:.8rem}footer.fixed-bottom{background-color:var(--global-footer-bg-color);font-size:.75rem}footer.fixed-bottom .container{color:var(--global-footer-text-color);padding-top:9px;padding-bottom:8px}footer.fixed-bottom a{color:var(--global-footer-link-color)}footer.fixed-bottom a:hover{color:var(--global-theme-color);text-decoration:none}footer.sticky-bottom{border-top:1px solid var(--global-divider-color);padding-top:40px;padding-bottom:40px;font-size:.9rem}.cv{margin-bottom:40px}.cv .card{background-color:var(--global-card-bg-color);border:1px solid var(--global-divider-color)}.cv .card .list-group-item{background-color:inherit}.cv .card .list-group-item .badge{color:var(--global-card-bg-color)!important;background-color:var(--global-theme-color)!important}@media(min-width:768px){.repo{max-width:50%}}.header-bar{border-bottom:1px solid var(--global-divider-color);text-align:center;padding-top:2rem;padding-bottom:3rem}.header-bar h1{color:var(--global-theme-color);font-size:5rem}.tag-list{border-bottom:1px solid var(--global-divider-color);text-align:center;padding-top:1rem}.tag-list ul{justify-content:center;display:flow-root}.tag-list ul p,.tag-list ul li{list-style:none;display:inline-block;padding:1rem .5rem;color:var(--global-text-color-light)}.post-list{margin:0;margin-bottom:40px;padding:0}.post-list li{border-bottom:1px solid var(--global-divider-color);list-style:none;padding-top:2rem;padding-bottom:2rem}.post-list li .post-meta{color:var(--global-text-color-light);font-size:.875rem;margin-bottom:0}.post-list li .post-tags{color:var(--global-text-color-light);font-size:.875rem;padding-top:.25rem;padding-bottom:0}.post-list li a{color:var(--global-text-color);text-decoration:none}.post-list li a:hover{color:var(--global-theme-color)}.pagination .page-item .page-link{color:var(--global-text-color)}.pagination .page-item .page-link:hover{color:#000}.pagination .page-item.active .page-link{color:#fff;background-color:var(--global-theme-color)}.pagination .page-item.active .page-link:hover{background-color:var(--global-theme-color)}.distill a:hover{border-bottom-color:var(--global-theme-color);text-decoration:none}.projects a{text-decoration:none}.projects a:hover .card-title{color:var(--global-theme-color)}.projects .card img{width:100%}.projects .card-item{width:auto;margin-bottom:10px}.projects .card-item .row{display:flex;align-items:center}.projects .grid-sizer,.projects .grid-item{width:250px;margin-bottom:10px}.projects h2.category{color:var(--global-divider-color);border-bottom:1px solid var(--global-divider-color);padding-top:.5rem;margin-top:2rem;margin-bottom:1rem;text-align:right}.publications{margin-top:2rem}.publications h1{color:var(--global-theme-color);font-size:2rem;text-align:center;margin-top:1em;margin-bottom:1em}.publications h2{margin-bottom:1rem}.publications h2 span{font-size:1.5rem}.publications h2.year{color:var(--global-divider-color);border-top:1px solid var(--global-divider-color);padding-top:1rem;margin-top:2rem;margin-bottom:-2rem;text-align:right}.publications ol.bibliography{list-style:none;padding:0;margin-top:0}.publications ol.bibliography li{margin-bottom:1rem}.publications ol.bibliography li .preview{width:100%;min-width:80px;max-width:200px}.publications ol.bibliography li .abbr{height:2rem;margin-bottom:.5rem}.publications ol.bibliography li .abbr abbr{display:inline-block;background-color:var(--global-theme-color);padding-left:1rem;padding-right:1rem}.publications ol.bibliography li .abbr abbr a{color:white}.publications ol.bibliography li .abbr abbr a:hover{text-decoration:none}.publications ol.bibliography li .abbr .award{color:var(--global-theme-color)!important;border:1px solid var(--global-theme-color)}.publications ol.bibliography li .title{font-weight:bolder}.publications ol.bibliography li .author a{border-bottom:1px dashed var(--global-theme-color)}.publications ol.bibliography li .author a:hover{border-bottom-style:solid;text-decoration:none}.publications ol.bibliography li .author>em{border-bottom:1px solid;font-style:normal}.publications ol.bibliography li .author>span.more-authors{color:var(--global-text-color-light);border-bottom:1px dashed var(--global-text-color-light);cursor:pointer}.publications ol.bibliography li .author>span.more-authors:hover{color:var(--global-text-color);border-bottom:1px dashed var(--global-text-color)}.publications ol.bibliography li .links a.btn{color:var(--global-text-color);border:1px solid var(--global-text-color);padding-left:1rem;padding-right:1rem;padding-top:.25rem;padding-bottom:.25rem} +.publications ol.bibliography li .links a.btn:hover{color:var(--global-theme-color);border-color:var(--global-theme-color)}.publications ol.bibliography li .hidden{font-size:.875rem;max-height:0;overflow:hidden;text-align:justify;transition-property:.15s ease;-moz-transition:.15s ease;-ms-transition:.15s ease;-o-transition:.15s ease;transition:all .15s ease}.publications ol.bibliography li .hidden p{line-height:1.4em;margin:10px}.publications ol.bibliography li .hidden pre{font-size:1em;line-height:1.4em;padding:10px}.publications ol.bibliography li .hidden.open{max-height:100em;transition-property:.15s ease;-moz-transition:.15s ease;-ms-transition:.15s ease;-o-transition:.15s ease;transition:all .15s ease}.publications ol.bibliography li div.abstract.hidden{border:dashed 1px var(--global-bg-color)}.publications ol.bibliography li div.abstract.hidden.open{border-color:var(--global-text-color)}figure.highlight{margin:0 0 1rem}pre{color:var(--global-theme-color);background-color:var(--global-code-bg-color);border-radius:6px;padding:6px 12px}pre pre,pre code{background-color:transparent;border-radius:0;padding:0}code{color:var(--global-theme-color);background-color:var(--global-code-bg-color);border-radius:3px;padding:3px 3px}html.transition,html.transition *,html.transition *:before,html.transition *:after{transition:all 750ms!important;transition-delay:0!important}.post .post-meta{color:var(--global-text-color-light);font-size:.875rem;margin-bottom:0}.post .post-tags{color:var(--global-text-color-light);font-size:.875rem;padding-top:.25rem;padding-bottom:1rem}.post .post-tags a{color:var(--global-text-color-light);text-decoration:none}.post .post-tags a:hover{color:var(--global-theme-color)}.post .post-content blockquote{border-left:5px solid var(--global-theme-color);padding:8px}d-byline{border-top-color:var(--global-divider-color)!important}d-byline h3{color:var(--global-text-color)!important}d-byline a,d-article d-byline a{color:var(--global-text-color)!important}d-byline a:hover,d-article d-byline a:hover{color:var(--global-hover-color)!important}d-article{border-top-color:var(--global-divider-color)!important}d-article a,d-article p,d-article h1,d-article h2,d-article h3,d-article h4,d-article h5,d-article h6,d-article li,d-article table{color:var(--global-text-color)!important}d-article a,d-article h1,d-article h2,d-article hr,d-article table,d-article table th,d-article table td{border-bottom-color:var(--global-divider-color)!important}d-article a:hover{border-bottom-color:var(--global-hover-color)!important}d-article b i{display:inline}d-article d-contents{align-self:start;grid-column:1/4;grid-row:auto/span 4;justify-self:end;margin-top:0;padding-left:2em;padding-right:3em;border-right:1px solid var(--global-divider-color);width:max(70%,300px);margin-right:0;margin-top:0;display:grid;grid-template-columns:minmax(8px,1fr) [toc] auto minmax(8px,1fr) [toc-line] 1px minmax(32px,2fr)}d-article d-contents nav{grid-column:toc}d-article d-contents nav a{border-bottom:none!important}d-article d-contents nav a:hover{border-bottom:1px solid var(--global-text-color)!important}d-article d-contents nav h3{margin-top:0;margin-bottom:1em}d-article d-contents nav div{display:block;outline:0;margin-bottom:.8em;color:rgba(0,0,0,0.8);font-weight:bold}d-article d-contents nav ul{padding-left:1em;margin-top:0;margin-bottom:6px;list-style-type:none}d-article d-contents nav ul li{margin-bottom:.25em}d-article d-contents .figcaption{line-height:1.4em}d-article d-contents toc-line{border-right:1px solid var(--global-divider-color);grid-column:toc-line}d-article d-footnote{scroll-margin-top:66px}d-appendix{border-top-color:var(--global-divider-color)!important;color:var(--global-distill-app-color)!important}d-appendix h3,d-appendix li,d-appendix span{color:var(--global-distill-app-color)!important}d-appendix a,d-appendix a.footnote-backlink{color:var(--global-distill-app-color)!important}d-appendix a:hover,d-appendix a.footnote-backlink:hover{color:var(--global-hover-color)!important}@media(max-width:1024px){d-article d-contents{display:block;grid-column-start:2;grid-column-end:-2;padding-bottom:.5em;margin-bottom:1em;padding-top:.5em;width:100%;border:1px solid var(--global-divider-color)}d-article d-contents nav{grid-column:none}} \ No newline at end of file diff --git a/assets/css/main.css.map b/assets/css/main.css.map new file mode 100644 index 00000000..275a423e --- /dev/null +++ b/assets/css/main.css.map @@ -0,0 +1 @@ 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* Variables used throughout the theme.\n * To adjust anything, simply edit the variables below and rebuild the theme.\n ******************************************************************************/\n\n\n// Colors\n$red-color: #FF3636 !default;\n$red-color-dark: #B71C1C !default;\n$orange-color: #F29105 !default;\n$blue-color: #0076df !default;\n$blue-color-dark: #00369f !default;\n$cyan-color: #2698BA !default;\n$light-cyan-color: lighten($cyan-color, 25%);\n$green-color: #00ab37 !default;\n$green-color-lime: #B7D12A !default;\n$green-color-dark: #009f06 !default;\n$green-color-light: #ddffdd !default;\n$green-color-bright: #11D68B !default;\n$purple-color: #B509AC !default;\n$light-purple-color: lighten($purple-color, 25%);\n$pink-color: #f92080 !default;\n$pink-color-light: #ffdddd !default;\n$yellow-color: #efcc00 !default;\n\n$grey-color: #828282 !default;\n$grey-color-light: lighten($grey-color, 40%);\n$grey-color-dark: #1C1C1D;\n$grey-900: #212529;\n\n$white-color: #ffffff !default;\n$black-color: #000000 !default;\n\n\n// Theme colors\n\n$code-bg-color-light: rgba($purple-color, 0.05);\n$code-bg-color-dark: #2c3237 !default;\n","/*******************************************************************************\r\n * Themes\r\n ******************************************************************************/\r\n \r\n:root {\r\n --global-bg-color: #{$white-color};\r\n --global-code-bg-color: #{$code-bg-color-light};\r\n --global-text-color: #{$black-color};\r\n --global-text-color-light: #{$grey-color};\r\n --global-theme-color: #{$cyan-color};\r\n --global-hover-color: #{$cyan-color};\r\n --global-footer-bg-color: #{$grey-color-dark};\r\n --global-footer-text-color: #{$grey-color-light};\r\n --global-footer-link-color: #{$white-color};\r\n --global-distill-app-color: #{$grey-color};\r\n --global-divider-color: rgba(0,0,0,.1);\r\n --global-card-bg-color: #{$white-color};\r\n\r\n .fa-sun {\r\n display : none;\r\n }\r\n .fa-moon {\r\n padding-left: 10px;\r\n padding-top: 12px;\r\n display : block;\r\n }\r\n\r\n .repo-img-light {\r\n display: block;\r\n }\r\n .repo-img-dark {\r\n display: none;\r\n }\r\n}\r\n\r\n.header-background .img {\r\n // background-image: url(\"../img/ICLR-logo.png\");\r\n background-repeat: no-repeat;\r\n background-size: 400px;\r\n background-position: center bottom;\r\n height: 12em;\r\n margin-bottom: 0em;\r\n margin-top: -2.7em; \r\n}\r\n\r\nhtml[data-theme='dark'] {\r\n --global-bg-color: #{$grey-color-dark};\r\n --global-code-bg-color: #{$code-bg-color-dark};\r\n --global-text-color: #{$grey-color-light};\r\n --global-text-color-light: #{$grey-color-light};\r\n --global-theme-color: #{$cyan-color};\r\n --global-hover-color: #{$cyan-color};\r\n --global-footer-bg-color: #{$grey-color-light};\r\n --global-footer-text-color: #{$grey-color-dark};\r\n --global-footer-link-color: #{$black-color};\r\n --global-distill-app-color: #{$grey-color-light};\r\n --global-divider-color: #424246;\r\n --global-card-bg-color: #{$grey-900};\r\n\r\n .fa-sun {\r\n padding-left: 10px;\r\n padding-top: 12px;\r\n display : block;\r\n }\r\n .fa-moon {\r\n display : none;\r\n }\r\n\r\n .repo-img-light {\r\n display: none;\r\n }\r\n .repo-img-dark {\r\n display: block;\r\n }\r\n\r\n.header-background .img {\r\n // background-image: url(\"../img/ICLR-logo-dark.png\");\r\n background-repeat: no-repeat;\r\n background-size: 400px;\r\n background-position: center bottom;\r\n height: 12em;\r\n margin-bottom: 0em;\r\n margin-top: -2.7em; \r\n // filter: invert(89%);\r\n}\r\n\r\n\r\n\r\n\r\n // .header-background .img {\r\n // background-image: url(\"../img/score_contour.jpg\");\r\n // background-repeat: no-repeat;\r\n // background-size: cover;\r\n // background-position: center bottom;\r\n // height: 15em;\r\n // margin-bottom: 2em;\r\n // margin-top: -2.7em;\r\n // filter: invert(89%);\r\n // }\r\n}\r\n","/******************************************************************************\n * Content\n ******************************************************************************/\n\nbody {\n padding-bottom: 70px;\n color: var(--global-text-color);\n background-color: var(--global-bg-color);\n\n h1, h2, h3, h4, h5, h6 {\n scroll-margin-top: 66px;\n }\n}\n\nbody.fixed-top-nav {\n // Add some padding for the nav-bar.\n padding-top: 56px;\n}\n\nbody.sticky-bottom-footer {\n // Remove padding below footer.\n padding-bottom: 0;\n}\n\n.container {\n max-width: $max-content-width;\n}\n\n// Profile\n.profile {\n img {\n width: 100%;\n }\n}\n\n// TODO: redefine content layout.\n\n\n/******************************************************************************\n * Publications\n ******************************************************************************/\n\n// TODO: redefine publications layout.\n\n\n/*****************************************************************************\n* Projects\n*****************************************************************************/\n\n// TODO: redefine projects layout.\n","@charset \"utf-8\";\n\n// Dimensions\n$max-content-width: 1000px;\n\n@import\n \"variables\",\n \"themes\",\n \"layout\",\n \"base\",\n \"distill\"\n;\n","/*******************************************************************************\n * Styles for the base elements of the theme.\n ******************************************************************************/\n\n// Typography\n\np, h1, h2, h3, h4, h5, h6, em, div, li, span, strong {\n color: var(--global-text-color);\n}\n\nhr {\n border-top: 1px solid var(--global-divider-color);\n}\n\ntable {\n td, th {\n color: var(--global-text-color);\n }\n td {\n font-size: 1rem;\n }\n}\n\na, table.table a {\n color: var(--global-theme-color);\n &:hover {\n color: var(--global-theme-color);\n text-decoration: underline;\n }\n &:hover:after :not(.nav-item.dropdown) {\n width: 100%;\n }\n}\n\nfigure, img {\n max-width: 90vw;\n}\n\nblockquote {\n background: var(--global-bg-color);\n border-left: 2px solid var(--global-theme-color);\n margin: 1.5em 10px;\n padding: 0.5em 10px;\n font-size: 1.1rem;\n}\n\n// Math\n\n.equation {\n margin-bottom: 1rem;\n text-align: center;\n}\n\n// Caption\n\n.caption {\n font-size: 0.875rem;\n margin-top: 0.75rem;\n margin-bottom: 1.5rem;\n text-align: center;\n}\n\n// Card\n\n.card {\n background-color: var(--global-card-bg-color);\n\n img {\n width: 100%;\n }\n\n .card-title {\n color: var(--global-text-color);\n }\n\n .card-item {\n width: auto;\n margin-bottom: 10px;\n\n .row {\n display: flex;\n align-items: center;\n }\n }\n}\n\n// Citation\n\n.citation, .citation-number {\n color: var(--global-theme-color);\n}\n\n// Profile\n\n.profile {\n width: 100%;\n\n .address {\n margin-bottom: 5px;\n margin-top: 5px;\n font-family: monospace;\n p {\n display: inline-block;\n margin: 0;\n }\n }\n}\n.profile.float-right{\n margin-left: 1rem;\n}\n.profile.float-left{\n margin-right: 1rem;\n}\n\n@media (min-width: 576px) {\n .profile {\n width: 30%;\n .address {\n p { display: block; }\n }\n }\n}\n\n.post-description {\n margin-bottom: 2rem;\n font-size: 0.875rem;\n a {\n color: inherit;\n &:hover {\n color: var(--global-theme-color);\n text-decoration: none;\n }\n }\n}\n\n\n// Navbar customization\n\n.navbar {\n box-shadow: none;\n border-bottom: 1px solid var(--global-divider-color);\n background-color: var(--global-bg-color);\n opacity: 0.95;\n}\n.navbar .dropdown-menu {\n background-color: var(--global-bg-color);\n border: 1px solid var(--global-divider-color);\n a:not(.active) {\n color: var(--global-text-color);\n }\n a:hover {\n color: var(--global-hover-color);\n }\n .dropdown-divider {\n border-top: 1px solid var(--global-divider-color) !important;\n }\n}\n.dropdown-item {\n color: var(--global-text-color);\n &:hover {\n color: var(--global-hover-color);\n background-color: var(--global-bg-color);\n }\n}\n.navbar.navbar-light {\n a {\n &:hover {\n text-decoration: none;\n }\n }\n .navbar-brand {\n color: var(--global-text-color);\n }\n .navbar-nav .nav-item .nav-link {\n color: var(--global-text-color);\n &:hover {\n color: var(--global-hover-color);\n }\n }\n .navbar-nav .nav-item.active>.nav-link {\n background-color: inherit;\n font-weight: bolder;\n color: var(--global-theme-color);\n &:hover {\n color: var(--global-hover-color);\n }\n }\n .navbar-brand.social {\n padding-bottom: 0;\n padding-top: 0;\n font-size: 1.7rem;\n a {\n i::before {\n color: var(--global-text-color);\n transition-property: all 0.2s ease-in-out;\n }\n &:hover {\n i::before {\n color: var(--global-theme-color);\n }\n }\n }\n }\n}\n\n.navbar-toggler {\n .icon-bar {\n display: block;\n width: 22px;\n height: 2px;\n background-color: var(--global-text-color);\n border-radius: 1px;\n margin-bottom: 4px;\n transition: all 0.2s;\n }\n .top-bar {\n transform: rotate(45deg);\n transform-origin: 10% 10%;\n }\n .middle-bar {\n opacity: 0;\n }\n .bottom-bar {\n transform: rotate(-45deg);\n transform-origin: 10% 90%;\n }\n}\n\n.navbar-toggler.collapsed {\n .top-bar {\n transform: rotate(0);\n }\n .middle-bar {\n opacity: 1;\n }\n .bottom-bar {\n transform: rotate(0);\n }\n}\n\n#light-toggle {\n padding: 0;\n border: 0;\n background-color: inherit;\n color: var(--global-text-color);\n &:hover {\n color: var(--global-hover-color);\n }\n}\n\n// Social (bottom)\n\n.social {\n text-align: center;\n .contact-icons {\n font-size: 4rem;\n a {\n i::before {\n color: var(--global-text-color);\n transition-property: all 0.2s ease-in-out;\n }\n &:hover {\n i::before {\n color: var(--global-theme-color);\n }\n }\n }\n }\n .contact-note {\n font-size: 0.8rem;\n }\n}\n\n\n// Footer\nfooter.fixed-bottom {\n background-color: var(--global-footer-bg-color);\n font-size: 0.75rem;\n .container {\n color: var(--global-footer-text-color);\n padding-top: 9px;\n padding-bottom: 8px;\n }\n a {\n color: var(--global-footer-link-color);\n &:hover {\n color: var(--global-theme-color);\n text-decoration: none;\n }\n }\n}\n\nfooter.sticky-bottom {\n border-top: 1px solid var(--global-divider-color);\n padding-top: 40px;\n padding-bottom: 40px;\n font-size: 0.9rem;\n}\n\n// CV\n\n.cv {\n margin-bottom: 40px;\n \n .card {\n background-color: var(--global-card-bg-color);\n border: 1px solid var(--global-divider-color);\n \n .list-group-item {\n background-color: inherit;\n\n .badge {\n color: var(--global-card-bg-color) !important;\n background-color: var(--global-theme-color) !important;\n }\n }\n }\n}\n\n// Repositories\n\n@media (min-width: 768px) {\n .repo {\n max-width: 50%;\n }\n}\n\n// Blog\n\n.header-bar {\n border-bottom: 1px solid var(--global-divider-color);\n text-align: center;\n padding-top: 2rem;\n padding-bottom: 3rem;\n h1 {\n color: var(--global-theme-color);\n font-size: 5rem;\n }\n}\n\n.tag-list {\n border-bottom: 1px solid var(--global-divider-color);\n text-align: center;\n padding-top: 1rem;\n\n ul {\n justify-content: center;\n display: flow-root;\n\n p, li {\n list-style: none;\n display: inline-block;\n padding: 1rem 0.5rem;\n color: var(--global-text-color-light);\n }\n }\n}\n\n.post-list {\n margin: 0;\n margin-bottom: 40px;\n padding: 0;\n li {\n border-bottom: 1px solid var(--global-divider-color);\n list-style: none;\n padding-top: 2rem;\n padding-bottom: 2rem;\n .post-meta {\n color: var(--global-text-color-light);\n font-size: 0.875rem;\n margin-bottom: 0;\n }\n .post-tags {\n color: var(--global-text-color-light);\n font-size: 0.875rem;\n padding-top: 0.25rem;\n padding-bottom: 0;\n }\n a {\n color: var(--global-text-color);\n text-decoration: none;\n &:hover {\n color: var(--global-theme-color);\n }\n }\n }\n}\n\n.pagination {\n .page-item {\n .page-link {\n color: var(--global-text-color);\n &:hover {\n color: $black-color;\n }\n }\n &.active .page-link {\n color: $white-color;\n background-color: var(--global-theme-color);\n &:hover {\n background-color: var(--global-theme-color);\n }\n }\n }\n}\n\n\n// Distill\n\n.distill {\n a:hover {\n border-bottom-color: var(--global-theme-color);\n text-decoration: none;\n }\n}\n\n\n// Projects\n\n.projects {\n a {\n text-decoration: none;\n\n &:hover {\n .card-title {\n color: var(--global-theme-color);\n }\n }\n }\n\n .card {\n img {\n width: 100%;\n }\n }\n\n .card-item {\n width: auto;\n margin-bottom: 10px;\n\n .row {\n display: flex;\n align-items: center;\n }\n }\n\n .grid-sizer, .grid-item {\n width: 250px;\n margin-bottom: 10px;\n }\n\n h2.category {\n color: var(--global-divider-color);\n border-bottom: 1px solid var(--global-divider-color);\n padding-top: 0.5rem;\n margin-top: 2rem;\n margin-bottom: 1rem;\n text-align: right;\n }\n}\n\n\n// Publications\n\n.publications {\n margin-top: 2rem;\n h1 {\n color: var(--global-theme-color);\n font-size: 2rem;\n text-align: center;\n margin-top: 1em;\n margin-bottom: 1em;\n }\n h2 {\n margin-bottom: 1rem;\n span {\n font-size: 1.5rem;\n }\n }\n h2.year {\n color: var(--global-divider-color);\n border-top: 1px solid var(--global-divider-color);\n padding-top: 1rem;\n margin-top: 2rem;\n margin-bottom: -2rem;\n text-align: right;\n }\n ol.bibliography {\n list-style: none;\n padding: 0;\n margin-top: 0;\n\n li {\n margin-bottom: 1rem;\n .preview {\n width: 100%;\n min-width: 80px;\n max-width: 200px;\n }\n .abbr {\n height: 2rem;\n margin-bottom: 0.5rem;\n abbr {\n display: inline-block;\n background-color: var(--global-theme-color);\n padding-left: 1rem;\n padding-right: 1rem;\n a {\n color: white;\n &:hover {\n text-decoration: none;\n }\n }\n }\n .award {\n color: var(--global-theme-color) !important;\n border: 1px solid var(--global-theme-color);\n }\n }\n .title {\n font-weight: bolder;\n }\n .author {\n a {\n border-bottom: 1px dashed var(--global-theme-color);\n &:hover {\n border-bottom-style: solid;\n text-decoration: none;\n }\n }\n > em {\n border-bottom: 1px solid;\n font-style: normal;\n }\n > span.more-authors {\n color: var(--global-text-color-light);\n border-bottom: 1px dashed 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+$(document).ready(function(){$("a.abstract").click(function(){$(this).parent().parent().find(".abstract.hidden").toggleClass("open")}),$("a.bibtex").click(function(){$(this).parent().parent().find(".bibtex.hidden").toggleClass("open")}),$("a").removeClass("waves-effect waves-light")}); \ No newline at end of file diff --git a/assets/js/dark_mode.js b/assets/js/dark_mode.js index 863b273f..26312e44 100644 --- a/assets/js/dark_mode.js +++ b/assets/js/dark_mode.js @@ -1,8 +1 @@ -document.addEventListener('DOMContentLoaded', function() { - const mode_toggle = document.getElementById("light-toggle"); - - mode_toggle.addEventListener("click", function() { - toggleTheme(localStorage.getItem("theme")); - }); -}); - +document.addEventListener("DOMContentLoaded",function(){document.getElementById("light-toggle").addEventListener("click",function(){toggleTheme(localStorage.getItem("theme"))})}); \ No newline at end of file diff --git a/assets/js/distillpub/overrides.js b/assets/js/distillpub/overrides.js index 2d839626..066b8efa 100644 --- a/assets/js/distillpub/overrides.js +++ b/assets/js/distillpub/overrides.js @@ -1,24 +1 @@ -$(document).ready(function() { - // Override styles of the footnotes. - document.querySelectorAll("d-footnote").forEach(function(footnote) { - footnote.shadowRoot.querySelector("sup > span") - .setAttribute("style", "color: var(--global-theme-color);"); - footnote.shadowRoot.querySelector("d-hover-box").shadowRoot.querySelector("style").sheet - .insertRule(".panel {background-color: var(--global-bg-color) !important;}"); - footnote.shadowRoot.querySelector("d-hover-box").shadowRoot.querySelector("style").sheet - .insertRule(".panel {border-color: var(--global-divider-color) !important;}"); - }); - // Override styles of the citations. - document.querySelectorAll("d-cite").forEach(function(cite) { - cite.shadowRoot.querySelector("div > span") - .setAttribute("style", "color: var(--global-theme-color);"); - cite.shadowRoot.querySelector("style").sheet - .insertRule("ul li a {color: var(--global-text-color) !important; text-decoration: none;}"); - cite.shadowRoot.querySelector("style").sheet - .insertRule("ul li a:hover {color: var(--global-theme-color) !important;}"); - cite.shadowRoot.querySelector("d-hover-box").shadowRoot.querySelector("style").sheet - .insertRule(".panel {background-color: var(--global-bg-color) !important;}"); - cite.shadowRoot.querySelector("d-hover-box").shadowRoot.querySelector("style").sheet - .insertRule(".panel {border-color: var(--global-divider-color) !important;}"); - }); -}) \ No newline at end of file +$(document).ready(function(){document.querySelectorAll("d-footnote").forEach(function(o){o.shadowRoot.querySelector("sup > span").setAttribute("style","color: var(--global-theme-color);"),o.shadowRoot.querySelector("d-hover-box").shadowRoot.querySelector("style").sheet.insertRule(".panel {background-color: var(--global-bg-color) 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b/assets/js/distillpub/template.v2.js index 4ddc61fc..a05e82bb 100644 --- a/assets/js/distillpub/template.v2.js +++ b/assets/js/distillpub/template.v2.js @@ -1,9247 +1,67 @@ -(function (factory) { - typeof define === 'function' && define.amd ? define(factory) : - factory(); -}((function () { 'use strict'; - - // Copyright 2018 The Distill Template Authors - // - // Licensed under the Apache License, Version 2.0 (the "License"); - // you may not use this file except in compliance with the License. - // You may obtain a copy of the License at - // - // http://www.apache.org/licenses/LICENSE-2.0 - // - // Unless required by applicable law or agreed to in writing, software - // distributed under the License is distributed on an "AS IS" BASIS, - // WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - // See the License for the specific language governing permissions and - // limitations under the License. - - const days = ['Sunday', 'Monday', 'Tuesday', 'Wednesday', 'Thursday', 'Friday', 'Saturday']; - const months = ['Jan.', 'Feb.', 'March', 'April', 'May', 'June', 'July', 'Aug.', 'Sept.', 'Oct.', 'Nov.', 'Dec.']; - const zeroPad = n => n < 10 ? '0' + n : n; - - const RFC = function(date) { - const day = days[date.getDay()].substring(0, 3); - const paddedDate = zeroPad(date.getDate()); - const month = months[date.getMonth()].substring(0,3); - const year = date.getFullYear().toString(); - const hours = date.getUTCHours().toString(); - const minutes = date.getUTCMinutes().toString(); - const seconds = date.getUTCSeconds().toString(); - return `${day}, ${paddedDate} ${month} ${year} ${hours}:${minutes}:${seconds} Z`; - }; - - const objectFromMap = function(map) { - const object = Array.from(map).reduce((object, [key, value]) => ( - Object.assign(object, { [key]: value }) // Be careful! Maps can have non-String keys; object literals can't. - ), {}); - return object; - }; - - const mapFromObject = function(object) { - const map = new Map(); - for (var property in object) { - if (object.hasOwnProperty(property)) { - map.set(property, object[property]); - } - } - return map; - }; - - class Author { - - // constructor(name='', personalURL='', affiliation='', affiliationURL='') { - // this.name = name; // 'Chris Olah' - // this.personalURL = personalURL; // 'https://colah.github.io' - // this.affiliation = affiliation; // 'Google Brain' - // this.affiliationURL = affiliationURL; // 'https://g.co/brain' - // } - - constructor(object) { - this.name = object.author; // 'Chris Olah' - this.personalURL = object.authorURL; // 'https://colah.github.io' - this.affiliation = object.affiliation; // 'Google Brain' - this.affiliationURL = object.affiliationURL; // 'https://g.co/brain' - this.affiliations = object.affiliations || []; // new-style affiliations - } - - // 'Chris' - get firstName() { - const names = this.name.split(' '); - return names.slice(0, names.length - 1).join(' '); - } - - // 'Olah' - get lastName() { - const names = this.name.split(' '); - return names[names.length -1]; - } - } - - function mergeFromYMLFrontmatter(target, source) { - target.title = source.title; - if (source.published) { - if (source.published instanceof Date) { - target.publishedDate = source.published; - } else if (source.published.constructor === String) { - target.publishedDate = new Date(source.published); - } - } - if (source.publishedDate) { - if (source.publishedDate instanceof Date) { - target.publishedDate = source.publishedDate; - } else if (source.publishedDate.constructor === String) { - target.publishedDate = new Date(source.publishedDate); - } else { - console.error('Don\'t know what to do with published date: ' + source.publishedDate); - } - } - target.description = source.description; - target.authors = source.authors.map( (authorObject) => new Author(authorObject)); - target.katex = source.katex; - target.password = source.password; - if (source.doi) { - target.doi = source.doi; - } - } - - class FrontMatter { - constructor() { - this.title = 'unnamed article'; // 'Attention and Augmented Recurrent Neural Networks' - this.description = ''; // 'A visual overview of neural attention...' - this.authors = []; // Array of Author(s) - - this.bibliography = new Map(); - this.bibliographyParsed = false; - // { - // 'gregor2015draw': { - // 'title': 'DRAW: A recurrent neural network for image generation', - // 'author': 'Gregor, Karol and Danihelka, Ivo and Graves, Alex and Rezende, Danilo Jimenez and Wierstra, Daan', - // 'journal': 'arXiv preprint arXiv:1502.04623', - // 'year': '2015', - // 'url': 'https://arxiv.org/pdf/1502.04623.pdf', - // 'type': 'article' - // }, - // } - - // Citation keys should be listed in the order that they are appear in the document. - // Each key refers to a key in the bibliography dictionary. - this.citations = []; // [ 'gregor2015draw', 'mercier2011humans' ] - this.citationsCollected = false; - - // - // Assigned from posts.csv - // - - // publishedDate: 2016-09-08T07:00:00.000Z, - // tags: [ 'rnn' ], - // distillPath: '2016/augmented-rnns', - // githubPath: 'distillpub/post--augmented-rnns', - // doiSuffix: 1, - - // - // Assigned from journal - // - this.journal = {}; - // journal: { - // 'title': 'Distill', - // 'full_title': 'Distill', - // 'abbrev_title': 'Distill', - // 'url': 'http://distill.pub', - // 'doi': '10.23915/distill', - // 'publisherName': 'Distill Working Group', - // 'publisherEmail': 'admin@distill.pub', - // 'issn': '2476-0757', - // 'editors': [...], - // 'committee': [...] - // } - // volume: 1, - // issue: 9, - - this.katex = {}; - - // - // Assigned from publishing process - // - - // githubCompareUpdatesUrl: 'https://github.com/distillpub/post--augmented-rnns/compare/1596e094d8943d2dc0ea445d92071129c6419c59...3bd9209e0c24d020f87cf6152dcecc6017cbc193', - // updatedDate: 2017-03-21T07:13:16.000Z, - // doi: '10.23915/distill.00001', - this.doi = undefined; - this.publishedDate = undefined; - } - - // Example: - // title: Demo Title Attention and Augmented Recurrent Neural Networks - // published: Jan 10, 2017 - // authors: - // - Chris Olah: - // - Shan Carter: http://shancarter.com - // affiliations: - // - Google Brain: - // - Google Brain: http://g.co/brain - - // - // Computed Properties - // - - // 'http://distill.pub/2016/augmented-rnns', - set url(value) { - this._url = value; - } - get url() { - if (this._url) { - return this._url; - } else if (this.distillPath && this.journal.url) { - return this.journal.url + '/' + this.distillPath; - } else if (this.journal.url) { - return this.journal.url; - } - } - - // 'https://github.com/distillpub/post--augmented-rnns', - get githubUrl() { - if (this.githubPath) { - return 'https://github.com/' + this.githubPath; - } else { - return undefined; - } - } - - // TODO resolve differences in naming of URL/Url/url. - // 'http://distill.pub/2016/augmented-rnns/thumbnail.jpg', - set previewURL(value) { - this._previewURL = value; - } - get previewURL() { - return this._previewURL ? this._previewURL : this.url + '/thumbnail.jpg'; - } - - // 'Thu, 08 Sep 2016 00:00:00 -0700', - get publishedDateRFC() { - return RFC(this.publishedDate); - } - - // 'Thu, 08 Sep 2016 00:00:00 -0700', - get updatedDateRFC() { - return RFC(this.updatedDate); - } - - // 2016, - get publishedYear() { - return this.publishedDate.getFullYear(); - } - - // 'Sept', - get publishedMonth() { - return months[this.publishedDate.getMonth()]; - } - - // 8, - get publishedDay() { - return this.publishedDate.getDate(); - } - - // '09', - get publishedMonthPadded() { - return zeroPad(this.publishedDate.getMonth() + 1); - } - - // '08', - get publishedDayPadded() { - return zeroPad(this.publishedDate.getDate()); - } - - get publishedISODateOnly() { - return this.publishedDate.toISOString().split('T')[0]; - } - - get volume() { - const volume = this.publishedYear - 2015; - if (volume < 1) { - throw new Error('Invalid publish date detected during computing volume'); - } - return volume; - } - - get issue() { - return this.publishedDate.getMonth() + 1; - } - - // 'Olah & Carter', - get concatenatedAuthors() { - if (this.authors.length > 2) { - return this.authors[0].lastName + ', et al.'; - } else if (this.authors.length === 2) { - return this.authors[0].lastName + ' & ' + this.authors[1].lastName; - } else if (this.authors.length === 1) { - return this.authors[0].lastName; - } - } - - // 'Olah, Chris and Carter, Shan', - get bibtexAuthors() { - return this.authors.map(author => { - return author.lastName + ', ' + author.firstName; - }).join(' and '); - } - - // 'olah2016attention' - get slug() { - let slug = ''; - if (this.authors.length) { - slug += this.authors[0].lastName.toLowerCase(); - slug += this.publishedYear; - slug += this.title.split(' ')[0].toLowerCase(); - } - return slug || 'Untitled'; - } - - get bibliographyEntries() { - return new Map(this.citations.map( citationKey => { - const entry = this.bibliography.get(citationKey); - return [citationKey, entry]; - })); - } - - set bibliography(bibliography) { - if (bibliography instanceof Map) { - this._bibliography = bibliography; - } else if (typeof bibliography === 'object') { - this._bibliography = mapFromObject(bibliography); - } - } - - get bibliography() { - return this._bibliography; - } - - static fromObject(source) { - const frontMatter = new FrontMatter(); - Object.assign(frontMatter, source); - return frontMatter; - } - - assignToObject(target) { - Object.assign(target, this); - target.bibliography = objectFromMap(this.bibliographyEntries); - target.url = this.url; - target.doi = this.doi; - target.githubUrl = this.githubUrl; - target.previewURL = this.previewURL; - if (this.publishedDate) { - target.volume = this.volume; - target.issue = this.issue; - target.publishedDateRFC = this.publishedDateRFC; - target.publishedYear = this.publishedYear; - target.publishedMonth = this.publishedMonth; - target.publishedDay = this.publishedDay; - target.publishedMonthPadded = this.publishedMonthPadded; - target.publishedDayPadded = this.publishedDayPadded; - } - if (this.updatedDate) { - target.updatedDateRFC = this.updatedDateRFC; - } - target.concatenatedAuthors = this.concatenatedAuthors; - target.bibtexAuthors = this.bibtexAuthors; - target.slug = this.slug; - } - - } - - // Copyright 2018 The Distill Template Authors - // - // Licensed under the Apache License, Version 2.0 (the "License"); - // you may not use this file except in compliance with the License. - // You may obtain a copy of the License at - // - // http://www.apache.org/licenses/LICENSE-2.0 - // - // Unless required by applicable law or agreed to in writing, software - // distributed under the License is distributed on an "AS IS" BASIS, - // WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - // See the License for the specific language governing permissions and - // limitations under the License. - - const Mutating = (superclass) => { - return class extends superclass { - - constructor() { - super(); - - // set up mutation observer - const options = {childList: true, characterData: true, subtree: true}; - const observer = new MutationObserver( () => { - observer.disconnect(); - this.renderIfPossible(); - observer.observe(this, options); - }); - - // ...and listen for changes - observer.observe(this, options); - } - - connectedCallback() { - super.connectedCallback(); - - this.renderIfPossible(); - } - - // potential TODO: check if this is enough for all our usecases - // maybe provide a custom function to tell if we have enough information to render - renderIfPossible() { - if (this.textContent && this.root) { - this.renderContent(); - } - } - - renderContent() { - console.error(`Your class ${this.constructor.name} must provide a custom renderContent() method!` ); - } - - }; // end class - }; // end mixin function - - // Copyright 2018 The Distill Template Authors - // - // Licensed under the Apache License, Version 2.0 (the "License"); - // you may not use this file except in compliance with the License. - // You may obtain a copy of the License at - // - // http://www.apache.org/licenses/LICENSE-2.0 - // - // Unless required by applicable law or agreed to in writing, software - // distributed under the License is distributed on an "AS IS" BASIS, - // WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - // See the License for the specific language governing permissions and - // limitations under the License. - - /*global ShadyCSS*/ - - const Template = (name, templateString, useShadow = true) => { - - return (superclass) => { - - const template = document.createElement('template'); - template.innerHTML = templateString; - - if (useShadow && 'ShadyCSS' in window) { - ShadyCSS.prepareTemplate(template, name); - } - - return class extends superclass { - - static get is() { return name; } - - constructor() { - super(); - - this.clone = document.importNode(template.content, true); - if (useShadow) { - this.attachShadow({mode: 'open'}); - this.shadowRoot.appendChild(this.clone); - } - } - - connectedCallback() { - if (this.hasAttribute('distill-prerendered')) { - return; - } - if (useShadow) { - if ('ShadyCSS' in window) { - ShadyCSS.styleElement(this); - } - } else { - this.insertBefore(this.clone, this.firstChild); - } - } - - get root() { - if (useShadow) { - return this.shadowRoot; - } else { - return this; - } - } - - /* TODO: Are we using these? Should we even? */ - $(query) { - return this.root.querySelector(query); - } - - $$(query) { - return this.root.querySelectorAll(query); - } - }; - }; - }; - - var math = "/*\n * Copyright 2018 The Distill Template Authors\n *\n * Licensed under the Apache License, Version 2.0 (the \"License\");\n * you may not use this file except in compliance with the License.\n * You may obtain a copy of the License at\n *\n * http://www.apache.org/licenses/LICENSE-2.0\n *\n * Unless required by applicable law or agreed to in writing, software\n * distributed under the License is distributed on an \"AS IS\" BASIS,\n * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\n * See the License for the specific language governing permissions and\n * limitations under the License.\n */\n\nspan.katex-display {\n text-align: left;\n padding: 8px 0 8px 0;\n margin: 0.5em 0 0.5em 1em;\n}\n\nspan.katex {\n -webkit-font-smoothing: antialiased;\n color: rgba(0, 0, 0, 0.8);\n font-size: 1.18em;\n}\n"; - - // Copyright 2018 The Distill Template Authors - // - // Licensed under the Apache License, Version 2.0 (the "License"); - // you may not use this file except in compliance with the License. - // You may obtain a copy of the License at - // - // http://www.apache.org/licenses/LICENSE-2.0 - // - // Unless required by applicable law or agreed to in writing, software - // distributed under the License is distributed on an "AS IS" BASIS, - // WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - // See the License for the specific language governing permissions and - // limitations under the License. - - // This is a straight concatenation of code from KaTeX's contrib folder, - // but we aren't using some of their helpers that don't work well outside a browser environment. - - /*global katex */ - - const findEndOfMath = function(delimiter, text, startIndex) { - // Adapted from - // https://github.com/Khan/perseus/blob/master/src/perseus-markdown.jsx - let index = startIndex; - let braceLevel = 0; - - const delimLength = delimiter.length; - - while (index < text.length) { - const character = text[index]; - - if ( - braceLevel <= 0 && - text.slice(index, index + delimLength) === delimiter - ) { - return index; - } else if (character === "\\") { - index++; - } else if (character === "{") { - braceLevel++; - } else if (character === "}") { - braceLevel--; - } - - index++; - } - - return -1; - }; - - const splitAtDelimiters = function(startData, leftDelim, rightDelim, display) { - const finalData = []; - - for (let i = 0; i < startData.length; i++) { - if (startData[i].type === "text") { - const text = startData[i].data; - - let lookingForLeft = true; - let currIndex = 0; - let nextIndex; - - nextIndex = text.indexOf(leftDelim); - if (nextIndex !== -1) { - currIndex = nextIndex; - finalData.push({ - type: "text", - data: text.slice(0, currIndex) - }); - lookingForLeft = false; - } - - while (true) { - // eslint-disable-line no-constant-condition - if (lookingForLeft) { - nextIndex = text.indexOf(leftDelim, currIndex); - if (nextIndex === -1) { - break; - } - - finalData.push({ - type: "text", - data: text.slice(currIndex, nextIndex) - }); - - currIndex = nextIndex; - } else { - nextIndex = findEndOfMath( - rightDelim, - text, - currIndex + leftDelim.length - ); - if (nextIndex === -1) { - break; - } - - finalData.push({ - type: "math", - data: text.slice(currIndex + leftDelim.length, nextIndex), - rawData: text.slice(currIndex, nextIndex + rightDelim.length), - display: display - }); - - currIndex = nextIndex + rightDelim.length; - } - - lookingForLeft = !lookingForLeft; - } - - finalData.push({ - type: "text", - data: text.slice(currIndex) - }); - } else { - finalData.push(startData[i]); - } - } - - return finalData; - }; - - const splitWithDelimiters = function(text, delimiters) { - let data = [{ type: "text", data: text }]; - for (let i = 0; i < delimiters.length; i++) { - const delimiter = delimiters[i]; - data = splitAtDelimiters( - data, - delimiter.left, - delimiter.right, - delimiter.display || false - ); - } - return data; - }; - - /* Note: optionsCopy is mutated by this method. If it is ever exposed in the - * API, we should copy it before mutating. - */ - const renderMathInText = function(text, optionsCopy) { - const data = splitWithDelimiters(text, optionsCopy.delimiters); - const fragment = document.createDocumentFragment(); - - for (let i = 0; i < data.length; i++) { - if (data[i].type === "text") { - fragment.appendChild(document.createTextNode(data[i].data)); - } else { - const tag = document.createElement("d-math"); - const math = data[i].data; - // Override any display mode defined in the settings with that - // defined by the text itself - optionsCopy.displayMode = data[i].display; - try { - tag.textContent = math; - if (optionsCopy.displayMode) { - tag.setAttribute("block", ""); - } - } catch (e) { - if (!(e instanceof katex.ParseError)) { - throw e; - } - optionsCopy.errorCallback( - "KaTeX auto-render: Failed to parse `" + data[i].data + "` with ", - e - ); - fragment.appendChild(document.createTextNode(data[i].rawData)); - continue; - } - fragment.appendChild(tag); - } - } - - return fragment; - }; - - const renderElem = function(elem, optionsCopy) { - for (let i = 0; i < elem.childNodes.length; i++) { - const childNode = elem.childNodes[i]; - if (childNode.nodeType === 3) { - // Text node - const text = childNode.textContent; - if (optionsCopy.mightHaveMath(text)) { - const frag = renderMathInText(text, optionsCopy); - i += frag.childNodes.length - 1; - elem.replaceChild(frag, childNode); - } - } else if (childNode.nodeType === 1) { - // Element node - const shouldRender = - optionsCopy.ignoredTags.indexOf(childNode.nodeName.toLowerCase()) === - -1; - - if (shouldRender) { - renderElem(childNode, optionsCopy); - } - } - // Otherwise, it's something else, and ignore it. - } - }; - - const defaultAutoRenderOptions = { - delimiters: [ - { left: "$$", right: "$$", display: true }, - { left: "\\[", right: "\\]", display: true }, - { left: "\\(", right: "\\)", display: false } - // LaTeX uses this, but it ruins the display of normal `$` in text: - // {left: '$', right: '$', display: false}, - ], - - ignoredTags: [ - "script", - "noscript", - "style", - "textarea", - "pre", - "code", - "svg" - ], - - errorCallback: function(msg, err) { - console.error(msg, err); - } - }; - - const renderMathInElement = function(elem, options) { - if (!elem) { - throw new Error("No element provided to render"); - } - - const optionsCopy = Object.assign({}, defaultAutoRenderOptions, options); - const delimiterStrings = optionsCopy.delimiters.flatMap(d => [ - d.left, - d.right - ]); - const mightHaveMath = text => - delimiterStrings.some(d => text.indexOf(d) !== -1); - optionsCopy.mightHaveMath = mightHaveMath; - renderElem(elem, optionsCopy); - }; - - // Copyright 2018 The Distill Template Authors - - const katexJSURL = 'https://distill.pub/third-party/katex/katex.min.js'; - const katexCSSTag = ''; - - const T = Template('d-math', ` -${katexCSSTag} - - -`); - - // DMath, not Math, because that would conflict with the JS built-in - class DMath extends Mutating(T(HTMLElement)) { - - static set katexOptions(options) { - DMath._katexOptions = options; - if (DMath.katexOptions.delimiters) { - if (!DMath.katexAdded) { - DMath.addKatex(); - } else { - DMath.katexLoadedCallback(); - } - } - } - - static get katexOptions() { - if (!DMath._katexOptions) { - DMath._katexOptions = { - delimiters: [ { 'left':'$$', 'right':'$$', 'display': false } ] - }; - } - return DMath._katexOptions; - } - - static katexLoadedCallback() { - // render all d-math tags - const mathTags = document.querySelectorAll('d-math'); - for (const mathTag of mathTags) { - mathTag.renderContent(); - } - // transform inline delimited math to d-math tags - if (DMath.katexOptions.delimiters) { - renderMathInElement(document.body, DMath.katexOptions); - } - } - - static addKatex() { - // css tag can use this convenience function - document.head.insertAdjacentHTML('beforeend', katexCSSTag); - // script tag has to be created to work properly - const scriptTag = document.createElement('script'); - scriptTag.src = katexJSURL; - scriptTag.async = true; - scriptTag.onload = DMath.katexLoadedCallback; - scriptTag.crossorigin = 'anonymous'; - document.head.appendChild(scriptTag); - - DMath.katexAdded = true; - } - - get options() { - const localOptions = { displayMode: this.hasAttribute('block') }; - return Object.assign(localOptions, DMath.katexOptions); - } - - connectedCallback() { - super.connectedCallback(); - if (!DMath.katexAdded) { - DMath.addKatex(); - } - } - - renderContent() { - if (typeof katex !== 'undefined') { - const container = this.root.querySelector('#katex-container'); - katex.render(this.textContent, container, this.options); - } - } - - } - - DMath.katexAdded = false; - DMath.inlineMathRendered = false; - window.DMath = DMath; // TODO: check if this can be removed, or if we should expose a distill global - - // Copyright 2018 The Distill Template Authors - // - // Licensed under the Apache License, Version 2.0 (the "License"); - // you may not use this file except in compliance with the License. - // You may obtain a copy of the License at - // - // http://www.apache.org/licenses/LICENSE-2.0 - // - // Unless required by applicable law or agreed to in writing, software - // distributed under the License is distributed on an "AS IS" BASIS, - // WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - // See the License for the specific language governing permissions and - // limitations under the License. - - function collect_citations(dom = document) { - const citations = new Set(); - const citeTags = dom.querySelectorAll("d-cite"); - for (const tag of citeTags) { - const keyString = tag.getAttribute("key") || tag.getAttribute("bibtex-key"); - const keys = keyString.split(",").map(k => k.trim()); - for (const key of keys) { - citations.add(key); - } - } - return [...citations]; - } - - function author_string(ent, template, sep, finalSep) { - if (ent.author == null) { - return ""; - } - var names = ent.author.split(" and "); - let name_strings = names.map(name => { - name = name.trim(); - if (name.indexOf(",") != -1) { - var last = name.split(",")[0].trim(); - var firsts = name.split(",")[1]; - } else if (name.indexOf(" ") != -1) { - var last = name - .split(" ") - .slice(-1)[0] - .trim(); - var firsts = name - .split(" ") - .slice(0, -1) - .join(" "); - } else { - var last = name.trim(); - } - var initials = ""; - if (firsts != undefined) { - initials = firsts - .trim() - .split(" ") - .map(s => s.trim()[0]); - initials = initials.join(".") + "."; - } - return template - .replace("${F}", firsts) - .replace("${L}", last) - .replace("${I}", initials) - .trim(); // in case one of first or last was empty - }); - if (names.length > 1) { - var str = name_strings.slice(0, names.length - 1).join(sep); - str += (finalSep || sep) + name_strings[names.length - 1]; - return str; - } else { - return name_strings[0]; - } - } - - function venue_string(ent) { - var cite = ent.journal || ent.booktitle || ""; - if ("volume" in ent) { - var issue = ent.issue || ent.number; - issue = issue != undefined ? "(" + issue + ")" : ""; - cite += ", Vol " + ent.volume + issue; - } - if ("pages" in ent) { - cite += ", pp. " + ent.pages; - } - if (cite != "") cite += ". "; - if ("publisher" in ent) { - cite += ent.publisher; - if (cite[cite.length - 1] != ".") cite += "."; - } - return cite; - } - - function link_string(ent) { - if ("url" in ent) { - var url = ent.url; - var arxiv_match = /arxiv\.org\/abs\/([0-9\.]*)/.exec(url); - if (arxiv_match != null) { - url = `http://arxiv.org/pdf/${arxiv_match[1]}.pdf`; - } - - if (url.slice(-4) == ".pdf") { - var label = "PDF"; - } else if (url.slice(-5) == ".html") { - var label = "HTML"; - } - return `  [${label || "link"}]`; - } /* else if ("doi" in ent){ - return `  [DOI]`; - }*/ else { - return ""; - } - } - function doi_string(ent, new_line) { - if ("doi" in ent) { - return `${new_line ? "
" : ""} DOI: ${ent.doi}`; - } else { - return ""; - } - } - - function title_string(ent) { - return '' + ent.title + " "; - } - - function bibliography_cite(ent, fancy) { - if (ent) { - var cite = title_string(ent); - cite += link_string(ent) + "
"; - if (ent.author) { - cite += author_string(ent, "${L}, ${I}", ", ", " and "); - if (ent.year || ent.date) { - cite += ", "; - } - } - if (ent.year || ent.date) { - cite += (ent.year || ent.date) + ". "; - } else { - cite += ". "; - } - cite += venue_string(ent); - cite += doi_string(ent); - return cite; - /*var cite = author_string(ent, "${L}, ${I}", ", ", " and "); - if (ent.year || ent.date){ - cite += ", " + (ent.year || ent.date) + ". " - } else { - cite += ". " - } - cite += "" + ent.title + ". "; - cite += venue_string(ent); - cite += doi_string(ent); - cite += link_string(ent); - return cite*/ - } else { - return "?"; - } - } - - function hover_cite(ent) { - if (ent) { - var cite = ""; - cite += "" + ent.title + ""; - cite += link_string(ent); - cite += "
"; - - var a_str = author_string(ent, "${I} ${L}", ", ") + "."; - var v_str = - venue_string(ent).trim() + " " + ent.year + ". " + doi_string(ent, true); - - if ((a_str + v_str).length < Math.min(40, ent.title.length)) { - cite += a_str + " " + v_str; - } else { - cite += a_str + "
" + v_str; - } - return cite; - } else { - return "?"; - } - } - - function domContentLoaded() { - return ['interactive', 'complete'].indexOf(document.readyState) !== -1; - } - - // Copyright 2018 The Distill Template Authors - // - // Licensed under the Apache License, Version 2.0 (the "License"); - // you may not use this file except in compliance with the License. - // You may obtain a copy of the License at - // - // http://www.apache.org/licenses/LICENSE-2.0 - // - // Unless required by applicable law or agreed to in writing, software - // distributed under the License is distributed on an "AS IS" BASIS, - // WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - // See the License for the specific language governing permissions and - // limitations under the License. - - function _moveLegacyAffiliationFormatIntoArray(frontMatter) { - // authors used to have propoerties "affiliation" and "affiliationURL". - // We now encourage using an array for affiliations containing objects with - // properties "name" and "url". - for (let author of frontMatter.authors) { - const hasOldStyle = Boolean(author.affiliation); - const hasNewStyle = Boolean(author.affiliations); - if (!hasOldStyle) continue; - if (hasNewStyle) { - console.warn(`Author ${author.author} has both old-style ("affiliation" & "affiliationURL") and new style ("affiliations") affiliation information!`); - } else { - let newAffiliation = { - "name": author.affiliation - }; - if (author.affiliationURL) newAffiliation.url = author.affiliationURL; - author.affiliations = [newAffiliation]; - } - } - return frontMatter - } - - function parseFrontmatter(element) { - const scriptTag = element.firstElementChild; - if (scriptTag) { - const type = scriptTag.getAttribute('type'); - if (type.split('/')[1] == 'json') { - const content = scriptTag.textContent; - const parsed = JSON.parse(content); - return _moveLegacyAffiliationFormatIntoArray(parsed); - } else { - console.error('Distill only supports JSON frontmatter tags anymore; no more YAML.'); - } - } else { - console.error('You added a frontmatter tag but did not provide a script tag with front matter data in it. Please take a look at our templates.'); - } - return {}; - } - - class FrontMatter$1 extends HTMLElement { - - static get is() { return 'd-front-matter'; } - - constructor() { - super(); - - const options = {childList: true, characterData: true, subtree: true}; - const observer = new MutationObserver( (entries) => { - for (const entry of entries) { - if (entry.target.nodeName === 'SCRIPT' || entry.type === 'characterData') { - const data = parseFrontmatter(this); - this.notify(data); - } - } - }); - observer.observe(this, options); - } - - notify(data) { - const options = { detail: data, bubbles: true }; - const event = new CustomEvent('onFrontMatterChanged', options); - document.dispatchEvent(event); - } - - } - - // Copyright 2018 The Distill Template Authors - // - // Licensed under the Apache License, Version 2.0 (the "License"); - // you may not use this file except in compliance with the License. - // You may obtain a copy of the License at - // - // http://www.apache.org/licenses/LICENSE-2.0 - // - // Unless required by applicable law or agreed to in writing, software - // distributed under the License is distributed on an "AS IS" BASIS, - // WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - // See the License for the specific language governing permissions and - // limitations under the License. - - // no appendix -> add appendix - // title in front, no h1 -> add it - // no title in front, h1 -> read and put into frontMatter - // footnote -> footnote list - // break up bib - // if citation, no bib-list -> add citation-list - - // if authors, no byline -> add byline - - function optionalComponents(dom, data) { - const body = dom.body; - const article = body.querySelector('d-article'); - - // If we don't have an article tag, something weird is going on—giving up. - if (!article) { - console.warn('No d-article tag found; skipping adding optional components!'); - return; - } - - let byline = dom.querySelector('d-byline'); - if (!byline) { - if (data.authors) { - byline = dom.createElement('d-byline'); - body.insertBefore(byline, article); - } else { - console.warn('No authors found in front matter; please add them before submission!'); - } - } - - let title = dom.querySelector('d-title'); - if (!title) { - title = dom.createElement('d-title'); - body.insertBefore(title, byline); - } - - let h1 = title.querySelector('h1'); - if (!h1) { - h1 = dom.createElement('h1'); - h1.textContent = data.title; - title.insertBefore(h1, title.firstChild); - } - - const hasPassword = typeof data.password !== 'undefined'; - let interstitial = body.querySelector('d-interstitial'); - if (hasPassword && !interstitial) { - const inBrowser = typeof window !== 'undefined'; - const onLocalhost = inBrowser && window.location.hostname.includes('localhost'); - if (!inBrowser || !onLocalhost) { - interstitial = dom.createElement('d-interstitial'); - interstitial.password = data.password; - body.insertBefore(interstitial, body.firstChild); - } - } else if (!hasPassword && interstitial) { - interstitial.parentElement.removeChild(this); - } - - let appendix = dom.querySelector('d-appendix'); - if (!appendix) { - appendix = dom.createElement('d-appendix'); - dom.body.appendChild(appendix); - } - - let footnoteList = dom.querySelector('d-footnote-list'); - if (!footnoteList) { - footnoteList = dom.createElement('d-footnote-list'); - appendix.appendChild(footnoteList); - } - - let citationList = dom.querySelector('d-citation-list'); - if (!citationList) { - citationList = dom.createElement('d-citation-list'); - appendix.appendChild(citationList); - } - - } - - // Copyright 2018 The Distill Template Authors - - const frontMatter = new FrontMatter(); - - const Controller = { - frontMatter: frontMatter, - waitingOn: { - bibliography: [], - citations: [] - }, - listeners: { - onCiteKeyCreated(event) { - const [citeTag, keys] = event.detail; - - // ensure we have citations - if (!frontMatter.citationsCollected) { - // console.debug('onCiteKeyCreated, but unresolved dependency ("citations"). Enqueing.'); - Controller.waitingOn.citations.push(() => - Controller.listeners.onCiteKeyCreated(event) - ); - return; - } - - // ensure we have a loaded bibliography - if (!frontMatter.bibliographyParsed) { - // console.debug('onCiteKeyCreated, but unresolved dependency ("bibliography"). Enqueing.'); - Controller.waitingOn.bibliography.push(() => - Controller.listeners.onCiteKeyCreated(event) - ); - return; - } - - const numbers = keys.map(key => frontMatter.citations.indexOf(key)); - citeTag.numbers = numbers; - const entries = keys.map(key => frontMatter.bibliography.get(key)); - citeTag.entries = entries; - }, - - onCiteKeyChanged() { - // const [citeTag, keys] = event.detail; - - // update citations - frontMatter.citations = collect_citations(); - frontMatter.citationsCollected = true; - for (const waitingCallback of Controller.waitingOn.citations.slice()) { - waitingCallback(); - } - - // update bibliography - const citationListTag = document.querySelector("d-citation-list"); - const bibliographyEntries = new Map( - frontMatter.citations.map(citationKey => { - return [citationKey, frontMatter.bibliography.get(citationKey)]; - }) - ); - citationListTag.citations = bibliographyEntries; - - const citeTags = document.querySelectorAll("d-cite"); - for (const citeTag of citeTags) { - console.log(citeTag); - const keys = citeTag.keys; - const numbers = keys.map(key => frontMatter.citations.indexOf(key)); - citeTag.numbers = numbers; - const entries = keys.map(key => frontMatter.bibliography.get(key)); - citeTag.entries = entries; - } - }, - - onCiteKeyRemoved(event) { - Controller.listeners.onCiteKeyChanged(event); - }, - - onBibliographyChanged(event) { - const citationListTag = document.querySelector("d-citation-list"); - - const bibliography = event.detail; - - frontMatter.bibliography = bibliography; - frontMatter.bibliographyParsed = true; - for (const waitingCallback of Controller.waitingOn.bibliography.slice()) { - waitingCallback(); - } - - // ensure we have citations - if (!frontMatter.citationsCollected) { - Controller.waitingOn.citations.push(function() { - Controller.listeners.onBibliographyChanged({ - target: event.target, - detail: event.detail - }); - }); - return; - } - - if (citationListTag.hasAttribute("distill-prerendered")) { - console.debug("Citation list was prerendered; not updating it."); - } else { - const entries = new Map( - frontMatter.citations.map(citationKey => { - return [citationKey, frontMatter.bibliography.get(citationKey)]; - }) - ); - citationListTag.citations = entries; - } - }, - - onFootnoteChanged() { - // const footnote = event.detail; - //TODO: optimize to only update current footnote - const footnotesList = document.querySelector("d-footnote-list"); - if (footnotesList) { - const footnotes = document.querySelectorAll("d-footnote"); - footnotesList.footnotes = footnotes; - } - }, - - onFrontMatterChanged(event) { - const data = event.detail; - mergeFromYMLFrontmatter(frontMatter, data); - - const interstitial = document.querySelector("d-interstitial"); - if (interstitial) { - if (typeof frontMatter.password !== "undefined") { - interstitial.password = frontMatter.password; - } else { - interstitial.parentElement.removeChild(interstitial); - } - } - - const prerendered = document.body.hasAttribute("distill-prerendered"); - if (!prerendered && domContentLoaded()) { - optionalComponents(document, frontMatter); - - const appendix = document.querySelector("distill-appendix"); - if (appendix) { - appendix.frontMatter = frontMatter; - } - - const byline = document.querySelector("d-byline"); - if (byline) { - byline.frontMatter = frontMatter; - } - - if (data.katex) { - DMath.katexOptions = data.katex; - } - } - }, - - DOMContentLoaded() { - if (Controller.loaded) { - console.warn( - "Controller received DOMContentLoaded but was already loaded!" - ); - return; - } else if (!domContentLoaded()) { - console.warn( - "Controller received DOMContentLoaded at document.readyState: " + - document.readyState + - "!" - ); - return; - } else { - Controller.loaded = true; - console.debug("Runlevel 4: Controller running DOMContentLoaded"); - } - - const frontMatterTag = document.querySelector("d-front-matter"); - if (frontMatterTag) { - const data = parseFrontmatter(frontMatterTag); - Controller.listeners.onFrontMatterChanged({ detail: data }); - } - - // Resolving "citations" dependency due to initial DOM load - frontMatter.citations = collect_citations(); - frontMatter.citationsCollected = true; - for (const waitingCallback of Controller.waitingOn.citations.slice()) { - waitingCallback(); - } - - if (frontMatter.bibliographyParsed) { - for (const waitingCallback of Controller.waitingOn.bibliography.slice()) { - waitingCallback(); - } - } - - const footnotesList = document.querySelector("d-footnote-list"); - if (footnotesList) { - const footnotes = document.querySelectorAll("d-footnote"); - footnotesList.footnotes = footnotes; - } - } - } // listeners - }; // Controller - - var base = "/*\n * Copyright 2018 The Distill Template Authors\n *\n * Licensed under the Apache License, Version 2.0 (the \"License\");\n * you may not use this file except in compliance with the License.\n * You may obtain a copy of the License at\n *\n * http://www.apache.org/licenses/LICENSE-2.0\n *\n * Unless required by applicable law or agreed to in writing, software\n * distributed under the License is distributed on an \"AS IS\" BASIS,\n * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\n * See the License for the specific language governing permissions and\n * limitations under the License.\n */\n\nhtml {\n font-size: 14px;\n\tline-height: 1.6em;\n /* font-family: \"Libre Franklin\", \"Helvetica Neue\", sans-serif; */\n font-family: -apple-system, BlinkMacSystemFont, \"Segoe UI\", Roboto, Oxygen, Ubuntu, Cantarell, \"Fira Sans\", \"Droid Sans\", \"Helvetica Neue\", Arial, sans-serif;\n /*, \"Apple Color Emoji\", \"Segoe UI Emoji\", \"Segoe UI Symbol\";*/\n text-size-adjust: 100%;\n -ms-text-size-adjust: 100%;\n -webkit-text-size-adjust: 100%;\n}\n\n@media(min-width: 768px) {\n html {\n font-size: 16px;\n }\n}\n\nbody {\n margin: 0;\n}\n\na {\n color: #004276;\n}\n\nfigure {\n margin: 0;\n}\n\ntable {\n\tborder-collapse: collapse;\n\tborder-spacing: 0;\n}\n\ntable th {\n\ttext-align: left;\n}\n\ntable thead {\n border-bottom: 1px solid rgba(0, 0, 0, 0.05);\n}\n\ntable thead th {\n padding-bottom: 0.5em;\n}\n\ntable tbody :first-child td {\n padding-top: 0.5em;\n}\n\npre {\n overflow: auto;\n max-width: 100%;\n}\n\np {\n margin-top: 0;\n margin-bottom: 1em;\n}\n\nsup, sub {\n vertical-align: baseline;\n position: relative;\n top: -0.4em;\n line-height: 1em;\n}\n\nsub {\n top: 0.4em;\n}\n\n.kicker,\n.marker {\n font-size: 15px;\n font-weight: 600;\n color: rgba(0, 0, 0, 0.5);\n}\n\n\n/* Headline */\n\n@media(min-width: 1024px) {\n d-title h1 span {\n display: block;\n }\n}\n\n/* Figure */\n\nfigure {\n position: relative;\n margin-bottom: 2.5em;\n margin-top: 1.5em;\n}\n\nfigcaption+figure {\n\n}\n\nfigure img {\n width: 100%;\n}\n\nfigure svg text,\nfigure svg tspan {\n}\n\nfigcaption,\n.figcaption {\n color: rgba(0, 0, 0, 0.6);\n font-size: 12px;\n line-height: 1.5em;\n}\n\n@media(min-width: 1024px) {\nfigcaption,\n.figcaption {\n font-size: 13px;\n }\n}\n\nfigure.external img {\n background: white;\n border: 1px solid rgba(0, 0, 0, 0.1);\n box-shadow: 0 1px 8px rgba(0, 0, 0, 0.1);\n padding: 18px;\n box-sizing: border-box;\n}\n\nfigcaption a {\n color: rgba(0, 0, 0, 0.6);\n}\n\nfigcaption b,\nfigcaption strong, {\n font-weight: 600;\n color: rgba(0, 0, 0, 1.0);\n}\n"; - - var layout = "/*\n * Copyright 2018 The Distill Template Authors\n *\n * Licensed under the Apache License, Version 2.0 (the \"License\");\n * you may not use this file except in compliance with the License.\n * You may obtain a copy of the License at\n *\n * http://www.apache.org/licenses/LICENSE-2.0\n *\n * Unless required by applicable law or agreed to in writing, software\n * distributed under the License is distributed on an \"AS IS\" BASIS,\n * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\n * See the License for the specific language governing permissions and\n * limitations under the License.\n */\n\n@supports not (display: grid) {\n .base-grid,\n distill-header,\n d-title,\n d-abstract,\n d-article,\n d-appendix,\n distill-appendix,\n d-byline,\n d-footnote-list,\n d-citation-list,\n distill-footer {\n display: block;\n padding: 8px;\n }\n}\n\n.base-grid,\ndistill-header,\nd-title,\nd-abstract,\nd-article,\nd-appendix,\ndistill-appendix,\nd-byline,\nd-footnote-list,\nd-citation-list,\ndistill-footer {\n display: grid;\n justify-items: stretch;\n grid-template-columns: [screen-start] 8px [page-start kicker-start text-start gutter-start middle-start] 1fr 1fr 1fr 1fr 1fr 1fr 1fr 1fr [text-end page-end gutter-end kicker-end middle-end] 8px [screen-end];\n grid-column-gap: 8px;\n}\n\n.grid {\n display: grid;\n grid-column-gap: 8px;\n}\n\n@media(min-width: 768px) {\n .base-grid,\n distill-header,\n d-title,\n d-abstract,\n d-article,\n d-appendix,\n distill-appendix,\n d-byline,\n d-footnote-list,\n d-citation-list,\n distill-footer {\n grid-template-columns: [screen-start] 1fr [page-start kicker-start middle-start text-start] 45px 45px 45px 45px 45px 45px 45px 45px [ kicker-end text-end gutter-start] 45px [middle-end] 45px [page-end gutter-end] 1fr [screen-end];\n grid-column-gap: 16px;\n }\n\n .grid {\n grid-column-gap: 16px;\n }\n}\n\n@media(min-width: 1000px) {\n .base-grid,\n distill-header,\n d-title,\n d-abstract,\n d-article,\n d-appendix,\n distill-appendix,\n d-byline,\n d-footnote-list,\n d-citation-list,\n distill-footer {\n grid-template-columns: [screen-start] 1fr [page-start kicker-start] 50px [middle-start] 50px [text-start kicker-end] 50px 50px 50px 50px 50px 50px 50px 50px [text-end gutter-start] 50px [middle-end] 50px [page-end gutter-end] 1fr [screen-end];\n grid-column-gap: 16px;\n }\n\n .grid {\n grid-column-gap: 16px;\n }\n}\n\n@media(min-width: 1180px) {\n .base-grid,\n distill-header,\n d-title,\n d-abstract,\n d-article,\n d-appendix,\n distill-appendix,\n d-byline,\n d-footnote-list,\n d-citation-list,\n distill-footer {\n grid-template-columns: [screen-start] 1fr [page-start kicker-start] 60px [middle-start] 60px [text-start kicker-end] 60px 60px 60px 60px 60px 60px 60px 60px [text-end gutter-start] 60px [middle-end] 60px [page-end gutter-end] 1fr [screen-end];\n grid-column-gap: 32px;\n }\n\n .grid {\n grid-column-gap: 32px;\n }\n}\n\n\n\n\n.base-grid {\n grid-column: screen;\n}\n\n/* .l-body,\nd-article > * {\n grid-column: text;\n}\n\n.l-page,\nd-title > *,\nd-figure {\n grid-column: page;\n} */\n\n.l-gutter {\n grid-column: gutter;\n}\n\n.l-text,\n.l-body {\n grid-column: text;\n}\n\n.l-page {\n grid-column: page;\n}\n\n.l-body-outset {\n grid-column: middle;\n}\n\n.l-page-outset {\n grid-column: page;\n}\n\n.l-screen {\n grid-column: screen;\n}\n\n.l-screen-inset {\n grid-column: screen;\n padding-left: 16px;\n padding-left: 16px;\n}\n\n\n/* Aside */\n\nd-article aside {\n grid-column: gutter;\n font-size: 12px;\n line-height: 1.6em;\n color: rgba(0, 0, 0, 0.6)\n}\n\n@media(min-width: 768px) {\n aside {\n grid-column: gutter;\n }\n\n .side {\n grid-column: gutter;\n }\n}\n"; - - var print = "/*\n * Copyright 2018 The Distill Template Authors\n *\n * Licensed under the Apache License, Version 2.0 (the \"License\");\n * you may not use this file except in compliance with the License.\n * You may obtain a copy of the License at\n *\n * http://www.apache.org/licenses/LICENSE-2.0\n *\n * Unless required by applicable law or agreed to in writing, software\n * distributed under the License is distributed on an \"AS IS\" BASIS,\n * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\n * See the License for the specific language governing permissions and\n * limitations under the License.\n */\n\n@media print {\n\n @page {\n size: 8in 11in;\n @bottom-right {\n content: counter(page) \" of \" counter(pages);\n }\n }\n\n html {\n /* no general margins -- CSS Grid takes care of those */\n }\n\n p, code {\n page-break-inside: avoid;\n }\n\n h2, h3 {\n page-break-after: avoid;\n }\n\n d-header {\n visibility: hidden;\n }\n\n d-footer {\n display: none!important;\n }\n\n}\n"; - - var byline = "/*\n * Copyright 2018 The Distill Template Authors\n *\n * Licensed under the Apache License, Version 2.0 (the \"License\");\n * you may not use this file except in compliance with the License.\n * You may obtain a copy of the License at\n *\n * http://www.apache.org/licenses/LICENSE-2.0\n *\n * Unless required by applicable law or agreed to in writing, software\n * distributed under the License is distributed on an \"AS IS\" BASIS,\n * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\n * See the License for the specific language governing permissions and\n * limitations under the License.\n */\n\nd-byline {\n contain: style;\n overflow: hidden;\n border-top: 1px solid rgba(0, 0, 0, 0.1);\n font-size: 0.8rem;\n line-height: 1.8em;\n padding: 1.5rem 0;\n min-height: 1.8em;\n}\n\n\nd-byline .byline {\n grid-template-columns: 1fr 1fr;\n grid-column: text;\n}\n\n@media(min-width: 768px) {\n d-byline .byline {\n grid-template-columns: 1fr 1fr 1fr 1fr;\n }\n}\n\nd-byline .authors-affiliations {\n grid-column-end: span 2;\n grid-template-columns: 1fr 1fr;\n margin-bottom: 1em;\n}\n\n@media(min-width: 768px) {\n d-byline .authors-affiliations {\n margin-bottom: 0;\n }\n}\n\nd-byline h3 {\n font-size: 0.6rem;\n font-weight: 400;\n color: rgba(0, 0, 0, 0.5);\n margin: 0;\n text-transform: uppercase;\n}\n\nd-byline p {\n margin: 0;\n}\n\nd-byline a,\nd-article d-byline a {\n color: rgba(0, 0, 0, 0.8);\n text-decoration: none;\n border-bottom: none;\n}\n\nd-article d-byline a:hover {\n text-decoration: underline;\n border-bottom: none;\n}\n\nd-byline p.author {\n font-weight: 500;\n}\n\nd-byline .affiliations {\n\n}\n"; - - var article = "/*\n * Copyright 2018 The Distill Template Authors\n *\n * Licensed under the Apache License, Version 2.0 (the \"License\");\n * you may not use this file except in compliance with the License.\n * You may obtain a copy of the License at\n *\n * http://www.apache.org/licenses/LICENSE-2.0\n *\n * Unless required by applicable law or agreed to in writing, software\n * distributed under the License is distributed on an \"AS IS\" BASIS,\n * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\n * See the License for the specific language governing permissions and\n * limitations under the License.\n */\n\nd-article {\n contain: layout style;\n overflow-x: hidden;\n border-top: 1px solid rgba(0, 0, 0, 0.1);\n padding-top: 2rem;\n color: rgba(0, 0, 0, 0.8);\n}\n\nd-article > * {\n grid-column: text;\n}\n\n@media(min-width: 768px) {\n d-article {\n font-size: 16px;\n }\n}\n\n@media(min-width: 1024px) {\n d-article {\n font-size: 1.06rem;\n line-height: 1.7em;\n }\n}\n\n\n/* H2 */\n\n\nd-article .marker {\n text-decoration: none;\n border: none;\n counter-reset: section;\n grid-column: kicker;\n line-height: 1.7em;\n}\n\nd-article .marker:hover {\n border: none;\n}\n\nd-article .marker span {\n padding: 0 3px 4px;\n border-bottom: 1px solid rgba(0, 0, 0, 0.2);\n position: relative;\n top: 4px;\n}\n\nd-article .marker:hover span {\n color: rgba(0, 0, 0, 0.7);\n border-bottom: 1px solid rgba(0, 0, 0, 0.7);\n}\n\nd-article h2 {\n font-weight: 600;\n font-size: 24px;\n line-height: 1.25em;\n margin: 2rem 0 1.5rem 0;\n border-bottom: 1px solid rgba(0, 0, 0, 0.1);\n padding-bottom: 1rem;\n}\n\n@media(min-width: 1024px) {\n d-article h2 {\n font-size: 36px;\n }\n}\n\n/* H3 */\n\nd-article h3 {\n font-weight: 700;\n font-size: 18px;\n line-height: 1.4em;\n margin-bottom: 1em;\n margin-top: 2em;\n}\n\n@media(min-width: 1024px) {\n d-article h3 {\n font-size: 20px;\n }\n}\n\n/* H4 */\n\nd-article h4 {\n font-weight: 600;\n text-transform: uppercase;\n font-size: 14px;\n line-height: 1.4em;\n}\n\nd-article a {\n color: inherit;\n}\n\nd-article p,\nd-article ul,\nd-article ol,\nd-article blockquote {\n margin-top: 0;\n margin-bottom: 1em;\n margin-left: 0;\n margin-right: 0;\n}\n\nd-article blockquote {\n border-left: 2px solid rgba(0, 0, 0, 0.2);\n padding-left: 2em;\n font-style: italic;\n color: rgba(0, 0, 0, 0.6);\n}\n\nd-article a {\n border-bottom: 1px solid rgba(0, 0, 0, 0.4);\n text-decoration: none;\n}\n\nd-article a:hover {\n border-bottom: 1px solid rgba(0, 0, 0, 0.8);\n}\n\nd-article .link {\n text-decoration: underline;\n cursor: pointer;\n}\n\nd-article ul,\nd-article ol {\n padding-left: 24px;\n}\n\nd-article li {\n margin-bottom: 1em;\n margin-left: 0;\n padding-left: 0;\n}\n\nd-article li:last-child {\n margin-bottom: 0;\n}\n\nd-article pre {\n font-size: 14px;\n margin-bottom: 20px;\n}\n\nd-article hr {\n grid-column: screen;\n width: 100%;\n border: none;\n border-bottom: 1px solid rgba(0, 0, 0, 0.1);\n margin-top: 60px;\n margin-bottom: 60px;\n}\n\nd-article section {\n margin-top: 60px;\n margin-bottom: 60px;\n}\n\nd-article span.equation-mimic {\n font-family: georgia;\n font-size: 115%;\n font-style: italic;\n}\n\nd-article > d-code,\nd-article section > d-code {\n display: block;\n}\n\nd-article > d-math[block],\nd-article section > d-math[block] {\n display: block;\n}\n\n@media (max-width: 768px) {\n d-article > d-code,\n d-article section > d-code,\n d-article > d-math[block],\n d-article section > d-math[block] {\n overflow-x: scroll;\n -ms-overflow-style: none; // IE 10+\n overflow: -moz-scrollbars-none; // Firefox\n }\n\n d-article > d-code::-webkit-scrollbar,\n d-article section > d-code::-webkit-scrollbar,\n d-article > d-math[block]::-webkit-scrollbar,\n d-article section > d-math[block]::-webkit-scrollbar {\n display: none; // Safari and Chrome\n }\n}\n\nd-article .citation {\n color: #668;\n cursor: pointer;\n}\n\nd-include {\n width: auto;\n display: block;\n}\n\nd-figure {\n contain: layout style;\n}\n\n/* KaTeX */\n\n.katex, .katex-prerendered {\n contain: style;\n display: inline-block;\n}\n\n/* Tables */\n\nd-article table {\n border-collapse: collapse;\n margin-bottom: 1.5rem;\n border-bottom: 1px solid rgba(0, 0, 0, 0.2);\n}\n\nd-article table th {\n border-bottom: 1px solid rgba(0, 0, 0, 0.2);\n}\n\nd-article table td {\n border-bottom: 1px solid rgba(0, 0, 0, 0.05);\n}\n\nd-article table tr:last-of-type td {\n border-bottom: none;\n}\n\nd-article table th,\nd-article table td {\n font-size: 15px;\n padding: 2px 8px;\n}\n\nd-article table tbody :first-child td {\n padding-top: 2px;\n}\n"; - - var title = "/*\n * Copyright 2018 The Distill Template Authors\n *\n * Licensed under the Apache License, Version 2.0 (the \"License\");\n * you may not use this file except in compliance with the License.\n * You may obtain a copy of the License at\n *\n * http://www.apache.org/licenses/LICENSE-2.0\n *\n * Unless required by applicable law or agreed to in writing, software\n * distributed under the License is distributed on an \"AS IS\" BASIS,\n * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\n * See the License for the specific language governing permissions and\n * limitations under the License.\n */\n\nd-title {\n padding: 2rem 0 1.5rem;\n contain: layout style;\n overflow-x: hidden;\n}\n\n@media(min-width: 768px) {\n d-title {\n padding: 4rem 0 1.5rem;\n }\n}\n\nd-title h1 {\n grid-column: text;\n font-size: 40px;\n font-weight: 700;\n line-height: 1.1em;\n margin: 0 0 0.5rem;\n}\n\n@media(min-width: 768px) {\n d-title h1 {\n font-size: 50px;\n }\n}\n\nd-title p {\n font-weight: 300;\n font-size: 1.2rem;\n line-height: 1.55em;\n grid-column: text;\n}\n\nd-title .status {\n margin-top: 0px;\n font-size: 12px;\n color: #009688;\n opacity: 0.8;\n grid-column: kicker;\n}\n\nd-title .status span {\n line-height: 1;\n display: inline-block;\n padding: 6px 0;\n border-bottom: 1px solid #80cbc4;\n font-size: 11px;\n text-transform: uppercase;\n}\n"; - - // Copyright 2018 The Distill Template Authors - - const styles = base + layout + title + byline + article + math + print; - - function makeStyleTag(dom) { - - const styleTagId = 'distill-prerendered-styles'; - const prerenderedTag = dom.getElementById(styleTagId); - if (!prerenderedTag) { - const styleTag = dom.createElement('style'); - styleTag.id = styleTagId; - styleTag.type = 'text/css'; - const cssTextTag = dom.createTextNode(styles); - styleTag.appendChild(cssTextTag); - const firstScriptTag = dom.head.querySelector('script'); - dom.head.insertBefore(styleTag, firstScriptTag); - } - - } - - // Copyright 2018 The Distill Template Authors - // - // Licensed under the Apache License, Version 2.0 (the "License"); - // you may not use this file except in compliance with the License. - // You may obtain a copy of the License at - // - // http://www.apache.org/licenses/LICENSE-2.0 - // - // Unless required by applicable law or agreed to in writing, software - // distributed under the License is distributed on an "AS IS" BASIS, - // WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - // See the License for the specific language governing permissions and - // limitations under the License. - - function addPolyfill(polyfill, polyfillLoadedCallback) { - console.debug('Runlevel 0: Polyfill required: ' + polyfill.name); - const script = document.createElement('script'); - script.src = polyfill.url; - script.async = false; - if (polyfillLoadedCallback) { - script.onload = function() { polyfillLoadedCallback(polyfill); }; - } - script.onerror = function() { - new Error('Runlevel 0: Polyfills failed to load script ' + polyfill.name); - }; - document.head.appendChild(script); - } - - const polyfills = [ - { - name: 'WebComponents', - support: function() { - return 'customElements' in window && - 'attachShadow' in Element.prototype && - 'getRootNode' in Element.prototype && - 'content' in document.createElement('template') && - 'Promise' in window && - 'from' in Array; - }, - url: 'https://distill.pub/third-party/polyfills/webcomponents-lite.js' - }, { - name: 'IntersectionObserver', - support: function() { - return 'IntersectionObserver' in window && - 'IntersectionObserverEntry' in window; - }, - url: 'https://distill.pub/third-party/polyfills/intersection-observer.js' - }, - ]; - - class Polyfills { - - static browserSupportsAllFeatures() { - return polyfills.every((poly) => poly.support()); - } - - static load(callback) { - // Define an intermediate callback that checks if all is loaded. - const polyfillLoaded = function(polyfill) { - polyfill.loaded = true; - console.debug('Runlevel 0: Polyfill has finished loading: ' + polyfill.name); - // console.debug(window[polyfill.name]); - if (Polyfills.neededPolyfills.every((poly) => poly.loaded)) { - console.debug('Runlevel 0: All required polyfills have finished loading.'); - console.debug('Runlevel 0->1.'); - window.distillRunlevel = 1; - callback(); - } - }; - // Add polyfill script tags - for (const polyfill of Polyfills.neededPolyfills) { - addPolyfill(polyfill, polyfillLoaded); - } - } - - static get neededPolyfills() { - if (!Polyfills._neededPolyfills) { - Polyfills._neededPolyfills = polyfills.filter((poly) => !poly.support()); - } - return Polyfills._neededPolyfills; - } - } - - // Copyright 2018 The Distill Template Authors - // - // Licensed under the Apache License, Version 2.0 (the "License"); - // you may not use this file except in compliance with the License. - // You may obtain a copy of the License at - // - // http://www.apache.org/licenses/LICENSE-2.0 - // - // Unless required by applicable law or agreed to in writing, software - // distributed under the License is distributed on an "AS IS" BASIS, - // WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - // See the License for the specific language governing permissions and - // limitations under the License. - - // const marginSmall = 16; - // const marginLarge = 3 * marginSmall; - // const margin = marginSmall + marginLarge; - // const gutter = marginSmall; - // const outsetAmount = margin / 2; - // const numCols = 4; - // const numGutters = numCols - 1; - // const columnWidth = (768 - 2 * marginLarge - numGutters * gutter) / numCols; - // - // const screenwidth = 768; - // const pageWidth = screenwidth - 2 * marginLarge; - // const bodyWidth = pageWidth - columnWidth - gutter; - - function body(selector) { - return `${selector} { - grid-column: left / text; - } - `; - } - - // Copyright 2018 The Distill Template Authors - - const T$1 = Template('d-abstract', ` - - - -`); - - class Abstract extends T$1(HTMLElement) { - - } - - // Copyright 2018 The Distill Template Authors - - const T$2 = Template('d-appendix', ` - - -`, false); - - class Appendix extends T$2(HTMLElement) { - - } - - // Copyright 2018 The Distill Template Authors - // - // Licensed under the Apache License, Version 2.0 (the "License"); - // you may not use this file except in compliance with the License. - // You may obtain a copy of the License at - // - // http://www.apache.org/licenses/LICENSE-2.0 - // - // Unless required by applicable law or agreed to in writing, software - // distributed under the License is distributed on an "AS IS" BASIS, - // WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - // See the License for the specific language governing permissions and - // limitations under the License. - - // import { Template } from '../mixins/template'; - // import { Controller } from '../controller'; - - const isOnlyWhitespace = /^\s*$/; - - class Article extends HTMLElement { - static get is() { return 'd-article'; } - - constructor() { - super(); - - new MutationObserver( (mutations) => { - for (const mutation of mutations) { - for (const addedNode of mutation.addedNodes) { - switch (addedNode.nodeName) { - case '#text': { // usually text nodes are only linebreaks. - const text = addedNode.nodeValue; - if (!isOnlyWhitespace.test(text)) { - console.warn('Use of unwrapped text in distill articles is discouraged as it breaks layout! Please wrap any text in a or

tag. We found the following text: ' + text); - const wrapper = document.createElement('span'); - wrapper.innerHTML = addedNode.nodeValue; - addedNode.parentNode.insertBefore(wrapper, addedNode); - addedNode.parentNode.removeChild(addedNode); - } - } break; - } - } - } - }).observe(this, {childList: true}); - } - - } - - var commonjsGlobal = typeof globalThis !== 'undefined' ? globalThis : typeof window !== 'undefined' ? window : typeof global !== 'undefined' ? global : typeof self !== 'undefined' ? self : {}; - - function createCommonjsModule(fn, module) { - return module = { exports: {} }, fn(module, module.exports), module.exports; - } - - var bibtexParse = createCommonjsModule(function (module, exports) { - /* start bibtexParse 0.0.22 */ - - //Original work by Henrik Muehe (c) 2010 - // - //CommonJS port by Mikola Lysenko 2013 - // - //Port to Browser lib by ORCID / RCPETERS - // - //Issues: - //no comment handling within strings - //no string concatenation - //no variable values yet - //Grammar implemented here: - //bibtex -> (string | preamble | comment | entry)*; - //string -> '@STRING' '{' key_equals_value '}'; - //preamble -> '@PREAMBLE' '{' value '}'; - //comment -> '@COMMENT' '{' value '}'; - //entry -> '@' key '{' key ',' key_value_list '}'; - //key_value_list -> key_equals_value (',' key_equals_value)*; - //key_equals_value -> key '=' value; - //value -> value_quotes | value_braces | key; - //value_quotes -> '"' .*? '"'; // not quite - //value_braces -> '{' .*? '"'; // not quite - (function(exports) { - - function BibtexParser() { - - this.months = ["jan", "feb", "mar", "apr", "may", "jun", "jul", "aug", "sep", "oct", "nov", "dec"]; - this.notKey = [',','{','}',' ','=']; - this.pos = 0; - this.input = ""; - this.entries = new Array(); - - this.currentEntry = ""; - - this.setInput = function(t) { - this.input = t; - }; - - this.getEntries = function() { - return this.entries; - }; - - this.isWhitespace = function(s) { - return (s == ' ' || s == '\r' || s == '\t' || s == '\n'); - }; - - this.match = function(s, canCommentOut) { - if (canCommentOut == undefined || canCommentOut == null) - canCommentOut = true; - this.skipWhitespace(canCommentOut); - if (this.input.substring(this.pos, this.pos + s.length) == s) { - this.pos += s.length; - } else { - throw "Token mismatch, expected " + s + ", found " - + this.input.substring(this.pos); - } this.skipWhitespace(canCommentOut); - }; - - this.tryMatch = function(s, canCommentOut) { - if (canCommentOut == undefined || canCommentOut == null) - canCommentOut = true; - this.skipWhitespace(canCommentOut); - if (this.input.substring(this.pos, this.pos + s.length) == s) { - return true; - } else { - return false; - } }; - - /* when search for a match all text can be ignored, not just white space */ - this.matchAt = function() { - while (this.input.length > this.pos && this.input[this.pos] != '@') { - this.pos++; - } - if (this.input[this.pos] == '@') { - return true; - } return false; - }; - - this.skipWhitespace = function(canCommentOut) { - while (this.isWhitespace(this.input[this.pos])) { - this.pos++; - } if (this.input[this.pos] == "%" && canCommentOut == true) { - while (this.input[this.pos] != "\n") { - this.pos++; - } this.skipWhitespace(canCommentOut); - } }; - - this.value_braces = function() { - var bracecount = 0; - this.match("{", false); - var start = this.pos; - var escaped = false; - while (true) { - if (!escaped) { - if (this.input[this.pos] == '}') { - if (bracecount > 0) { - bracecount--; - } else { - var end = this.pos; - this.match("}", false); - return this.input.substring(start, end); - } } else if (this.input[this.pos] == '{') { - bracecount++; - } else if (this.pos >= this.input.length - 1) { - throw "Unterminated value"; - } } if (this.input[this.pos] == '\\' && escaped == false) - escaped = true; - else - escaped = false; - this.pos++; - } }; - - this.value_comment = function() { - var str = ''; - var brcktCnt = 0; - while (!(this.tryMatch("}", false) && brcktCnt == 0)) { - str = str + this.input[this.pos]; - if (this.input[this.pos] == '{') - brcktCnt++; - if (this.input[this.pos] == '}') - brcktCnt--; - if (this.pos >= this.input.length - 1) { - throw "Unterminated value:" + this.input.substring(start); - } this.pos++; - } return str; - }; - - this.value_quotes = function() { - this.match('"', false); - var start = this.pos; - var escaped = false; - while (true) { - if (!escaped) { - if (this.input[this.pos] == '"') { - var end = this.pos; - this.match('"', false); - return this.input.substring(start, end); - } else if (this.pos >= this.input.length - 1) { - throw "Unterminated value:" + this.input.substring(start); - } } - if (this.input[this.pos] == '\\' && escaped == false) - escaped = true; - else - escaped = false; - this.pos++; - } }; - - this.single_value = function() { - var start = this.pos; - if (this.tryMatch("{")) { - return this.value_braces(); - } else if (this.tryMatch('"')) { - return this.value_quotes(); - } else { - var k = this.key(); - if (k.match("^[0-9]+$")) - return k; - else if (this.months.indexOf(k.toLowerCase()) >= 0) - return k.toLowerCase(); - else - throw "Value expected:" + this.input.substring(start) + ' for key: ' + k; - - } }; - - this.value = function() { - var values = []; - values.push(this.single_value()); - while (this.tryMatch("#")) { - this.match("#"); - values.push(this.single_value()); - } return values.join(""); - }; - - this.key = function() { - var start = this.pos; - while (true) { - if (this.pos >= this.input.length) { - throw "Runaway key"; - } // а-яА-Я is Cyrillic - //console.log(this.input[this.pos]); - if (this.notKey.indexOf(this.input[this.pos]) >= 0) { - return this.input.substring(start, this.pos); - } else { - this.pos++; - - } } }; - - this.key_equals_value = function() { - var key = this.key(); - if (this.tryMatch("=")) { - this.match("="); - var val = this.value(); - return [ key, val ]; - } else { - throw "... = value expected, equals sign missing:" - + this.input.substring(this.pos); - } }; - - this.key_value_list = function() { - var kv = this.key_equals_value(); - this.currentEntry['entryTags'] = {}; - this.currentEntry['entryTags'][kv[0]] = kv[1]; - while (this.tryMatch(",")) { - this.match(","); - // fixes problems with commas at the end of a list - if (this.tryMatch("}")) { - break; - } - kv = this.key_equals_value(); - this.currentEntry['entryTags'][kv[0]] = kv[1]; - } }; - - this.entry_body = function(d) { - this.currentEntry = {}; - this.currentEntry['citationKey'] = this.key(); - this.currentEntry['entryType'] = d.substring(1); - this.match(","); - this.key_value_list(); - this.entries.push(this.currentEntry); - }; - - this.directive = function() { - this.match("@"); - return "@" + this.key(); - }; - - this.preamble = function() { - this.currentEntry = {}; - this.currentEntry['entryType'] = 'PREAMBLE'; - this.currentEntry['entry'] = this.value_comment(); - this.entries.push(this.currentEntry); - }; - - this.comment = function() { - this.currentEntry = {}; - this.currentEntry['entryType'] = 'COMMENT'; - this.currentEntry['entry'] = this.value_comment(); - this.entries.push(this.currentEntry); - }; - - this.entry = function(d) { - this.entry_body(d); - }; - - this.bibtex = function() { - while (this.matchAt()) { - var d = this.directive(); - this.match("{"); - if (d == "@STRING") { - this.string(); - } else if (d == "@PREAMBLE") { - this.preamble(); - } else if (d == "@COMMENT") { - this.comment(); - } else { - this.entry(d); - } - this.match("}"); - } }; - } - exports.toJSON = function(bibtex) { - var b = new BibtexParser(); - b.setInput(bibtex); - b.bibtex(); - return b.entries; - }; - - /* added during hackathon don't hate on me */ - exports.toBibtex = function(json) { - var out = ''; - for ( var i in json) { - out += "@" + json[i].entryType; - out += '{'; - if (json[i].citationKey) - out += json[i].citationKey + ', '; - if (json[i].entry) - out += json[i].entry ; - if (json[i].entryTags) { - var tags = ''; - for (var jdx in json[i].entryTags) { - if (tags.length != 0) - tags += ', '; - tags += jdx + '= {' + json[i].entryTags[jdx] + '}'; - } - out += tags; - } - out += '}\n\n'; - } - return out; - - }; - - })( exports); - - /* end bibtexParse */ - }); - - // Copyright 2018 The Distill Template Authors - - function normalizeTag(string) { - return string - .replace(/[\t\n ]+/g, ' ') - .replace(/{\\["^`.'acu~Hvs]( )?([a-zA-Z])}/g, (full, x, char) => char) - .replace(/{\\([a-zA-Z])}/g, (full, char) => char); - } - - function parseBibtex(bibtex) { - const bibliography = new Map(); - const parsedEntries = bibtexParse.toJSON(bibtex); - for (const entry of parsedEntries) { - // normalize tags; note entryTags is an object, not Map - for (const [key, value] of Object.entries(entry.entryTags)) { - entry.entryTags[key.toLowerCase()] = normalizeTag(value); - } - entry.entryTags.type = entry.entryType; - // add to bibliography - bibliography.set(entry.citationKey, entry.entryTags); - } - return bibliography; - } - - function serializeFrontmatterToBibtex(frontMatter) { - return `@article{${frontMatter.slug}, - author = {${frontMatter.bibtexAuthors}}, - title = {${frontMatter.title}}, - journal = {${frontMatter.journal.title}}, - year = {${frontMatter.publishedYear}}, - note = {${frontMatter.url}}, - doi = {${frontMatter.doi}} -}`; - } - - // Copyright 2018 The Distill Template Authors - - class Bibliography extends HTMLElement { - - static get is() { return 'd-bibliography'; } - - constructor() { - super(); - - // set up mutation observer - const options = {childList: true, characterData: true, subtree: true}; - const observer = new MutationObserver( (entries) => { - for (const entry of entries) { - if (entry.target.nodeName === 'SCRIPT' || entry.type === 'characterData') { - this.parseIfPossible(); - } - } - }); - observer.observe(this, options); - } - - connectedCallback() { - requestAnimationFrame(() => { - this.parseIfPossible(); - }); - } - - parseIfPossible() { - const scriptTag = this.querySelector('script'); - if (!scriptTag) return; - if (scriptTag.type == 'text/bibtex') { - const newBibtex = scriptTag.textContent; - if (this.bibtex !== newBibtex) { - this.bibtex = newBibtex; - const bibliography = parseBibtex(this.bibtex); - this.notify(bibliography); - } - } else if (scriptTag.type == 'text/json') { - const bibliography = new Map(JSON.parse(scriptTag.textContent)); - this.notify(bibliography); - } else { - console.warn('Unsupported bibliography script tag type: ' + scriptTag.type); - } - } - - notify(bibliography) { - const options = { detail: bibliography, bubbles: true }; - const event = new CustomEvent('onBibliographyChanged', options); - this.dispatchEvent(event); - } - - /* observe 'src' attribute */ - - static get observedAttributes() { - return ['src']; - } - - receivedBibtex(event) { - const bibliography = parseBibtex(event.target.response); - this.notify(bibliography); - } - - attributeChangedCallback(name, oldValue, newValue) { - var oReq = new XMLHttpRequest(); - oReq.onload = (e) => this.receivedBibtex(e); - oReq.onerror = () => console.warn(`Could not load Bibtex! (tried ${newValue})`); - oReq.responseType = 'text'; - oReq.open('GET', newValue, true); - oReq.send(); - } - - - } - - // Copyright 2018 The Distill Template Authors - // - // Licensed under the Apache License, Version 2.0 (the "License"); - // you may not use this file except in compliance with the License. - // You may obtain a copy of the License at - // - // http://www.apache.org/licenses/LICENSE-2.0 - // - // Unless required by applicable law or agreed to in writing, software - // distributed under the License is distributed on an "AS IS" BASIS, - // WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - // See the License for the specific language governing permissions and - // limitations under the License. - - // import style from '../styles/d-byline.css'; - - function bylineTemplate(frontMatter) { - return ` -

-
-

Authors

-

Affiliations

- ${frontMatter.authors.map(author => ` -

- ${author.personalURL ? ` - ${author.name}` : ` - ${author.name}`} -

-

- ${author.affiliations.map(affiliation => - affiliation.url ? `${affiliation.name}` : `${affiliation.name}` - ).join(', ')} -

- `).join('')} -
-
-

Published

- ${frontMatter.publishedDate ? ` -

${frontMatter.publishedMonth} ${frontMatter.publishedDay}, ${frontMatter.publishedYear}

` : ` -

Not published yet.

`} -
-
-`; - } - - class Byline extends HTMLElement { - - static get is() { return 'd-byline'; } - - set frontMatter(frontMatter) { - this.innerHTML = bylineTemplate(frontMatter); - } - - } - - // Copyright 2018 The Distill Template Authors - - const T$3 = Template( - "d-cite", - ` - - - - -
- -
-` - ); - - class Cite extends T$3(HTMLElement) { - /* Lifecycle */ - constructor() { - super(); - this._numbers = []; - this._entries = []; - } - - connectedCallback() { - this.outerSpan = this.root.querySelector("#citation-"); - this.innerSpan = this.root.querySelector(".citation-number"); - this.hoverBox = this.root.querySelector("d-hover-box"); - window.customElements.whenDefined("d-hover-box").then(() => { - this.hoverBox.listen(this); - }); - // in case this component got connected after values were set - if (this.numbers) { - this.displayNumbers(this.numbers); - } - if (this.entries) { - this.displayEntries(this.entries); - } - } - - //TODO This causes an infinite loop on firefox with polyfills. - // This is only needed for interactive editing so no priority. - // disconnectedCallback() { - // const options = { detail: [this, this.keys], bubbles: true }; - // const event = new CustomEvent('onCiteKeyRemoved', options); - // document.dispatchEvent(event); - // } - - /* observe 'key' attribute */ - - static get observedAttributes() { - return ["key", "bibtex-key"]; - } - - attributeChangedCallback(name, oldValue, newValue) { - const eventName = oldValue ? "onCiteKeyChanged" : "onCiteKeyCreated"; - const keys = newValue.split(",").map(k => k.trim()); - const options = { detail: [this, keys], bubbles: true }; - const event = new CustomEvent(eventName, options); - document.dispatchEvent(event); - } - - set key(value) { - this.setAttribute("key", value); - } - - get key() { - return this.getAttribute("key") || this.getAttribute("bibtex-key"); - } - - get keys() { - const result = this.key.split(","); - console.log(result); - return result; - } - - /* Setters & Rendering */ - - set numbers(numbers) { - this._numbers = numbers; - this.displayNumbers(numbers); - } - - get numbers() { - return this._numbers; - } - - displayNumbers(numbers) { - if (!this.innerSpan) return; - const numberStrings = numbers.map(index => { - return index == -1 ? "?" : index + 1 + ""; - }); - const textContent = "[" + numberStrings.join(", ") + "]"; - this.innerSpan.textContent = textContent; - } - - set entries(entries) { - this._entries = entries; - this.displayEntries(entries); - } - - get entries() { - return this._entries; - } - - displayEntries(entries) { - if (!this.hoverBox) return; - this.hoverBox.innerHTML = `
    - ${entries - .map(hover_cite) - .map(html => `
  • ${html}
    • `) - .join("\n")} -
`; - } - } - - // Copyright 2018 The Distill Template Authors - - const styles$1 = ` -d-citation-list { - contain: style; -} - -d-citation-list .references { - grid-column: text; -} - -d-citation-list .references .title { - font-weight: 500; -} -`; - - function renderCitationList(element, entries, dom=document) { - if (entries.size > 0) { - element.style.display = ''; - let list = element.querySelector('.references'); - if (list) { - list.innerHTML = ''; - } else { - const stylesTag = dom.createElement('style'); - stylesTag.innerHTML = styles$1; - element.appendChild(stylesTag); - - const heading = dom.createElement('h3'); - heading.id = 'references'; - heading.textContent = 'References'; - element.appendChild(heading); - - list = dom.createElement('ol'); - list.id = 'references-list'; - list.className = 'references'; - element.appendChild(list); - } - - for (const [key, entry] of entries) { - const listItem = dom.createElement('li'); - listItem.id = key; - listItem.innerHTML = bibliography_cite(entry); - list.appendChild(listItem); - } - } else { - element.style.display = 'none'; - } - } - - class CitationList extends HTMLElement { - - static get is() { return 'd-citation-list'; } - - connectedCallback() { - if (!this.hasAttribute('distill-prerendered')) { - this.style.display = 'none'; - } - } - - set citations(citations) { - renderCitationList(this, citations); - } - - } - - var prism = createCommonjsModule(function (module) { - /* ********************************************** - Begin prism-core.js - ********************************************** */ - - var _self = (typeof window !== 'undefined') - ? window // if in browser - : ( - (typeof WorkerGlobalScope !== 'undefined' && self instanceof WorkerGlobalScope) - ? self // if in worker - : {} // if in node js - ); - - /** - * Prism: Lightweight, robust, elegant syntax highlighting - * MIT license http://www.opensource.org/licenses/mit-license.php/ - * @author Lea Verou http://lea.verou.me - */ - - var Prism = (function (_self){ - - // Private helper vars - var lang = /\blang(?:uage)?-([\w-]+)\b/i; - var uniqueId = 0; - - - var _ = { - manual: _self.Prism && _self.Prism.manual, - disableWorkerMessageHandler: _self.Prism && _self.Prism.disableWorkerMessageHandler, - util: { - encode: function encode(tokens) { - if (tokens instanceof Token) { - return new Token(tokens.type, encode(tokens.content), tokens.alias); - } else if (Array.isArray(tokens)) { - return tokens.map(encode); - } else { - return tokens.replace(/&/g, '&').replace(/' + env.content + ''; - }; - - /** - * @param {string} text - * @param {LinkedList} tokenList - * @param {any} grammar - * @param {LinkedListNode} startNode - * @param {number} startPos - * @param {boolean} [oneshot=false] - * @param {string} [target] - */ - function matchGrammar(text, tokenList, grammar, startNode, startPos, oneshot, target) { - for (var token in grammar) { - if (!grammar.hasOwnProperty(token) || !grammar[token]) { - continue; - } - - var patterns = grammar[token]; - patterns = Array.isArray(patterns) ? patterns : [patterns]; - - for (var j = 0; j < patterns.length; ++j) { - if (target && target == token + ',' + j) { - return; - } - - var pattern = patterns[j], - inside = pattern.inside, - lookbehind = !!pattern.lookbehind, - greedy = !!pattern.greedy, - lookbehindLength = 0, - alias = pattern.alias; - - if (greedy && !pattern.pattern.global) { - // Without the global flag, lastIndex won't work - var flags = pattern.pattern.toString().match(/[imsuy]*$/)[0]; - pattern.pattern = RegExp(pattern.pattern.source, flags + 'g'); - } - - pattern = pattern.pattern || pattern; - - for ( // iterate the token list and keep track of the current token/string position - var currentNode = startNode.next, pos = startPos; - currentNode !== tokenList.tail; - pos += currentNode.value.length, currentNode = currentNode.next - ) { - - var str = currentNode.value; - - if (tokenList.length > text.length) { - // Something went terribly wrong, ABORT, ABORT! - return; - } - - if (str instanceof Token) { - continue; - } - - var removeCount = 1; // this is the to parameter of removeBetween - - if (greedy && currentNode != tokenList.tail.prev) { - pattern.lastIndex = pos; - var match = pattern.exec(text); - if (!match) { - break; - } - - var from = match.index + (lookbehind && match[1] ? match[1].length : 0); - var to = match.index + match[0].length; - var p = pos; - - // find the node that contains the match - p += currentNode.value.length; - while (from >= p) { - currentNode = currentNode.next; - p += currentNode.value.length; - } - // adjust pos (and p) - p -= currentNode.value.length; - pos = p; - - // the current node is a Token, then the match starts inside another Token, which is invalid - if (currentNode.value instanceof Token) { - continue; - } - - // find the last node which is affected by this match - for ( - var k = currentNode; - k !== tokenList.tail && (p < to || (typeof k.value === 'string' && !k.prev.value.greedy)); - k = k.next - ) { - removeCount++; - p += k.value.length; - } - removeCount--; - - // replace with the new match - str = text.slice(pos, p); - match.index -= pos; - } else { - pattern.lastIndex = 0; - - var match = pattern.exec(str); - } - - if (!match) { - if (oneshot) { - break; - } - - continue; - } - - if (lookbehind) { - lookbehindLength = match[1] ? match[1].length : 0; - } - - var from = match.index + lookbehindLength, - match = match[0].slice(lookbehindLength), - to = from + match.length, - before = str.slice(0, from), - after = str.slice(to); - - var removeFrom = currentNode.prev; - - if (before) { - removeFrom = addAfter(tokenList, removeFrom, before); - pos += before.length; - } - - removeRange(tokenList, removeFrom, removeCount); - - var wrapped = new Token(token, inside ? _.tokenize(match, inside) : match, alias, match, greedy); - currentNode = addAfter(tokenList, removeFrom, wrapped); - - if (after) { - addAfter(tokenList, currentNode, after); - } - - - if (removeCount > 1) - matchGrammar(text, tokenList, grammar, currentNode.prev, pos, true, token + ',' + j); - - if (oneshot) - break; - } - } - } - } - - /** - * @typedef LinkedListNode - * @property {T} value - * @property {LinkedListNode | null} prev The previous node. - * @property {LinkedListNode | null} next The next node. - * @template T - */ - - /** - * @template T - */ - function LinkedList() { - /** @type {LinkedListNode} */ - var head = { value: null, prev: null, next: null }; - /** @type {LinkedListNode} */ - var tail = { value: null, prev: head, next: null }; - head.next = tail; - - /** @type {LinkedListNode} */ - this.head = head; - /** @type {LinkedListNode} */ - this.tail = tail; - this.length = 0; - } - - /** - * Adds a new node with the given value to the list. - * @param {LinkedList} list - * @param {LinkedListNode} node - * @param {T} value - * @returns {LinkedListNode} The added node. - * @template T - */ - function addAfter(list, node, value) { - // assumes that node != list.tail && values.length >= 0 - var next = node.next; - - var newNode = { value: value, prev: node, next: next }; - node.next = newNode; - next.prev = newNode; - list.length++; - - return newNode; - } - /** - * Removes `count` nodes after the given node. The given node will not be removed. - * @param {LinkedList} list - * @param {LinkedListNode} node - * @param {number} count - * @template T - */ - function removeRange(list, node, count) { - var next = node.next; - for (var i = 0; i < count && next !== list.tail; i++) { - next = next.next; - } - node.next = next; - next.prev = node; - list.length -= i; - } - /** - * @param {LinkedList} list - * @returns {T[]} - * @template T - */ - function toArray(list) { - var array = []; - var node = list.head.next; - while (node !== list.tail) { - array.push(node.value); - node = node.next; - } - return array; - } - - - if (!_self.document) { - if (!_self.addEventListener) { - // in Node.js - return _; - } - - if (!_.disableWorkerMessageHandler) { - // In worker - _self.addEventListener('message', function (evt) { - var message = JSON.parse(evt.data), - lang = message.language, - code = message.code, - immediateClose = message.immediateClose; - - _self.postMessage(_.highlight(code, _.languages[lang], lang)); - if (immediateClose) { - _self.close(); - } - }, false); - } - - return _; - } - - //Get current script and highlight - var script = _.util.currentScript(); - - if (script) { - _.filename = script.src; - - if (script.hasAttribute('data-manual')) { - _.manual = true; - } - } - - function highlightAutomaticallyCallback() { - if (!_.manual) { - _.highlightAll(); - } - } - - if (!_.manual) { - // If the document state is "loading", then we'll use DOMContentLoaded. - // If the document state is "interactive" and the prism.js script is deferred, then we'll also use the - // DOMContentLoaded event because there might be some plugins or languages which have also been deferred and they - // might take longer one animation frame to execute which can create a race condition where only some plugins have - // been loaded when Prism.highlightAll() is executed, depending on how fast resources are loaded. - // See https://github.com/PrismJS/prism/issues/2102 - var readyState = document.readyState; - if (readyState === 'loading' || readyState === 'interactive' && script && script.defer) { - document.addEventListener('DOMContentLoaded', highlightAutomaticallyCallback); - } else { - if (window.requestAnimationFrame) { - window.requestAnimationFrame(highlightAutomaticallyCallback); - } else { - window.setTimeout(highlightAutomaticallyCallback, 16); - } - } - } - - return _; - - })(_self); - - if ( module.exports) { - module.exports = Prism; - } - - // hack for components to work correctly in node.js - if (typeof commonjsGlobal !== 'undefined') { - commonjsGlobal.Prism = Prism; - } - - - /* ********************************************** - Begin prism-markup.js - ********************************************** */ - - Prism.languages.markup = { - 'comment': //, - 'prolog': /<\?[\s\S]+?\?>/, - 'doctype': { - pattern: /"'[\]]|"[^"]*"|'[^']*')+(?:\[(?:(?!)*\]\s*)?>/i, - greedy: true - }, - 'cdata': //i, - 'tag': { - pattern: /<\/?(?!\d)[^\s>\/=$<%]+(?:\s(?:\s*[^\s>\/=]+(?:\s*=\s*(?:"[^"]*"|'[^']*'|[^\s'">=]+(?=[\s>]))|(?=[\s/>])))+)?\s*\/?>/i, - greedy: true, - inside: { - 'tag': { - pattern: /^<\/?[^\s>\/]+/i, - inside: { - 'punctuation': /^<\/?/, - 'namespace': /^[^\s>\/:]+:/ - } - }, - 'attr-value': { - pattern: /=\s*(?:"[^"]*"|'[^']*'|[^\s'">=]+)/i, - inside: { - 'punctuation': [ - /^=/, - { - pattern: /^(\s*)["']|["']$/, - lookbehind: true - } - ] - } - }, - 'punctuation': /\/?>/, - 'attr-name': { - pattern: /[^\s>\/]+/, - inside: { - 'namespace': /^[^\s>\/:]+:/ - } - } - - } - }, - 'entity': /&#?[\da-z]{1,8};/i - }; - - Prism.languages.markup['tag'].inside['attr-value'].inside['entity'] = - Prism.languages.markup['entity']; - - // Plugin to make entity title show the real entity, idea by Roman Komarov - Prism.hooks.add('wrap', function(env) { - - if (env.type === 'entity') { - env.attributes['title'] = env.content.replace(/&/, '&'); - } - }); - - Object.defineProperty(Prism.languages.markup.tag, 'addInlined', { - /** - * Adds an inlined language to markup. - * - * An example of an inlined language is CSS with ` - - - -`); - - class Code extends Mutating(T$4(HTMLElement)) { - - renderContent() { - - // check if language can be highlighted - this.languageName = this.getAttribute('language'); - if (!this.languageName) { - console.warn('You need to provide a language attribute to your block to let us know how to highlight your code; e.g.:\n zeros = np.zeros(shape).'); - return; - } - const language = prism.languages[this.languageName]; - if (language == undefined) { - console.warn(`Distill does not yet support highlighting your code block in "${this.languageName}'.`); - return; - } - - let content = this.textContent; - const codeTag = this.shadowRoot.querySelector('#code-container'); - - if (this.hasAttribute('block')) { - // normalize the tab indents - content = content.replace(/\n/, ''); - const tabs = content.match(/\s*/); - content = content.replace(new RegExp('\n' + tabs, 'g'), '\n'); - content = content.trim(); - // wrap code block in pre tag if needed - if (codeTag.parentNode instanceof ShadowRoot) { - const preTag = document.createElement('pre'); - this.shadowRoot.removeChild(codeTag); - preTag.appendChild(codeTag); - this.shadowRoot.appendChild(preTag); - } - - } - - codeTag.className = `language-${this.languageName}`; - codeTag.innerHTML = prism.highlight(content, language); - } - - } - - // Copyright 2018 The Distill Template Authors - - const T$5 = Template('d-footnote', ` - - - -
- -
- - - - - - -`); - - class Footnote extends T$5(HTMLElement) { - - constructor() { - super(); - - const options = {childList: true, characterData: true, subtree: true}; - const observer = new MutationObserver(this.notify); - observer.observe(this, options); - } - - notify() { - const options = { detail: this, bubbles: true }; - const event = new CustomEvent('onFootnoteChanged', options); - document.dispatchEvent(event); - } - - connectedCallback() { - // listen and notify about changes to slotted content - // const slot = this.shadowRoot.querySelector('#slot'); - // console.warn(slot.textContent); - // slot.addEventListener('slotchange', this.notify); - this.hoverBox = this.root.querySelector('d-hover-box'); - window.customElements.whenDefined('d-hover-box').then(() => { - this.hoverBox.listen(this); - }); - // create numeric ID - Footnote.currentFootnoteId += 1; - const IdString = Footnote.currentFootnoteId.toString(); - this.root.host.id = 'd-footnote-' + IdString; - - // set up hidden hover box - const id = 'dt-fn-hover-box-' + IdString; - this.hoverBox.id = id; - - // set up visible footnote marker - const span = this.root.querySelector('#fn-'); - span.setAttribute('id', 'fn-' + IdString); - span.setAttribute('data-hover-ref', id); - span.textContent = IdString; - } - - } - - Footnote.currentFootnoteId = 0; - - // Copyright 2018 The Distill Template Authors - - const T$6 = Template('d-footnote-list', ` - - -

Footnotes

-
    -`, false); - - class FootnoteList extends T$6(HTMLElement) { - - connectedCallback() { - super.connectedCallback(); - - this.list = this.root.querySelector('ol'); - // footnotes list is initially hidden - this.root.style.display = 'none'; - // look through document and register existing footnotes - // Store.subscribeTo('footnotes', (footnote) => { - // this.renderFootnote(footnote); - // }); - } - - // TODO: could optimize this to accept individual footnotes? - set footnotes(footnotes) { - this.list.innerHTML = ''; - if (footnotes.length) { - // ensure footnote list is visible - this.root.style.display = ''; - - for (const footnote of footnotes) { - // construct and append list item to show footnote - const listItem = document.createElement('li'); - listItem.id = footnote.id + '-listing'; - listItem.innerHTML = footnote.innerHTML; - - const backlink = document.createElement('a'); - backlink.setAttribute('class', 'footnote-backlink'); - backlink.textContent = '[↩]'; - backlink.href = '#' + footnote.id; - - listItem.appendChild(backlink); - this.list.appendChild(listItem); - } - } else { - // ensure footnote list is invisible - this.root.style.display = 'none'; - } - } - - } - - // Copyright 2018 The Distill Template Authors - - const T$7 = Template('d-hover-box', ` - - -
    -
    - -
    -
    -`); - - class HoverBox extends T$7(HTMLElement) { - - constructor() { - super(); - } - - connectedCallback() { - - } - - listen(element) { - // console.log(element) - this.bindDivEvents(this); - this.bindTriggerEvents(element); - // this.style.display = "block"; - } - - bindDivEvents(element) { - // For mice, same behavior as hovering on links - element.addEventListener('mouseover', () => { - if (!this.visible) this.showAtNode(element); - this.stopTimeout(); - }); - element.addEventListener('mouseout', () => { - this.extendTimeout(500); - }); - // Don't trigger body touchstart event when touching within box - element.addEventListener('touchstart', (event) => { - event.stopPropagation(); - }, {passive: true}); - // Close box when touching outside box - document.body.addEventListener('touchstart', () => { - this.hide(); - }, {passive: true}); - } - - bindTriggerEvents(node) { - node.addEventListener('mouseover', () => { - if (!this.visible) { - this.showAtNode(node); - } - this.stopTimeout(); - }); - - node.addEventListener('mouseout', () => { - this.extendTimeout(300); - }); - - node.addEventListener('touchstart', (event) => { - if (this.visible) { - this.hide(); - } else { - this.showAtNode(node); - } - // Don't trigger body touchstart event when touching link - event.stopPropagation(); - }, {passive: true}); - } - - show(position) { - this.visible = true; - this.style.display = 'block'; - // 10px extra offset from element - this.style.top = Math.round(position[1] + 10) + 'px'; - } - - showAtNode(node) { - // https://developer.mozilla.org/en-US/docs/Web/API/HTMLElement/offsetTop - const bbox = node.getBoundingClientRect(); - this.show([node.offsetLeft + bbox.width, node.offsetTop + bbox.height]); - } - - hide() { - this.visible = false; - this.style.display = 'none'; - this.stopTimeout(); - } - - stopTimeout() { - if (this.timeout) { - clearTimeout(this.timeout); - } - } - - extendTimeout(time) { - this.stopTimeout(); - this.timeout = setTimeout(() => { - this.hide(); - }, time); - } - - } - - // Copyright 2018 The Distill Template Authors - // - // Licensed under the Apache License, Version 2.0 (the "License"); - // you may not use this file except in compliance with the License. - // You may obtain a copy of the License at - // - // http://www.apache.org/licenses/LICENSE-2.0 - // - // Unless required by applicable law or agreed to in writing, software - // distributed under the License is distributed on an "AS IS" BASIS, - // WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - // See the License for the specific language governing permissions and - // limitations under the License. - - class Title extends HTMLElement { - static get is() { return 'd-title'; } - } - - // Copyright 2018 The Distill Template Authors - - const T$8 = Template('d-references', ` - -`, false); - - class References extends T$8(HTMLElement) { - - } - - // Copyright 2018 The Distill Template Authors - // - // Licensed under the Apache License, Version 2.0 (the "License"); - // you may not use this file except in compliance with the License. - // You may obtain a copy of the License at - // - // http://www.apache.org/licenses/LICENSE-2.0 - // - // Unless required by applicable law or agreed to in writing, software - // distributed under the License is distributed on an "AS IS" BASIS, - // WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - // See the License for the specific language governing permissions and - // limitations under the License. - - class TOC extends HTMLElement { - - static get is() { return 'd-toc'; } - - connectedCallback() { - if (!this.getAttribute('prerendered')) { - window.onload = () => { - const article = document.querySelector('d-article'); - const headings = article.querySelectorAll('h2, h3'); - renderTOC(this, headings); - }; - } - } - - } - - function renderTOC(element, headings) { - - let ToC =` - - -

    Table of contents

    -
      `; - - for (const el of headings) { - // should element be included in TOC? - const isInTitle = el.parentElement.tagName == 'D-TITLE'; - const isException = el.getAttribute('no-toc'); - if (isInTitle || isException) continue; - // create TOC entry - const title = el.textContent; - const link = '#' + el.getAttribute('id'); - - let newLine = '
    • ' + '' + title + '' + '
      • '; - if (el.tagName == 'H3') { - newLine = '
        ' + newLine + '
      '; - } else { - newLine += '
      '; - } - ToC += newLine; - - } - - ToC += '
    '; - element.innerHTML = ToC; - } - - // Copyright 2018 The Distill Template Authors - // - // Licensed under the Apache License, Version 2.0 (the "License"); - // you may not use this file except in compliance with the License. - // You may obtain a copy of the License at - // - // http://www.apache.org/licenses/LICENSE-2.0 - // - // Unless required by applicable law or agreed to in writing, software - // distributed under the License is distributed on an "AS IS" BASIS, - // WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - // See the License for the specific language governing permissions and - // limitations under the License. - - // Figure - // - // d-figure provides a state-machine of visibility events: - // - // scroll out of view - // +----------------+ - // *do work here* | | - // +----------------+ +-+---------+ +-v---------+ - // | ready +----> onscreen | | offscreen | - // +----------------+ +---------^-+ +---------+-+ - // | | - // +----------------+ - // scroll into view - // - - class Figure extends HTMLElement { - - static get is() { return 'd-figure'; } - - static get readyQueue() { - if (!Figure._readyQueue) { - Figure._readyQueue = []; - } - return Figure._readyQueue; - } - - static addToReadyQueue(figure) { - if (Figure.readyQueue.indexOf(figure) === -1) { - Figure.readyQueue.push(figure); - Figure.runReadyQueue(); - } - } - - static runReadyQueue() { - // console.log("Checking to run readyQueue, length: " + Figure.readyQueue.length + ", scrolling: " + Figure.isScrolling); - // if (Figure.isScrolling) return; - // console.log("Running ready Queue"); - const figure = Figure.readyQueue - .sort((a,b) => a._seenOnScreen - b._seenOnScreen ) - .filter((figure) => !figure._ready) - .pop(); - if (figure) { - figure.ready(); - requestAnimationFrame(Figure.runReadyQueue); - } - - } - - constructor() { - super(); - // debugger - this._ready = false; - this._onscreen = false; - this._offscreen = true; - } - - connectedCallback() { - this.loadsWhileScrolling = this.hasAttribute('loadsWhileScrolling'); - Figure.marginObserver.observe(this); - Figure.directObserver.observe(this); - } - - disconnectedCallback() { - Figure.marginObserver.unobserve(this); - Figure.directObserver.unobserve(this); - } - - // We use two separate observers: - // One with an extra 1000px margin to warn if the viewpoint gets close, - // And one for the actual on/off screen events - - static get marginObserver() { - if (!Figure._marginObserver) { - // if (!('IntersectionObserver' in window)) { - // throw new Error('no interscetionobbserver!'); - // } - const viewportHeight = window.innerHeight; - const margin = Math.floor(2 * viewportHeight); - const options = {rootMargin: margin + 'px 0px ' + margin + 'px 0px', threshold: 0.01}; - const callback = Figure.didObserveMarginIntersection; - const observer = new IntersectionObserver(callback, options); - Figure._marginObserver = observer; - } - return Figure._marginObserver; - } - - static didObserveMarginIntersection(entries) { - for (const entry of entries) { - const figure = entry.target; - if (entry.isIntersecting && !figure._ready) { - Figure.addToReadyQueue(figure); - } - } - } - - static get directObserver() { - if (!Figure._directObserver) { - Figure._directObserver = new IntersectionObserver( - Figure.didObserveDirectIntersection, { - rootMargin: '0px', threshold: [0, 1.0], - } - ); - } - return Figure._directObserver; - } - - static didObserveDirectIntersection(entries) { - for (const entry of entries) { - const figure = entry.target; - if (entry.isIntersecting) { - figure._seenOnScreen = new Date(); - // if (!figure._ready) { figure.ready(); } - if (figure._offscreen) { figure.onscreen(); } - } else { - if (figure._onscreen) { figure.offscreen(); } - } - } - } - - // Notify listeners that registered late, too: - - addEventListener(eventName, callback) { - super.addEventListener(eventName, callback); - // if we had already dispatched something while presumingly no one was listening, we do so again - // debugger - if (eventName === 'ready') { - if (Figure.readyQueue.indexOf(this) !== -1) { - this._ready = false; - Figure.runReadyQueue(); - } - } - if (eventName === 'onscreen') { - this.onscreen(); - } - } - - // Custom Events - - ready() { - // debugger - this._ready = true; - Figure.marginObserver.unobserve(this); - const event = new CustomEvent('ready'); - this.dispatchEvent(event); - } - - onscreen() { - this._onscreen = true; - this._offscreen = false; - const event = new CustomEvent('onscreen'); - this.dispatchEvent(event); - } - - offscreen() { - this._onscreen = false; - this._offscreen = true; - const event = new CustomEvent('offscreen'); - this.dispatchEvent(event); - } - - } - - if (typeof window !== 'undefined') { - - Figure.isScrolling = false; - let timeout; - const resetTimer = () => { - Figure.isScrolling = true; - clearTimeout(timeout); - timeout = setTimeout(() => { - Figure.isScrolling = false; - Figure.runReadyQueue(); - }, 500); - }; - window.addEventListener('scroll', resetTimer, true); - - } - - // Copyright 2018 The Distill Template Authors - - // This overlay is not secure. - // It is only meant as a social deterrent. - - const productionHostname = 'distill.pub'; - const T$9 = Template('d-interstitial', ` - - -
    -
    -

    This article is in review.

    -

    Do not share this URL or the contents of this article. Thank you!

    - -

    Enter the password we shared with you as part of the review process to view the article.

    -
    -
    -`); - - class Interstitial extends T$9(HTMLElement) { - - connectedCallback() { - if (this.shouldRemoveSelf()) { - this.parentElement.removeChild(this); - } else { - const passwordInput = this.root.querySelector('#interstitial-password-input'); - passwordInput.oninput = (event) => this.passwordChanged(event); - } - } - - passwordChanged(event) { - const entered = event.target.value; - if (entered === this.password) { - console.log('Correct password entered.'); - this.parentElement.removeChild(this); - if (typeof(Storage) !== 'undefined') { - console.log('Saved that correct password was entered.'); - localStorage.setItem(this.localStorageIdentifier(), 'true'); - } - } - } - - shouldRemoveSelf() { - // should never be visible in production - if (window && window.location.hostname === productionHostname) { - console.warn('Interstitial found on production, hiding it.'); - return true - } - // should only have to enter password once - if (typeof(Storage) !== 'undefined') { - if (localStorage.getItem(this.localStorageIdentifier()) === 'true') { - console.log('Loaded that correct password was entered before; skipping interstitial.'); - return true; - } - } - // otherwise, leave visible - return false; - } - - localStorageIdentifier() { - const prefix = 'distill-drafts'; - const suffix = 'interstitial-password-correct'; - return prefix + (window ? window.location.pathname : '-') + suffix - } - - } - - function ascending(a, b) { - return a < b ? -1 : a > b ? 1 : a >= b ? 0 : NaN; - } - - function bisector(compare) { - if (compare.length === 1) compare = ascendingComparator(compare); - return { - left: function(a, x, lo, hi) { - if (lo == null) lo = 0; - if (hi == null) hi = a.length; - while (lo < hi) { - var mid = lo + hi >>> 1; - if (compare(a[mid], x) < 0) lo = mid + 1; - else hi = mid; - } - return lo; - }, - right: function(a, x, lo, hi) { - if (lo == null) lo = 0; - if (hi == null) hi = a.length; - while (lo < hi) { - var mid = lo + hi >>> 1; - if (compare(a[mid], x) > 0) hi = mid; - else lo = mid + 1; - } - return lo; - } - }; - } - - function ascendingComparator(f) { - return function(d, x) { - return ascending(f(d), x); - }; - } - - var ascendingBisect = bisector(ascending); - var bisectRight = ascendingBisect.right; - - function range(start, stop, step) { - start = +start, stop = +stop, step = (n = arguments.length) < 2 ? (stop = start, start = 0, 1) : n < 3 ? 1 : +step; - - var i = -1, - n = Math.max(0, Math.ceil((stop - start) / step)) | 0, - range = new Array(n); - - while (++i < n) { - range[i] = start + i * step; - } - - return range; - } - - var e10 = Math.sqrt(50), - e5 = Math.sqrt(10), - e2 = Math.sqrt(2); - - function ticks(start, stop, count) { - var reverse, - i = -1, - n, - ticks, - step; - - stop = +stop, start = +start, count = +count; - if (start === stop && count > 0) return [start]; - if (reverse = stop < start) n = start, start = stop, stop = n; - if ((step = tickIncrement(start, stop, count)) === 0 || !isFinite(step)) return []; - - if (step > 0) { - start = Math.ceil(start / step); - stop = Math.floor(stop / step); - ticks = new Array(n = Math.ceil(stop - start + 1)); - while (++i < n) ticks[i] = (start + i) * step; - } else { - start = Math.floor(start * step); - stop = Math.ceil(stop * step); - ticks = new Array(n = Math.ceil(start - stop + 1)); - while (++i < n) ticks[i] = (start - i) / step; - } - - if (reverse) ticks.reverse(); - - return ticks; - } - - function tickIncrement(start, stop, count) { - var step = (stop - start) / Math.max(0, count), - power = Math.floor(Math.log(step) / Math.LN10), - error = step / Math.pow(10, power); - return power >= 0 - ? (error >= e10 ? 10 : error >= e5 ? 5 : error >= e2 ? 2 : 1) * Math.pow(10, power) - : -Math.pow(10, -power) / (error >= e10 ? 10 : error >= e5 ? 5 : error >= e2 ? 2 : 1); - } - - function tickStep(start, stop, count) { - var step0 = Math.abs(stop - start) / Math.max(0, count), - step1 = Math.pow(10, Math.floor(Math.log(step0) / Math.LN10)), - error = step0 / step1; - if (error >= e10) step1 *= 10; - else if (error >= e5) step1 *= 5; - else if (error >= e2) step1 *= 2; - return stop < start ? -step1 : step1; - } - - function initRange(domain, range) { - switch (arguments.length) { - case 0: break; - case 1: this.range(domain); break; - default: this.range(range).domain(domain); break; - } - return this; - } - - function define(constructor, factory, prototype) { - constructor.prototype = factory.prototype = prototype; - prototype.constructor = constructor; - } - - function extend(parent, definition) { - var prototype = Object.create(parent.prototype); - for (var key in definition) prototype[key] = definition[key]; - return prototype; - } - - function Color() {} - - var darker = 0.7; - var brighter = 1 / darker; - - var reI = "\\s*([+-]?\\d+)\\s*", - reN = "\\s*([+-]?\\d*\\.?\\d+(?:[eE][+-]?\\d+)?)\\s*", - reP = "\\s*([+-]?\\d*\\.?\\d+(?:[eE][+-]?\\d+)?)%\\s*", - reHex = /^#([0-9a-f]{3,8})$/, - reRgbInteger = new RegExp("^rgb\\(" + [reI, reI, reI] + "\\)$"), - reRgbPercent = new RegExp("^rgb\\(" + [reP, reP, reP] + "\\)$"), - reRgbaInteger = new RegExp("^rgba\\(" + [reI, reI, reI, reN] + "\\)$"), - reRgbaPercent = new RegExp("^rgba\\(" + [reP, reP, reP, reN] + "\\)$"), - reHslPercent = new RegExp("^hsl\\(" + [reN, reP, reP] + "\\)$"), - reHslaPercent = new RegExp("^hsla\\(" + [reN, reP, reP, reN] + "\\)$"); - - var named = { - aliceblue: 0xf0f8ff, - antiquewhite: 0xfaebd7, - aqua: 0x00ffff, - aquamarine: 0x7fffd4, - azure: 0xf0ffff, - beige: 0xf5f5dc, - bisque: 0xffe4c4, - black: 0x000000, - blanchedalmond: 0xffebcd, - blue: 0x0000ff, - blueviolet: 0x8a2be2, - brown: 0xa52a2a, - burlywood: 0xdeb887, - cadetblue: 0x5f9ea0, - chartreuse: 0x7fff00, - chocolate: 0xd2691e, - coral: 0xff7f50, - cornflowerblue: 0x6495ed, - cornsilk: 0xfff8dc, - crimson: 0xdc143c, - cyan: 0x00ffff, - darkblue: 0x00008b, - darkcyan: 0x008b8b, - darkgoldenrod: 0xb8860b, - darkgray: 0xa9a9a9, - darkgreen: 0x006400, - darkgrey: 0xa9a9a9, - darkkhaki: 0xbdb76b, - darkmagenta: 0x8b008b, - darkolivegreen: 0x556b2f, - darkorange: 0xff8c00, - darkorchid: 0x9932cc, - darkred: 0x8b0000, - darksalmon: 0xe9967a, - darkseagreen: 0x8fbc8f, - darkslateblue: 0x483d8b, - darkslategray: 0x2f4f4f, - darkslategrey: 0x2f4f4f, - darkturquoise: 0x00ced1, - darkviolet: 0x9400d3, - deeppink: 0xff1493, - deepskyblue: 0x00bfff, - dimgray: 0x696969, - dimgrey: 0x696969, - dodgerblue: 0x1e90ff, - firebrick: 0xb22222, - floralwhite: 0xfffaf0, - forestgreen: 0x228b22, - fuchsia: 0xff00ff, - gainsboro: 0xdcdcdc, - ghostwhite: 0xf8f8ff, - gold: 0xffd700, - goldenrod: 0xdaa520, - gray: 0x808080, - green: 0x008000, - greenyellow: 0xadff2f, - grey: 0x808080, - honeydew: 0xf0fff0, - hotpink: 0xff69b4, - indianred: 0xcd5c5c, - indigo: 0x4b0082, - ivory: 0xfffff0, - khaki: 0xf0e68c, - lavender: 0xe6e6fa, - lavenderblush: 0xfff0f5, - lawngreen: 0x7cfc00, - lemonchiffon: 0xfffacd, - lightblue: 0xadd8e6, - lightcoral: 0xf08080, - lightcyan: 0xe0ffff, - lightgoldenrodyellow: 0xfafad2, - lightgray: 0xd3d3d3, - lightgreen: 0x90ee90, - lightgrey: 0xd3d3d3, - lightpink: 0xffb6c1, - lightsalmon: 0xffa07a, - lightseagreen: 0x20b2aa, - lightskyblue: 0x87cefa, - lightslategray: 0x778899, - lightslategrey: 0x778899, - lightsteelblue: 0xb0c4de, - lightyellow: 0xffffe0, - lime: 0x00ff00, - limegreen: 0x32cd32, - linen: 0xfaf0e6, - magenta: 0xff00ff, - maroon: 0x800000, - mediumaquamarine: 0x66cdaa, - mediumblue: 0x0000cd, - mediumorchid: 0xba55d3, - mediumpurple: 0x9370db, - mediumseagreen: 0x3cb371, - mediumslateblue: 0x7b68ee, - mediumspringgreen: 0x00fa9a, - mediumturquoise: 0x48d1cc, - mediumvioletred: 0xc71585, - midnightblue: 0x191970, - mintcream: 0xf5fffa, - mistyrose: 0xffe4e1, - moccasin: 0xffe4b5, - navajowhite: 0xffdead, - navy: 0x000080, - oldlace: 0xfdf5e6, - olive: 0x808000, - olivedrab: 0x6b8e23, - orange: 0xffa500, - orangered: 0xff4500, - orchid: 0xda70d6, - palegoldenrod: 0xeee8aa, - palegreen: 0x98fb98, - paleturquoise: 0xafeeee, - palevioletred: 0xdb7093, - papayawhip: 0xffefd5, - peachpuff: 0xffdab9, - peru: 0xcd853f, - pink: 0xffc0cb, - plum: 0xdda0dd, - powderblue: 0xb0e0e6, - purple: 0x800080, - rebeccapurple: 0x663399, - red: 0xff0000, - rosybrown: 0xbc8f8f, - royalblue: 0x4169e1, - saddlebrown: 0x8b4513, - salmon: 0xfa8072, - sandybrown: 0xf4a460, - seagreen: 0x2e8b57, - seashell: 0xfff5ee, - sienna: 0xa0522d, - silver: 0xc0c0c0, - skyblue: 0x87ceeb, - slateblue: 0x6a5acd, - slategray: 0x708090, - slategrey: 0x708090, - snow: 0xfffafa, - springgreen: 0x00ff7f, - steelblue: 0x4682b4, - tan: 0xd2b48c, - teal: 0x008080, - thistle: 0xd8bfd8, - tomato: 0xff6347, - turquoise: 0x40e0d0, - violet: 0xee82ee, - wheat: 0xf5deb3, - white: 0xffffff, - whitesmoke: 0xf5f5f5, - yellow: 0xffff00, - yellowgreen: 0x9acd32 - }; - - define(Color, color, { - copy: function(channels) { - return Object.assign(new this.constructor, this, channels); - }, - displayable: function() { - return this.rgb().displayable(); - }, - hex: color_formatHex, // Deprecated! Use color.formatHex. - formatHex: color_formatHex, - formatHsl: color_formatHsl, - formatRgb: color_formatRgb, - toString: color_formatRgb - }); - - function color_formatHex() { - return this.rgb().formatHex(); - } - - function color_formatHsl() { - return hslConvert(this).formatHsl(); - } - - function color_formatRgb() { - return this.rgb().formatRgb(); - } - - function color(format) { - var m, l; - format = (format + "").trim().toLowerCase(); - return (m = reHex.exec(format)) ? (l = m[1].length, m = parseInt(m[1], 16), l === 6 ? rgbn(m) // #ff0000 - : l === 3 ? new Rgb((m >> 8 & 0xf) | (m >> 4 & 0xf0), (m >> 4 & 0xf) | (m & 0xf0), ((m & 0xf) << 4) | (m & 0xf), 1) // #f00 - : l === 8 ? rgba(m >> 24 & 0xff, m >> 16 & 0xff, m >> 8 & 0xff, (m & 0xff) / 0xff) // #ff000000 - : l === 4 ? rgba((m >> 12 & 0xf) | (m >> 8 & 0xf0), (m >> 8 & 0xf) | (m >> 4 & 0xf0), (m >> 4 & 0xf) | (m & 0xf0), (((m & 0xf) << 4) | (m & 0xf)) / 0xff) // #f000 - : null) // invalid hex - : (m = reRgbInteger.exec(format)) ? new Rgb(m[1], m[2], m[3], 1) // rgb(255, 0, 0) - : (m = reRgbPercent.exec(format)) ? new Rgb(m[1] * 255 / 100, m[2] * 255 / 100, m[3] * 255 / 100, 1) // rgb(100%, 0%, 0%) - : (m = reRgbaInteger.exec(format)) ? rgba(m[1], m[2], m[3], m[4]) // rgba(255, 0, 0, 1) - : (m = reRgbaPercent.exec(format)) ? rgba(m[1] * 255 / 100, m[2] * 255 / 100, m[3] * 255 / 100, m[4]) // rgb(100%, 0%, 0%, 1) - : (m = reHslPercent.exec(format)) ? hsla(m[1], m[2] / 100, m[3] / 100, 1) // hsl(120, 50%, 50%) - : (m = reHslaPercent.exec(format)) ? hsla(m[1], m[2] / 100, m[3] / 100, m[4]) // hsla(120, 50%, 50%, 1) - : named.hasOwnProperty(format) ? rgbn(named[format]) // eslint-disable-line no-prototype-builtins - : format === "transparent" ? new Rgb(NaN, NaN, NaN, 0) - : null; - } - - function rgbn(n) { - return new Rgb(n >> 16 & 0xff, n >> 8 & 0xff, n & 0xff, 1); - } - - function rgba(r, g, b, a) { - if (a <= 0) r = g = b = NaN; - return new Rgb(r, g, b, a); - } - - function rgbConvert(o) { - if (!(o instanceof Color)) o = color(o); - if (!o) return new Rgb; - o = o.rgb(); - return new Rgb(o.r, o.g, o.b, o.opacity); - } - - function rgb(r, g, b, opacity) { - return arguments.length === 1 ? rgbConvert(r) : new Rgb(r, g, b, opacity == null ? 1 : opacity); - } - - function Rgb(r, g, b, opacity) { - this.r = +r; - this.g = +g; - this.b = +b; - this.opacity = +opacity; - } - - define(Rgb, rgb, extend(Color, { - brighter: function(k) { - k = k == null ? brighter : Math.pow(brighter, k); - return new Rgb(this.r * k, this.g * k, this.b * k, this.opacity); - }, - darker: function(k) { - k = k == null ? darker : Math.pow(darker, k); - return new Rgb(this.r * k, this.g * k, this.b * k, this.opacity); - }, - rgb: function() { - return this; - }, - displayable: function() { - return (-0.5 <= this.r && this.r < 255.5) - && (-0.5 <= this.g && this.g < 255.5) - && (-0.5 <= this.b && this.b < 255.5) - && (0 <= this.opacity && this.opacity <= 1); - }, - hex: rgb_formatHex, // Deprecated! Use color.formatHex. - formatHex: rgb_formatHex, - formatRgb: rgb_formatRgb, - toString: rgb_formatRgb - })); - - function rgb_formatHex() { - return "#" + hex(this.r) + hex(this.g) + hex(this.b); - } - - function rgb_formatRgb() { - var a = this.opacity; a = isNaN(a) ? 1 : Math.max(0, Math.min(1, a)); - return (a === 1 ? "rgb(" : "rgba(") - + Math.max(0, Math.min(255, Math.round(this.r) || 0)) + ", " - + Math.max(0, Math.min(255, Math.round(this.g) || 0)) + ", " - + Math.max(0, Math.min(255, Math.round(this.b) || 0)) - + (a === 1 ? ")" : ", " + a + ")"); - } - - function hex(value) { - value = Math.max(0, Math.min(255, Math.round(value) || 0)); - return (value < 16 ? "0" : "") + value.toString(16); - } - - function hsla(h, s, l, a) { - if (a <= 0) h = s = l = NaN; - else if (l <= 0 || l >= 1) h = s = NaN; - else if (s <= 0) h = NaN; - return new Hsl(h, s, l, a); - } - - function hslConvert(o) { - if (o instanceof Hsl) return new Hsl(o.h, o.s, o.l, o.opacity); - if (!(o instanceof Color)) o = color(o); - if (!o) return new Hsl; - if (o instanceof Hsl) return o; - o = o.rgb(); - var r = o.r / 255, - g = o.g / 255, - b = o.b / 255, - min = Math.min(r, g, b), - max = Math.max(r, g, b), - h = NaN, - s = max - min, - l = (max + min) / 2; - if (s) { - if (r === max) h = (g - b) / s + (g < b) * 6; - else if (g === max) h = (b - r) / s + 2; - else h = (r - g) / s + 4; - s /= l < 0.5 ? max + min : 2 - max - min; - h *= 60; - } else { - s = l > 0 && l < 1 ? 0 : h; - } - return new Hsl(h, s, l, o.opacity); - } - - function hsl(h, s, l, opacity) { - return arguments.length === 1 ? hslConvert(h) : new Hsl(h, s, l, opacity == null ? 1 : opacity); - } - - function Hsl(h, s, l, opacity) { - this.h = +h; - this.s = +s; - this.l = +l; - this.opacity = +opacity; - } - - define(Hsl, hsl, extend(Color, { - brighter: function(k) { - k = k == null ? brighter : Math.pow(brighter, k); - return new Hsl(this.h, this.s, this.l * k, this.opacity); - }, - darker: function(k) { - k = k == null ? darker : Math.pow(darker, k); - return new Hsl(this.h, this.s, this.l * k, this.opacity); - }, - rgb: function() { - var h = this.h % 360 + (this.h < 0) * 360, - s = isNaN(h) || isNaN(this.s) ? 0 : this.s, - l = this.l, - m2 = l + (l < 0.5 ? l : 1 - l) * s, - m1 = 2 * l - m2; - return new Rgb( - hsl2rgb(h >= 240 ? h - 240 : h + 120, m1, m2), - hsl2rgb(h, m1, m2), - hsl2rgb(h < 120 ? h + 240 : h - 120, m1, m2), - this.opacity - ); - }, - displayable: function() { - return (0 <= this.s && this.s <= 1 || isNaN(this.s)) - && (0 <= this.l && this.l <= 1) - && (0 <= this.opacity && this.opacity <= 1); - }, - formatHsl: function() { - var a = this.opacity; a = isNaN(a) ? 1 : Math.max(0, Math.min(1, a)); - return (a === 1 ? "hsl(" : "hsla(") - + (this.h || 0) + ", " - + (this.s || 0) * 100 + "%, " - + (this.l || 0) * 100 + "%" - + (a === 1 ? ")" : ", " + a + ")"); - } - })); - - /* From FvD 13.37, CSS Color Module Level 3 */ - function hsl2rgb(h, m1, m2) { - return (h < 60 ? m1 + (m2 - m1) * h / 60 - : h < 180 ? m2 - : h < 240 ? m1 + (m2 - m1) * (240 - h) / 60 - : m1) * 255; - } - - var deg2rad = Math.PI / 180; - var rad2deg = 180 / Math.PI; - - // https://observablehq.com/@mbostock/lab-and-rgb - var K = 18, - Xn = 0.96422, - Yn = 1, - Zn = 0.82521, - t0 = 4 / 29, - t1 = 6 / 29, - t2 = 3 * t1 * t1, - t3 = t1 * t1 * t1; - - function labConvert(o) { - if (o instanceof Lab) return new Lab(o.l, o.a, o.b, o.opacity); - if (o instanceof Hcl) return hcl2lab(o); - if (!(o instanceof Rgb)) o = rgbConvert(o); - var r = rgb2lrgb(o.r), - g = rgb2lrgb(o.g), - b = rgb2lrgb(o.b), - y = xyz2lab((0.2225045 * r + 0.7168786 * g + 0.0606169 * b) / Yn), x, z; - if (r === g && g === b) x = z = y; else { - x = xyz2lab((0.4360747 * r + 0.3850649 * g + 0.1430804 * b) / Xn); - z = xyz2lab((0.0139322 * r + 0.0971045 * g + 0.7141733 * b) / Zn); - } - return new Lab(116 * y - 16, 500 * (x - y), 200 * (y - z), o.opacity); - } - - function lab(l, a, b, opacity) { - return arguments.length === 1 ? labConvert(l) : new Lab(l, a, b, opacity == null ? 1 : opacity); - } - - function Lab(l, a, b, opacity) { - this.l = +l; - this.a = +a; - this.b = +b; - this.opacity = +opacity; - } - - define(Lab, lab, extend(Color, { - brighter: function(k) { - return new Lab(this.l + K * (k == null ? 1 : k), this.a, this.b, this.opacity); - }, - darker: function(k) { - return new Lab(this.l - K * (k == null ? 1 : k), this.a, this.b, this.opacity); - }, - rgb: function() { - var y = (this.l + 16) / 116, - x = isNaN(this.a) ? y : y + this.a / 500, - z = isNaN(this.b) ? y : y - this.b / 200; - x = Xn * lab2xyz(x); - y = Yn * lab2xyz(y); - z = Zn * lab2xyz(z); - return new Rgb( - lrgb2rgb( 3.1338561 * x - 1.6168667 * y - 0.4906146 * z), - lrgb2rgb(-0.9787684 * x + 1.9161415 * y + 0.0334540 * z), - lrgb2rgb( 0.0719453 * x - 0.2289914 * y + 1.4052427 * z), - this.opacity - ); - } - })); - - function xyz2lab(t) { - return t > t3 ? Math.pow(t, 1 / 3) : t / t2 + t0; - } - - function lab2xyz(t) { - return t > t1 ? t * t * t : t2 * (t - t0); - } - - function lrgb2rgb(x) { - return 255 * (x <= 0.0031308 ? 12.92 * x : 1.055 * Math.pow(x, 1 / 2.4) - 0.055); - } - - function rgb2lrgb(x) { - return (x /= 255) <= 0.04045 ? x / 12.92 : Math.pow((x + 0.055) / 1.055, 2.4); - } - - function hclConvert(o) { - if (o instanceof Hcl) return new Hcl(o.h, o.c, o.l, o.opacity); - if (!(o instanceof Lab)) o = labConvert(o); - if (o.a === 0 && o.b === 0) return new Hcl(NaN, 0 < o.l && o.l < 100 ? 0 : NaN, o.l, o.opacity); - var h = Math.atan2(o.b, o.a) * rad2deg; - return new Hcl(h < 0 ? h + 360 : h, Math.sqrt(o.a * o.a + o.b * o.b), o.l, o.opacity); - } - - function hcl(h, c, l, opacity) { - return arguments.length === 1 ? hclConvert(h) : new Hcl(h, c, l, opacity == null ? 1 : opacity); - } - - function Hcl(h, c, l, opacity) { - this.h = +h; - this.c = +c; - this.l = +l; - this.opacity = +opacity; - } - - function hcl2lab(o) { - if (isNaN(o.h)) return new Lab(o.l, 0, 0, o.opacity); - var h = o.h * deg2rad; - return new Lab(o.l, Math.cos(h) * o.c, Math.sin(h) * o.c, o.opacity); - } - - define(Hcl, hcl, extend(Color, { - brighter: function(k) { - return new Hcl(this.h, this.c, this.l + K * (k == null ? 1 : k), this.opacity); - }, - darker: function(k) { - return new Hcl(this.h, this.c, this.l - K * (k == null ? 1 : k), this.opacity); - }, - rgb: function() { - return hcl2lab(this).rgb(); - } - })); - - var A = -0.14861, - B = +1.78277, - C = -0.29227, - D = -0.90649, - E = +1.97294, - ED = E * D, - EB = E * B, - BC_DA = B * C - D * A; - - function cubehelixConvert(o) { - if (o instanceof Cubehelix) return new Cubehelix(o.h, o.s, o.l, o.opacity); - if (!(o instanceof Rgb)) o = rgbConvert(o); - var r = o.r / 255, - g = o.g / 255, - b = o.b / 255, - l = (BC_DA * b + ED * r - EB * g) / (BC_DA + ED - EB), - bl = b - l, - k = (E * (g - l) - C * bl) / D, - s = Math.sqrt(k * k + bl * bl) / (E * l * (1 - l)), // NaN if l=0 or l=1 - h = s ? Math.atan2(k, bl) * rad2deg - 120 : NaN; - return new Cubehelix(h < 0 ? h + 360 : h, s, l, o.opacity); - } - - function cubehelix(h, s, l, opacity) { - return arguments.length === 1 ? cubehelixConvert(h) : new Cubehelix(h, s, l, opacity == null ? 1 : opacity); - } - - function Cubehelix(h, s, l, opacity) { - this.h = +h; - this.s = +s; - this.l = +l; - this.opacity = +opacity; - } - - define(Cubehelix, cubehelix, extend(Color, { - brighter: function(k) { - k = k == null ? brighter : Math.pow(brighter, k); - return new Cubehelix(this.h, this.s, this.l * k, this.opacity); - }, - darker: function(k) { - k = k == null ? darker : Math.pow(darker, k); - return new Cubehelix(this.h, this.s, this.l * k, this.opacity); - }, - rgb: function() { - var h = isNaN(this.h) ? 0 : (this.h + 120) * deg2rad, - l = +this.l, - a = isNaN(this.s) ? 0 : this.s * l * (1 - l), - cosh = Math.cos(h), - sinh = Math.sin(h); - return new Rgb( - 255 * (l + a * (A * cosh + B * sinh)), - 255 * (l + a * (C * cosh + D * sinh)), - 255 * (l + a * (E * cosh)), - this.opacity - ); - } - })); - - function constant(x) { - return function() { - return x; - }; - } - - function linear(a, d) { - return function(t) { - return a + t * d; - }; - } - - function exponential(a, b, y) { - return a = Math.pow(a, y), b = Math.pow(b, y) - a, y = 1 / y, function(t) { - return Math.pow(a + t * b, y); - }; - } - - function gamma(y) { - return (y = +y) === 1 ? nogamma : function(a, b) { - return b - a ? exponential(a, b, y) : constant(isNaN(a) ? b : a); - }; - } - - function nogamma(a, b) { - var d = b - a; - return d ? linear(a, d) : constant(isNaN(a) ? b : a); - } - - var rgb$1 = (function rgbGamma(y) { - var color = gamma(y); - - function rgb$1(start, end) { - var r = color((start = rgb(start)).r, (end = rgb(end)).r), - g = color(start.g, end.g), - b = color(start.b, end.b), - opacity = nogamma(start.opacity, end.opacity); - return function(t) { - start.r = r(t); - start.g = g(t); - start.b = b(t); - start.opacity = opacity(t); - return start + ""; - }; - } - - rgb$1.gamma = rgbGamma; - - return rgb$1; - })(1); - - function numberArray(a, b) { - if (!b) b = []; - var n = a ? Math.min(b.length, a.length) : 0, - c = b.slice(), - i; - return function(t) { - for (i = 0; i < n; ++i) c[i] = a[i] * (1 - t) + b[i] * t; - return c; - }; - } - - function isNumberArray(x) { - return ArrayBuffer.isView(x) && !(x instanceof DataView); - } - - function genericArray(a, b) { - var nb = b ? b.length : 0, - na = a ? Math.min(nb, a.length) : 0, - x = new Array(na), - c = new Array(nb), - i; - - for (i = 0; i < na; ++i) x[i] = interpolate(a[i], b[i]); - for (; i < nb; ++i) c[i] = b[i]; - - return function(t) { - for (i = 0; i < na; ++i) c[i] = x[i](t); - return c; - }; - } - - function date(a, b) { - var d = new Date; - return a = +a, b = +b, function(t) { - return d.setTime(a * (1 - t) + b * t), d; - }; - } - - function interpolateNumber(a, b) { - return a = +a, b = +b, function(t) { - return a * (1 - t) + b * t; - }; - } - - function object(a, b) { - var i = {}, - c = {}, - k; - - if (a === null || typeof a !== "object") a = {}; - if (b === null || typeof b !== "object") b = {}; - - for (k in b) { - if (k in a) { - i[k] = interpolate(a[k], b[k]); - } else { - c[k] = b[k]; - } - } - - return function(t) { - for (k in i) c[k] = i[k](t); - return c; - }; - } - - var reA = /[-+]?(?:\d+\.?\d*|\.?\d+)(?:[eE][-+]?\d+)?/g, - reB = new RegExp(reA.source, "g"); - - function zero(b) { - return function() { - return b; - }; - } - - function one(b) { - return function(t) { - return b(t) + ""; - }; - } - - function string(a, b) { - var bi = reA.lastIndex = reB.lastIndex = 0, // scan index for next number in b - am, // current match in a - bm, // current match in b - bs, // string preceding current number in b, if any - i = -1, // index in s - s = [], // string constants and placeholders - q = []; // number interpolators - - // Coerce inputs to strings. - a = a + "", b = b + ""; - - // Interpolate pairs of numbers in a & b. - while ((am = reA.exec(a)) - && (bm = reB.exec(b))) { - if ((bs = bm.index) > bi) { // a string precedes the next number in b - bs = b.slice(bi, bs); - if (s[i]) s[i] += bs; // coalesce with previous string - else s[++i] = bs; - } - if ((am = am[0]) === (bm = bm[0])) { // numbers in a & b match - if (s[i]) s[i] += bm; // coalesce with previous string - else s[++i] = bm; - } else { // interpolate non-matching numbers - s[++i] = null; - q.push({i: i, x: interpolateNumber(am, bm)}); - } - bi = reB.lastIndex; - } - - // Add remains of b. - if (bi < b.length) { - bs = b.slice(bi); - if (s[i]) s[i] += bs; // coalesce with previous string - else s[++i] = bs; - } - - // Special optimization for only a single match. - // Otherwise, interpolate each of the numbers and rejoin the string. - return s.length < 2 ? (q[0] - ? one(q[0].x) - : zero(b)) - : (b = q.length, function(t) { - for (var i = 0, o; i < b; ++i) s[(o = q[i]).i] = o.x(t); - return s.join(""); - }); - } - - function interpolate(a, b) { - var t = typeof b, c; - return b == null || t === "boolean" ? constant(b) - : (t === "number" ? interpolateNumber - : t === "string" ? ((c = color(b)) ? (b = c, rgb$1) : string) - : b instanceof color ? rgb$1 - : b instanceof Date ? date - : isNumberArray(b) ? numberArray - : Array.isArray(b) ? genericArray - : typeof b.valueOf !== "function" && typeof b.toString !== "function" || isNaN(b) ? object - : interpolateNumber)(a, b); - } - - function interpolateRound(a, b) { - return a = +a, b = +b, function(t) { - return Math.round(a * (1 - t) + b * t); - }; - } - - function constant$1(x) { - return function() { - return x; - }; - } - - function number(x) { - return +x; - } - - var unit = [0, 1]; - - function identity(x) { - return x; - } - - function normalize(a, b) { - return (b -= (a = +a)) - ? function(x) { return (x - a) / b; } - : constant$1(isNaN(b) ? NaN : 0.5); - } - - function clamper(a, b) { - var t; - if (a > b) t = a, a = b, b = t; - return function(x) { return Math.max(a, Math.min(b, x)); }; - } - - // normalize(a, b)(x) takes a domain value x in [a,b] and returns the corresponding parameter t in [0,1]. - // interpolate(a, b)(t) takes a parameter t in [0,1] and returns the corresponding range value x in [a,b]. - function bimap(domain, range, interpolate) { - var d0 = domain[0], d1 = domain[1], r0 = range[0], r1 = range[1]; - if (d1 < d0) d0 = normalize(d1, d0), r0 = interpolate(r1, r0); - else d0 = normalize(d0, d1), r0 = interpolate(r0, r1); - return function(x) { return r0(d0(x)); }; - } - - function polymap(domain, range, interpolate) { - var j = Math.min(domain.length, range.length) - 1, - d = new Array(j), - r = new Array(j), - i = -1; - - // Reverse descending domains. - if (domain[j] < domain[0]) { - domain = domain.slice().reverse(); - range = range.slice().reverse(); - } - - while (++i < j) { - d[i] = normalize(domain[i], domain[i + 1]); - r[i] = interpolate(range[i], range[i + 1]); - } - - return function(x) { - var i = bisectRight(domain, x, 1, j) - 1; - return r[i](d[i](x)); - }; - } - - function copy(source, target) { - return target - .domain(source.domain()) - .range(source.range()) - .interpolate(source.interpolate()) - .clamp(source.clamp()) - .unknown(source.unknown()); - } - - function transformer() { - var domain = unit, - range = unit, - interpolate$1 = interpolate, - transform, - untransform, - unknown, - clamp = identity, - piecewise, - output, - input; - - function rescale() { - var n = Math.min(domain.length, range.length); - if (clamp !== identity) clamp = clamper(domain[0], domain[n - 1]); - piecewise = n > 2 ? polymap : bimap; - output = input = null; - return scale; - } - - function scale(x) { - return isNaN(x = +x) ? unknown : (output || (output = piecewise(domain.map(transform), range, interpolate$1)))(transform(clamp(x))); - } - - scale.invert = function(y) { - return clamp(untransform((input || (input = piecewise(range, domain.map(transform), interpolateNumber)))(y))); - }; - - scale.domain = function(_) { - return arguments.length ? (domain = Array.from(_, number), rescale()) : domain.slice(); - }; - - scale.range = function(_) { - return arguments.length ? (range = Array.from(_), rescale()) : range.slice(); - }; - - scale.rangeRound = function(_) { - return range = Array.from(_), interpolate$1 = interpolateRound, rescale(); - }; - - scale.clamp = function(_) { - return arguments.length ? (clamp = _ ? true : identity, rescale()) : clamp !== identity; - }; - - scale.interpolate = function(_) { - return arguments.length ? (interpolate$1 = _, rescale()) : interpolate$1; - }; - - scale.unknown = function(_) { - return arguments.length ? (unknown = _, scale) : unknown; - }; - - return function(t, u) { - transform = t, untransform = u; - return rescale(); - }; - } - - function continuous() { - return transformer()(identity, identity); - } - - // Computes the decimal coefficient and exponent of the specified number x with - // significant digits p, where x is positive and p is in [1, 21] or undefined. - // For example, formatDecimal(1.23) returns ["123", 0]. - function formatDecimal(x, p) { - if ((i = (x = p ? x.toExponential(p - 1) : x.toExponential()).indexOf("e")) < 0) return null; // NaN, ±Infinity - var i, coefficient = x.slice(0, i); - - // The string returned by toExponential either has the form \d\.\d+e[-+]\d+ - // (e.g., 1.2e+3) or the form \de[-+]\d+ (e.g., 1e+3). - return [ - coefficient.length > 1 ? coefficient[0] + coefficient.slice(2) : coefficient, - +x.slice(i + 1) - ]; - } - - function exponent(x) { - return x = formatDecimal(Math.abs(x)), x ? x[1] : NaN; - } - - function formatGroup(grouping, thousands) { - return function(value, width) { - var i = value.length, - t = [], - j = 0, - g = grouping[0], - length = 0; - - while (i > 0 && g > 0) { - if (length + g + 1 > width) g = Math.max(1, width - length); - t.push(value.substring(i -= g, i + g)); - if ((length += g + 1) > width) break; - g = grouping[j = (j + 1) % grouping.length]; - } - - return t.reverse().join(thousands); - }; - } - - function formatNumerals(numerals) { - return function(value) { - return value.replace(/[0-9]/g, function(i) { - return numerals[+i]; - }); - }; - } - - // [[fill]align][sign][symbol][0][width][,][.precision][~][type] - var re = /^(?:(.)?([<>=^]))?([+\-( ])?([$#])?(0)?(\d+)?(,)?(\.\d+)?(~)?([a-z%])?$/i; - - function formatSpecifier(specifier) { - if (!(match = re.exec(specifier))) throw new Error("invalid format: " + specifier); - var match; - return new FormatSpecifier({ - fill: match[1], - align: match[2], - sign: match[3], - symbol: match[4], - zero: match[5], - width: match[6], - comma: match[7], - precision: match[8] && match[8].slice(1), - trim: match[9], - type: match[10] - }); - } - - formatSpecifier.prototype = FormatSpecifier.prototype; // instanceof - - function FormatSpecifier(specifier) { - this.fill = specifier.fill === undefined ? " " : specifier.fill + ""; - this.align = specifier.align === undefined ? ">" : specifier.align + ""; - this.sign = specifier.sign === undefined ? "-" : specifier.sign + ""; - this.symbol = specifier.symbol === undefined ? "" : specifier.symbol + ""; - this.zero = !!specifier.zero; - this.width = specifier.width === undefined ? undefined : +specifier.width; - this.comma = !!specifier.comma; - this.precision = specifier.precision === undefined ? undefined : +specifier.precision; - this.trim = !!specifier.trim; - this.type = specifier.type === undefined ? "" : specifier.type + ""; - } - - FormatSpecifier.prototype.toString = function() { - return this.fill - + this.align - + this.sign - + this.symbol - + (this.zero ? "0" : "") - + (this.width === undefined ? "" : Math.max(1, this.width | 0)) - + (this.comma ? "," : "") - + (this.precision === undefined ? "" : "." + Math.max(0, this.precision | 0)) - + (this.trim ? "~" : "") - + this.type; - }; - - // Trims insignificant zeros, e.g., replaces 1.2000k with 1.2k. - function formatTrim(s) { - out: for (var n = s.length, i = 1, i0 = -1, i1; i < n; ++i) { - switch (s[i]) { - case ".": i0 = i1 = i; break; - case "0": if (i0 === 0) i0 = i; i1 = i; break; - default: if (!+s[i]) break out; if (i0 > 0) i0 = 0; break; - } - } - return i0 > 0 ? s.slice(0, i0) + s.slice(i1 + 1) : s; - } - - var prefixExponent; - - function formatPrefixAuto(x, p) { - var d = formatDecimal(x, p); - if (!d) return x + ""; - var coefficient = d[0], - exponent = d[1], - i = exponent - (prefixExponent = Math.max(-8, Math.min(8, Math.floor(exponent / 3))) * 3) + 1, - n = coefficient.length; - return i === n ? coefficient - : i > n ? coefficient + new Array(i - n + 1).join("0") - : i > 0 ? coefficient.slice(0, i) + "." + coefficient.slice(i) - : "0." + new Array(1 - i).join("0") + formatDecimal(x, Math.max(0, p + i - 1))[0]; // less than 1y! - } - - function formatRounded(x, p) { - var d = formatDecimal(x, p); - if (!d) return x + ""; - var coefficient = d[0], - exponent = d[1]; - return exponent < 0 ? "0." + new Array(-exponent).join("0") + coefficient - : coefficient.length > exponent + 1 ? coefficient.slice(0, exponent + 1) + "." + coefficient.slice(exponent + 1) - : coefficient + new Array(exponent - coefficient.length + 2).join("0"); - } - - var formatTypes = { - "%": function(x, p) { return (x * 100).toFixed(p); }, - "b": function(x) { return Math.round(x).toString(2); }, - "c": function(x) { return x + ""; }, - "d": function(x) { return Math.round(x).toString(10); }, - "e": function(x, p) { return x.toExponential(p); }, - "f": function(x, p) { return x.toFixed(p); }, - "g": function(x, p) { return x.toPrecision(p); }, - "o": function(x) { return Math.round(x).toString(8); }, - "p": function(x, p) { return formatRounded(x * 100, p); }, - "r": formatRounded, - "s": formatPrefixAuto, - "X": function(x) { return Math.round(x).toString(16).toUpperCase(); }, - "x": function(x) { return Math.round(x).toString(16); } - }; - - function identity$1(x) { - return x; - } - - var map = Array.prototype.map, - prefixes = ["y","z","a","f","p","n","µ","m","","k","M","G","T","P","E","Z","Y"]; - - function formatLocale(locale) { - var group = locale.grouping === undefined || locale.thousands === undefined ? identity$1 : formatGroup(map.call(locale.grouping, Number), locale.thousands + ""), - currencyPrefix = locale.currency === undefined ? "" : locale.currency[0] + "", - currencySuffix = locale.currency === undefined ? "" : locale.currency[1] + "", - decimal = locale.decimal === undefined ? "." : locale.decimal + "", - numerals = locale.numerals === undefined ? identity$1 : formatNumerals(map.call(locale.numerals, String)), - percent = locale.percent === undefined ? "%" : locale.percent + "", - minus = locale.minus === undefined ? "-" : locale.minus + "", - nan = locale.nan === undefined ? "NaN" : locale.nan + ""; - - function newFormat(specifier) { - specifier = formatSpecifier(specifier); - - var fill = specifier.fill, - align = specifier.align, - sign = specifier.sign, - symbol = specifier.symbol, - zero = specifier.zero, - width = specifier.width, - comma = specifier.comma, - precision = specifier.precision, - trim = specifier.trim, - type = specifier.type; - - // The "n" type is an alias for ",g". - if (type === "n") comma = true, type = "g"; - - // The "" type, and any invalid type, is an alias for ".12~g". - else if (!formatTypes[type]) precision === undefined && (precision = 12), trim = true, type = "g"; - - // If zero fill is specified, padding goes after sign and before digits. - if (zero || (fill === "0" && align === "=")) zero = true, fill = "0", align = "="; - - // Compute the prefix and suffix. - // For SI-prefix, the suffix is lazily computed. - var prefix = symbol === "$" ? currencyPrefix : symbol === "#" && /[boxX]/.test(type) ? "0" + type.toLowerCase() : "", - suffix = symbol === "$" ? currencySuffix : /[%p]/.test(type) ? percent : ""; - - // What format function should we use? - // Is this an integer type? - // Can this type generate exponential notation? - var formatType = formatTypes[type], - maybeSuffix = /[defgprs%]/.test(type); - - // Set the default precision if not specified, - // or clamp the specified precision to the supported range. - // For significant precision, it must be in [1, 21]. - // For fixed precision, it must be in [0, 20]. - precision = precision === undefined ? 6 - : /[gprs]/.test(type) ? Math.max(1, Math.min(21, precision)) - : Math.max(0, Math.min(20, precision)); - - function format(value) { - var valuePrefix = prefix, - valueSuffix = suffix, - i, n, c; - - if (type === "c") { - valueSuffix = formatType(value) + valueSuffix; - value = ""; - } else { - value = +value; - - // Determine the sign. -0 is not less than 0, but 1 / -0 is! - var valueNegative = value < 0 || 1 / value < 0; - - // Perform the initial formatting. - value = isNaN(value) ? nan : formatType(Math.abs(value), precision); - - // Trim insignificant zeros. - if (trim) value = formatTrim(value); - - // If a negative value rounds to zero after formatting, and no explicit positive sign is requested, hide the sign. - if (valueNegative && +value === 0 && sign !== "+") valueNegative = false; - - // Compute the prefix and suffix. - valuePrefix = (valueNegative ? (sign === "(" ? sign : minus) : sign === "-" || sign === "(" ? "" : sign) + valuePrefix; - valueSuffix = (type === "s" ? prefixes[8 + prefixExponent / 3] : "") + valueSuffix + (valueNegative && sign === "(" ? ")" : ""); - - // Break the formatted value into the integer “value” part that can be - // grouped, and fractional or exponential “suffix” part that is not. - if (maybeSuffix) { - i = -1, n = value.length; - while (++i < n) { - if (c = value.charCodeAt(i), 48 > c || c > 57) { - valueSuffix = (c === 46 ? decimal + value.slice(i + 1) : value.slice(i)) + valueSuffix; - value = value.slice(0, i); - break; - } - } - } - } - - // If the fill character is not "0", grouping is applied before padding. - if (comma && !zero) value = group(value, Infinity); - - // Compute the padding. - var length = valuePrefix.length + value.length + valueSuffix.length, - padding = length < width ? new Array(width - length + 1).join(fill) : ""; - - // If the fill character is "0", grouping is applied after padding. - if (comma && zero) value = group(padding + value, padding.length ? width - valueSuffix.length : Infinity), padding = ""; - - // Reconstruct the final output based on the desired alignment. - switch (align) { - case "<": value = valuePrefix + value + valueSuffix + padding; break; - case "=": value = valuePrefix + padding + value + valueSuffix; break; - case "^": value = padding.slice(0, length = padding.length >> 1) + valuePrefix + value + valueSuffix + padding.slice(length); break; - default: value = padding + valuePrefix + value + valueSuffix; break; - } - - return numerals(value); - } - - format.toString = function() { - return specifier + ""; - }; - - return format; - } - - function formatPrefix(specifier, value) { - var f = newFormat((specifier = formatSpecifier(specifier), specifier.type = "f", specifier)), - e = Math.max(-8, Math.min(8, Math.floor(exponent(value) / 3))) * 3, - k = Math.pow(10, -e), - prefix = prefixes[8 + e / 3]; - return function(value) { - return f(k * value) + prefix; - }; - } - - return { - format: newFormat, - formatPrefix: formatPrefix - }; - } - - var locale; - var format; - var formatPrefix; - - defaultLocale({ - decimal: ".", - thousands: ",", - grouping: [3], - currency: ["$", ""], - minus: "-" - }); - - function defaultLocale(definition) { - locale = formatLocale(definition); - format = locale.format; - formatPrefix = locale.formatPrefix; - return locale; - } - - function precisionFixed(step) { - return Math.max(0, -exponent(Math.abs(step))); - } - - function precisionPrefix(step, value) { - return Math.max(0, Math.max(-8, Math.min(8, Math.floor(exponent(value) / 3))) * 3 - exponent(Math.abs(step))); - } - - function precisionRound(step, max) { - step = Math.abs(step), max = Math.abs(max) - step; - return Math.max(0, exponent(max) - exponent(step)) + 1; - } - - function tickFormat(start, stop, count, specifier) { - var step = tickStep(start, stop, count), - precision; - specifier = formatSpecifier(specifier == null ? ",f" : specifier); - switch (specifier.type) { - case "s": { - var value = Math.max(Math.abs(start), Math.abs(stop)); - if (specifier.precision == null && !isNaN(precision = precisionPrefix(step, value))) specifier.precision = precision; - return formatPrefix(specifier, value); - } - case "": - case "e": - case "g": - case "p": - case "r": { - if (specifier.precision == null && !isNaN(precision = precisionRound(step, Math.max(Math.abs(start), Math.abs(stop))))) specifier.precision = precision - (specifier.type === "e"); - break; - } - case "f": - case "%": { - if (specifier.precision == null && !isNaN(precision = precisionFixed(step))) specifier.precision = precision - (specifier.type === "%") * 2; - break; - } - } - return format(specifier); - } - - function linearish(scale) { - var domain = scale.domain; - - scale.ticks = function(count) { - var d = domain(); - return ticks(d[0], d[d.length - 1], count == null ? 10 : count); - }; - - scale.tickFormat = function(count, specifier) { - var d = domain(); - return tickFormat(d[0], d[d.length - 1], count == null ? 10 : count, specifier); - }; - - scale.nice = function(count) { - if (count == null) count = 10; - - var d = domain(), - i0 = 0, - i1 = d.length - 1, - start = d[i0], - stop = d[i1], - step; - - if (stop < start) { - step = start, start = stop, stop = step; - step = i0, i0 = i1, i1 = step; - } - - step = tickIncrement(start, stop, count); - - if (step > 0) { - start = Math.floor(start / step) * step; - stop = Math.ceil(stop / step) * step; - step = tickIncrement(start, stop, count); - } else if (step < 0) { - start = Math.ceil(start * step) / step; - stop = Math.floor(stop * step) / step; - step = tickIncrement(start, stop, count); - } - - if (step > 0) { - d[i0] = Math.floor(start / step) * step; - d[i1] = Math.ceil(stop / step) * step; - domain(d); - } else if (step < 0) { - d[i0] = Math.ceil(start * step) / step; - d[i1] = Math.floor(stop * step) / step; - domain(d); - } - - return scale; - }; - - return scale; - } - - function linear$1() { - var scale = continuous(); - - scale.copy = function() { - return copy(scale, linear$1()); - }; - - initRange.apply(scale, arguments); - - return linearish(scale); - } - - var t0$1 = new Date, - t1$1 = new Date; - - function newInterval(floori, offseti, count, field) { - - function interval(date) { - return floori(date = arguments.length === 0 ? new Date : new Date(+date)), date; - } - - interval.floor = function(date) { - return floori(date = new Date(+date)), date; - }; - - interval.ceil = function(date) { - return floori(date = new Date(date - 1)), offseti(date, 1), floori(date), date; - }; - - interval.round = function(date) { - var d0 = interval(date), - d1 = interval.ceil(date); - return date - d0 < d1 - date ? d0 : d1; - }; - - interval.offset = function(date, step) { - return offseti(date = new Date(+date), step == null ? 1 : Math.floor(step)), date; - }; - - interval.range = function(start, stop, step) { - var range = [], previous; - start = interval.ceil(start); - step = step == null ? 1 : Math.floor(step); - if (!(start < stop) || !(step > 0)) return range; // also handles Invalid Date - do range.push(previous = new Date(+start)), offseti(start, step), floori(start); - while (previous < start && start < stop); - return range; - }; - - interval.filter = function(test) { - return newInterval(function(date) { - if (date >= date) while (floori(date), !test(date)) date.setTime(date - 1); - }, function(date, step) { - if (date >= date) { - if (step < 0) while (++step <= 0) { - while (offseti(date, -1), !test(date)) {} // eslint-disable-line no-empty - } else while (--step >= 0) { - while (offseti(date, +1), !test(date)) {} // eslint-disable-line no-empty - } - } - }); - }; - - if (count) { - interval.count = function(start, end) { - t0$1.setTime(+start), t1$1.setTime(+end); - floori(t0$1), floori(t1$1); - return Math.floor(count(t0$1, t1$1)); - }; - - interval.every = function(step) { - step = Math.floor(step); - return !isFinite(step) || !(step > 0) ? null - : !(step > 1) ? interval - : interval.filter(field - ? function(d) { return field(d) % step === 0; } - : function(d) { return interval.count(0, d) % step === 0; }); - }; - } - - return interval; - } - - var millisecond = newInterval(function() { - // noop - }, function(date, step) { - date.setTime(+date + step); - }, function(start, end) { - return end - start; - }); - - // An optimized implementation for this simple case. - millisecond.every = function(k) { - k = Math.floor(k); - if (!isFinite(k) || !(k > 0)) return null; - if (!(k > 1)) return millisecond; - return newInterval(function(date) { - date.setTime(Math.floor(date / k) * k); - }, function(date, step) { - date.setTime(+date + step * k); - }, function(start, end) { - return (end - start) / k; - }); - }; - - var durationSecond = 1e3; - var durationMinute = 6e4; - var durationHour = 36e5; - var durationDay = 864e5; - var durationWeek = 6048e5; - - var second = newInterval(function(date) { - date.setTime(date - date.getMilliseconds()); - }, function(date, step) { - date.setTime(+date + step * durationSecond); - }, function(start, end) { - return (end - start) / durationSecond; - }, function(date) { - return date.getUTCSeconds(); - }); - - var minute = newInterval(function(date) { - date.setTime(date - date.getMilliseconds() - date.getSeconds() * durationSecond); - }, function(date, step) { - date.setTime(+date + step * durationMinute); - }, function(start, end) { - return (end - start) / durationMinute; - }, function(date) { - return date.getMinutes(); - }); - - var hour = newInterval(function(date) { - date.setTime(date - date.getMilliseconds() - date.getSeconds() * durationSecond - date.getMinutes() * durationMinute); - }, function(date, step) { - date.setTime(+date + step * durationHour); - }, function(start, end) { - return (end - start) / durationHour; - }, function(date) { - return date.getHours(); - }); - - var day = newInterval(function(date) { - date.setHours(0, 0, 0, 0); - }, function(date, step) { - date.setDate(date.getDate() + step); - }, function(start, end) { - return (end - start - (end.getTimezoneOffset() - start.getTimezoneOffset()) * durationMinute) / durationDay; - }, function(date) { - return date.getDate() - 1; - }); - - function weekday(i) { - return newInterval(function(date) { - date.setDate(date.getDate() - (date.getDay() + 7 - i) % 7); - date.setHours(0, 0, 0, 0); - }, function(date, step) { - date.setDate(date.getDate() + step * 7); - }, function(start, end) { - return (end - start - (end.getTimezoneOffset() - start.getTimezoneOffset()) * durationMinute) / durationWeek; - }); - } - - var sunday = weekday(0); - var monday = weekday(1); - var tuesday = weekday(2); - var wednesday = weekday(3); - var thursday = weekday(4); - var friday = weekday(5); - var saturday = weekday(6); - - var month = newInterval(function(date) { - date.setDate(1); - date.setHours(0, 0, 0, 0); - }, function(date, step) { - date.setMonth(date.getMonth() + step); - }, function(start, end) { - return end.getMonth() - start.getMonth() + (end.getFullYear() - start.getFullYear()) * 12; - }, function(date) { - return date.getMonth(); - }); - - var year = newInterval(function(date) { - date.setMonth(0, 1); - date.setHours(0, 0, 0, 0); - }, function(date, step) { - date.setFullYear(date.getFullYear() + step); - }, function(start, end) { - return end.getFullYear() - start.getFullYear(); - }, function(date) { - return date.getFullYear(); - }); - - // An optimized implementation for this simple case. - year.every = function(k) { - return !isFinite(k = Math.floor(k)) || !(k > 0) ? null : newInterval(function(date) { - date.setFullYear(Math.floor(date.getFullYear() / k) * k); - date.setMonth(0, 1); - date.setHours(0, 0, 0, 0); - }, function(date, step) { - date.setFullYear(date.getFullYear() + step * k); - }); - }; - - var utcMinute = newInterval(function(date) { - date.setUTCSeconds(0, 0); - }, function(date, step) { - date.setTime(+date + step * durationMinute); - }, function(start, end) { - return (end - start) / durationMinute; - }, function(date) { - return date.getUTCMinutes(); - }); - - var utcHour = newInterval(function(date) { - date.setUTCMinutes(0, 0, 0); - }, function(date, step) { - date.setTime(+date + step * durationHour); - }, function(start, end) { - return (end - start) / durationHour; - }, function(date) { - return date.getUTCHours(); - }); - - var utcDay = newInterval(function(date) { - date.setUTCHours(0, 0, 0, 0); - }, function(date, step) { - date.setUTCDate(date.getUTCDate() + step); - }, function(start, end) { - return (end - start) / durationDay; - }, function(date) { - return date.getUTCDate() - 1; - }); - - function utcWeekday(i) { - return newInterval(function(date) { - date.setUTCDate(date.getUTCDate() - (date.getUTCDay() + 7 - i) % 7); - date.setUTCHours(0, 0, 0, 0); - }, function(date, step) { - date.setUTCDate(date.getUTCDate() + step * 7); - }, function(start, end) { - return (end - start) / durationWeek; - }); - } - - var utcSunday = utcWeekday(0); - var utcMonday = utcWeekday(1); - var utcTuesday = utcWeekday(2); - var utcWednesday = utcWeekday(3); - var utcThursday = utcWeekday(4); - var utcFriday = utcWeekday(5); - var utcSaturday = utcWeekday(6); - - var utcMonth = newInterval(function(date) { - date.setUTCDate(1); - date.setUTCHours(0, 0, 0, 0); - }, function(date, step) { - date.setUTCMonth(date.getUTCMonth() + step); - }, function(start, end) { - return end.getUTCMonth() - start.getUTCMonth() + (end.getUTCFullYear() - start.getUTCFullYear()) * 12; - }, function(date) { - return date.getUTCMonth(); - }); - - var utcYear = newInterval(function(date) { - date.setUTCMonth(0, 1); - date.setUTCHours(0, 0, 0, 0); - }, function(date, step) { - date.setUTCFullYear(date.getUTCFullYear() + step); - }, function(start, end) { - return end.getUTCFullYear() - start.getUTCFullYear(); - }, function(date) { - return date.getUTCFullYear(); - }); - - // An optimized implementation for this simple case. - utcYear.every = function(k) { - return !isFinite(k = Math.floor(k)) || !(k > 0) ? null : newInterval(function(date) { - date.setUTCFullYear(Math.floor(date.getUTCFullYear() / k) * k); - date.setUTCMonth(0, 1); - date.setUTCHours(0, 0, 0, 0); - }, function(date, step) { - date.setUTCFullYear(date.getUTCFullYear() + step * k); - }); - }; - - function localDate(d) { - if (0 <= d.y && d.y < 100) { - var date = new Date(-1, d.m, d.d, d.H, d.M, d.S, d.L); - date.setFullYear(d.y); - return date; - } - return new Date(d.y, d.m, d.d, d.H, d.M, d.S, d.L); - } - - function utcDate(d) { - if (0 <= d.y && d.y < 100) { - var date = new Date(Date.UTC(-1, d.m, d.d, d.H, d.M, d.S, d.L)); - date.setUTCFullYear(d.y); - return date; - } - return new Date(Date.UTC(d.y, d.m, d.d, d.H, d.M, d.S, d.L)); - } - - function newDate(y, m, d) { - return {y: y, m: m, d: d, H: 0, M: 0, S: 0, L: 0}; - } - - function formatLocale$1(locale) { - var locale_dateTime = locale.dateTime, - locale_date = locale.date, - locale_time = locale.time, - locale_periods = locale.periods, - locale_weekdays = locale.days, - locale_shortWeekdays = locale.shortDays, - locale_months = locale.months, - locale_shortMonths = locale.shortMonths; - - var periodRe = formatRe(locale_periods), - periodLookup = formatLookup(locale_periods), - weekdayRe = formatRe(locale_weekdays), - weekdayLookup = formatLookup(locale_weekdays), - shortWeekdayRe = formatRe(locale_shortWeekdays), - shortWeekdayLookup = formatLookup(locale_shortWeekdays), - monthRe = formatRe(locale_months), - monthLookup = formatLookup(locale_months), - shortMonthRe = formatRe(locale_shortMonths), - shortMonthLookup = formatLookup(locale_shortMonths); - - var formats = { - "a": formatShortWeekday, - "A": formatWeekday, - "b": formatShortMonth, - "B": formatMonth, - "c": null, - "d": formatDayOfMonth, - "e": formatDayOfMonth, - "f": formatMicroseconds, - "H": formatHour24, - "I": formatHour12, - "j": formatDayOfYear, - "L": formatMilliseconds, - "m": formatMonthNumber, - "M": formatMinutes, - "p": formatPeriod, - "q": formatQuarter, - "Q": formatUnixTimestamp, - "s": formatUnixTimestampSeconds, - "S": formatSeconds, - "u": formatWeekdayNumberMonday, - "U": formatWeekNumberSunday, - "V": formatWeekNumberISO, - "w": formatWeekdayNumberSunday, - "W": formatWeekNumberMonday, - "x": null, - "X": null, - "y": formatYear, - "Y": formatFullYear, - "Z": formatZone, - "%": formatLiteralPercent - }; - - var utcFormats = { - "a": formatUTCShortWeekday, - "A": formatUTCWeekday, - "b": formatUTCShortMonth, - "B": formatUTCMonth, - "c": null, - "d": formatUTCDayOfMonth, - "e": formatUTCDayOfMonth, - "f": formatUTCMicroseconds, - "H": formatUTCHour24, - "I": formatUTCHour12, - "j": formatUTCDayOfYear, - "L": formatUTCMilliseconds, - "m": formatUTCMonthNumber, - "M": formatUTCMinutes, - "p": formatUTCPeriod, - "q": formatUTCQuarter, - "Q": formatUnixTimestamp, - "s": formatUnixTimestampSeconds, - "S": formatUTCSeconds, - "u": formatUTCWeekdayNumberMonday, - "U": formatUTCWeekNumberSunday, - "V": formatUTCWeekNumberISO, - "w": formatUTCWeekdayNumberSunday, - "W": formatUTCWeekNumberMonday, - "x": null, - "X": null, - "y": formatUTCYear, - "Y": formatUTCFullYear, - "Z": formatUTCZone, - "%": formatLiteralPercent - }; - - var parses = { - "a": parseShortWeekday, - "A": parseWeekday, - "b": parseShortMonth, - "B": parseMonth, - "c": parseLocaleDateTime, - "d": parseDayOfMonth, - "e": parseDayOfMonth, - "f": parseMicroseconds, - "H": parseHour24, - "I": parseHour24, - "j": parseDayOfYear, - "L": parseMilliseconds, - "m": parseMonthNumber, - "M": parseMinutes, - "p": parsePeriod, - "q": parseQuarter, - "Q": parseUnixTimestamp, - "s": parseUnixTimestampSeconds, - "S": parseSeconds, - "u": parseWeekdayNumberMonday, - "U": parseWeekNumberSunday, - "V": parseWeekNumberISO, - "w": parseWeekdayNumberSunday, - "W": parseWeekNumberMonday, - "x": parseLocaleDate, - "X": parseLocaleTime, - "y": parseYear, - "Y": parseFullYear, - "Z": parseZone, - "%": parseLiteralPercent - }; - - // These recursive directive definitions must be deferred. - formats.x = newFormat(locale_date, formats); - formats.X = newFormat(locale_time, formats); - formats.c = newFormat(locale_dateTime, formats); - utcFormats.x = newFormat(locale_date, utcFormats); - utcFormats.X = newFormat(locale_time, utcFormats); - utcFormats.c = newFormat(locale_dateTime, utcFormats); - - function newFormat(specifier, formats) { - return function(date) { - var string = [], - i = -1, - j = 0, - n = specifier.length, - c, - pad, - format; - - if (!(date instanceof Date)) date = new Date(+date); - - while (++i < n) { - if (specifier.charCodeAt(i) === 37) { - string.push(specifier.slice(j, i)); - if ((pad = pads[c = specifier.charAt(++i)]) != null) c = specifier.charAt(++i); - else pad = c === "e" ? " " : "0"; - if (format = formats[c]) c = format(date, pad); - string.push(c); - j = i + 1; - } - } - - string.push(specifier.slice(j, i)); - return string.join(""); - }; - } - - function newParse(specifier, Z) { - return function(string) { - var d = newDate(1900, undefined, 1), - i = parseSpecifier(d, specifier, string += "", 0), - week, day$1; - if (i != string.length) return null; - - // If a UNIX timestamp is specified, return it. - if ("Q" in d) return new Date(d.Q); - if ("s" in d) return new Date(d.s * 1000 + ("L" in d ? d.L : 0)); - - // If this is utcParse, never use the local timezone. - if (Z && !("Z" in d)) d.Z = 0; - - // The am-pm flag is 0 for AM, and 1 for PM. - if ("p" in d) d.H = d.H % 12 + d.p * 12; - - // If the month was not specified, inherit from the quarter. - if (d.m === undefined) d.m = "q" in d ? d.q : 0; - - // Convert day-of-week and week-of-year to day-of-year. - if ("V" in d) { - if (d.V < 1 || d.V > 53) return null; - if (!("w" in d)) d.w = 1; - if ("Z" in d) { - week = utcDate(newDate(d.y, 0, 1)), day$1 = week.getUTCDay(); - week = day$1 > 4 || day$1 === 0 ? utcMonday.ceil(week) : utcMonday(week); - week = utcDay.offset(week, (d.V - 1) * 7); - d.y = week.getUTCFullYear(); - d.m = week.getUTCMonth(); - d.d = week.getUTCDate() + (d.w + 6) % 7; - } else { - week = localDate(newDate(d.y, 0, 1)), day$1 = week.getDay(); - week = day$1 > 4 || day$1 === 0 ? monday.ceil(week) : monday(week); - week = day.offset(week, (d.V - 1) * 7); - d.y = week.getFullYear(); - d.m = week.getMonth(); - d.d = week.getDate() + (d.w + 6) % 7; - } - } else if ("W" in d || "U" in d) { - if (!("w" in d)) d.w = "u" in d ? d.u % 7 : "W" in d ? 1 : 0; - day$1 = "Z" in d ? utcDate(newDate(d.y, 0, 1)).getUTCDay() : localDate(newDate(d.y, 0, 1)).getDay(); - d.m = 0; - d.d = "W" in d ? (d.w + 6) % 7 + d.W * 7 - (day$1 + 5) % 7 : d.w + d.U * 7 - (day$1 + 6) % 7; - } - - // If a time zone is specified, all fields are interpreted as UTC and then - // offset according to the specified time zone. - if ("Z" in d) { - d.H += d.Z / 100 | 0; - d.M += d.Z % 100; - return utcDate(d); - } - - // Otherwise, all fields are in local time. - return localDate(d); - }; - } - - function parseSpecifier(d, specifier, string, j) { - var i = 0, - n = specifier.length, - m = string.length, - c, - parse; - - while (i < n) { - if (j >= m) return -1; - c = specifier.charCodeAt(i++); - if (c === 37) { - c = specifier.charAt(i++); - parse = parses[c in pads ? specifier.charAt(i++) : c]; - if (!parse || ((j = parse(d, string, j)) < 0)) return -1; - } else if (c != string.charCodeAt(j++)) { - return -1; - } - } - - return j; - } - - function parsePeriod(d, string, i) { - var n = periodRe.exec(string.slice(i)); - return n ? (d.p = periodLookup[n[0].toLowerCase()], i + n[0].length) : -1; - } - - function parseShortWeekday(d, string, i) { - var n = shortWeekdayRe.exec(string.slice(i)); - return n ? (d.w = shortWeekdayLookup[n[0].toLowerCase()], i + n[0].length) : -1; - } - - function parseWeekday(d, string, i) { - var n = weekdayRe.exec(string.slice(i)); - return n ? (d.w = weekdayLookup[n[0].toLowerCase()], i + n[0].length) : -1; - } - - function parseShortMonth(d, string, i) { - var n = shortMonthRe.exec(string.slice(i)); - return n ? (d.m = shortMonthLookup[n[0].toLowerCase()], i + n[0].length) : -1; - } - - function parseMonth(d, string, i) { - var n = monthRe.exec(string.slice(i)); - return n ? (d.m = monthLookup[n[0].toLowerCase()], i + n[0].length) : -1; - } - - function parseLocaleDateTime(d, string, i) { - return parseSpecifier(d, locale_dateTime, string, i); - } - - function parseLocaleDate(d, string, i) { - return parseSpecifier(d, locale_date, string, i); - } - - function parseLocaleTime(d, string, i) { - return parseSpecifier(d, locale_time, string, i); - } - - function formatShortWeekday(d) { - return locale_shortWeekdays[d.getDay()]; - } - - function formatWeekday(d) { - return locale_weekdays[d.getDay()]; - } - - function formatShortMonth(d) { - return locale_shortMonths[d.getMonth()]; - } - - function formatMonth(d) { - return locale_months[d.getMonth()]; - } - - function formatPeriod(d) { - return locale_periods[+(d.getHours() >= 12)]; - } - - function formatQuarter(d) { - return 1 + ~~(d.getMonth() / 3); - } - - function formatUTCShortWeekday(d) { - return locale_shortWeekdays[d.getUTCDay()]; - } - - function formatUTCWeekday(d) { - return locale_weekdays[d.getUTCDay()]; - } - - function formatUTCShortMonth(d) { - return locale_shortMonths[d.getUTCMonth()]; - } - - function formatUTCMonth(d) { - return locale_months[d.getUTCMonth()]; - } - - function formatUTCPeriod(d) { - return locale_periods[+(d.getUTCHours() >= 12)]; - } - - function formatUTCQuarter(d) { - return 1 + ~~(d.getUTCMonth() / 3); - } - - return { - format: function(specifier) { - var f = newFormat(specifier += "", formats); - f.toString = function() { return specifier; }; - return f; - }, - parse: function(specifier) { - var p = newParse(specifier += "", false); - p.toString = function() { return specifier; }; - return p; - }, - utcFormat: function(specifier) { - var f = newFormat(specifier += "", utcFormats); - f.toString = function() { return specifier; }; - return f; - }, - utcParse: function(specifier) { - var p = newParse(specifier += "", true); - p.toString = function() { return specifier; }; - return p; - } - }; - } - - var pads = {"-": "", "_": " ", "0": "0"}, - numberRe = /^\s*\d+/, // note: ignores next directive - percentRe = /^%/, - requoteRe = /[\\^$*+?|[\]().{}]/g; - - function pad(value, fill, width) { - var sign = value < 0 ? "-" : "", - string = (sign ? -value : value) + "", - length = string.length; - return sign + (length < width ? new Array(width - length + 1).join(fill) + string : string); - } - - function requote(s) { - return s.replace(requoteRe, "\\$&"); - } - - function formatRe(names) { - return new RegExp("^(?:" + names.map(requote).join("|") + ")", "i"); - } - - function formatLookup(names) { - var map = {}, i = -1, n = names.length; - while (++i < n) map[names[i].toLowerCase()] = i; - return map; - } - - function parseWeekdayNumberSunday(d, string, i) { - var n = numberRe.exec(string.slice(i, i + 1)); - return n ? (d.w = +n[0], i + n[0].length) : -1; - } - - function parseWeekdayNumberMonday(d, string, i) { - var n = numberRe.exec(string.slice(i, i + 1)); - return n ? (d.u = +n[0], i + n[0].length) : -1; - } - - function parseWeekNumberSunday(d, string, i) { - var n = numberRe.exec(string.slice(i, i + 2)); - return n ? (d.U = +n[0], i + n[0].length) : -1; - } - - function parseWeekNumberISO(d, string, i) { - var n = numberRe.exec(string.slice(i, i + 2)); - return n ? (d.V = +n[0], i + n[0].length) : -1; - } - - function parseWeekNumberMonday(d, string, i) { - var n = numberRe.exec(string.slice(i, i + 2)); - return n ? (d.W = +n[0], i + n[0].length) : -1; - } - - function parseFullYear(d, string, i) { - var n = numberRe.exec(string.slice(i, i + 4)); - return n ? (d.y = +n[0], i + n[0].length) : -1; - } - - function parseYear(d, string, i) { - var n = numberRe.exec(string.slice(i, i + 2)); - return n ? (d.y = +n[0] + (+n[0] > 68 ? 1900 : 2000), i + n[0].length) : -1; - } - - function parseZone(d, string, i) { - var n = /^(Z)|([+-]\d\d)(?::?(\d\d))?/.exec(string.slice(i, i + 6)); - return n ? (d.Z = n[1] ? 0 : -(n[2] + (n[3] || "00")), i + n[0].length) : -1; - } - - function parseQuarter(d, string, i) { - var n = numberRe.exec(string.slice(i, i + 1)); - return n ? (d.q = n[0] * 3 - 3, i + n[0].length) : -1; - } - - function parseMonthNumber(d, string, i) { - var n = numberRe.exec(string.slice(i, i + 2)); - return n ? (d.m = n[0] - 1, i + n[0].length) : -1; - } - - function parseDayOfMonth(d, string, i) { - var n = numberRe.exec(string.slice(i, i + 2)); - return n ? (d.d = +n[0], i + n[0].length) : -1; - } - - function parseDayOfYear(d, string, i) { - var n = numberRe.exec(string.slice(i, i + 3)); - return n ? (d.m = 0, d.d = +n[0], i + n[0].length) : -1; - } - - function parseHour24(d, string, i) { - var n = numberRe.exec(string.slice(i, i + 2)); - return n ? (d.H = +n[0], i + n[0].length) : -1; - } - - function parseMinutes(d, string, i) { - var n = numberRe.exec(string.slice(i, i + 2)); - return n ? (d.M = +n[0], i + n[0].length) : -1; - } - - function parseSeconds(d, string, i) { - var n = numberRe.exec(string.slice(i, i + 2)); - return n ? (d.S = +n[0], i + n[0].length) : -1; - } - - function parseMilliseconds(d, string, i) { - var n = numberRe.exec(string.slice(i, i + 3)); - return n ? (d.L = +n[0], i + n[0].length) : -1; - } - - function parseMicroseconds(d, string, i) { - var n = numberRe.exec(string.slice(i, i + 6)); - return n ? (d.L = Math.floor(n[0] / 1000), i + n[0].length) : -1; - } - - function parseLiteralPercent(d, string, i) { - var n = percentRe.exec(string.slice(i, i + 1)); - return n ? i + n[0].length : -1; - } - - function parseUnixTimestamp(d, string, i) { - var n = numberRe.exec(string.slice(i)); - return n ? (d.Q = +n[0], i + n[0].length) : -1; - } - - function parseUnixTimestampSeconds(d, string, i) { - var n = numberRe.exec(string.slice(i)); - return n ? (d.s = +n[0], i + n[0].length) : -1; - } - - function formatDayOfMonth(d, p) { - return pad(d.getDate(), p, 2); - } - - function formatHour24(d, p) { - return pad(d.getHours(), p, 2); - } - - function formatHour12(d, p) { - return pad(d.getHours() % 12 || 12, p, 2); - } - - function formatDayOfYear(d, p) { - return pad(1 + day.count(year(d), d), p, 3); - } - - function formatMilliseconds(d, p) { - return pad(d.getMilliseconds(), p, 3); - } - - function formatMicroseconds(d, p) { - return formatMilliseconds(d, p) + "000"; - } - - function formatMonthNumber(d, p) { - return pad(d.getMonth() + 1, p, 2); - } - - function formatMinutes(d, p) { - return pad(d.getMinutes(), p, 2); - } - - function formatSeconds(d, p) { - return pad(d.getSeconds(), p, 2); - } - - function formatWeekdayNumberMonday(d) { - var day = d.getDay(); - return day === 0 ? 7 : day; - } - - function formatWeekNumberSunday(d, p) { - return pad(sunday.count(year(d) - 1, d), p, 2); - } - - function formatWeekNumberISO(d, p) { - var day = d.getDay(); - d = (day >= 4 || day === 0) ? thursday(d) : thursday.ceil(d); - return pad(thursday.count(year(d), d) + (year(d).getDay() === 4), p, 2); - } - - function formatWeekdayNumberSunday(d) { - return d.getDay(); - } - - function formatWeekNumberMonday(d, p) { - return pad(monday.count(year(d) - 1, d), p, 2); - } - - function formatYear(d, p) { - return pad(d.getFullYear() % 100, p, 2); - } - - function formatFullYear(d, p) { - return pad(d.getFullYear() % 10000, p, 4); - } - - function formatZone(d) { - var z = d.getTimezoneOffset(); - return (z > 0 ? "-" : (z *= -1, "+")) - + pad(z / 60 | 0, "0", 2) - + pad(z % 60, "0", 2); - } - - function formatUTCDayOfMonth(d, p) { - return pad(d.getUTCDate(), p, 2); - } - - function formatUTCHour24(d, p) { - return pad(d.getUTCHours(), p, 2); - } - - function formatUTCHour12(d, p) { - return pad(d.getUTCHours() % 12 || 12, p, 2); - } - - function formatUTCDayOfYear(d, p) { - return pad(1 + utcDay.count(utcYear(d), d), p, 3); - } - - function formatUTCMilliseconds(d, p) { - return pad(d.getUTCMilliseconds(), p, 3); - } - - function formatUTCMicroseconds(d, p) { - return formatUTCMilliseconds(d, p) + "000"; - } - - function formatUTCMonthNumber(d, p) { - return pad(d.getUTCMonth() + 1, p, 2); - } - - function formatUTCMinutes(d, p) { - return pad(d.getUTCMinutes(), p, 2); - } - - function formatUTCSeconds(d, p) { - return pad(d.getUTCSeconds(), p, 2); - } - - function formatUTCWeekdayNumberMonday(d) { - var dow = d.getUTCDay(); - return dow === 0 ? 7 : dow; - } - - function formatUTCWeekNumberSunday(d, p) { - return pad(utcSunday.count(utcYear(d) - 1, d), p, 2); - } - - function formatUTCWeekNumberISO(d, p) { - var day = d.getUTCDay(); - d = (day >= 4 || day === 0) ? utcThursday(d) : utcThursday.ceil(d); - return pad(utcThursday.count(utcYear(d), d) + (utcYear(d).getUTCDay() === 4), p, 2); - } - - function formatUTCWeekdayNumberSunday(d) { - return d.getUTCDay(); - } - - function formatUTCWeekNumberMonday(d, p) { - return pad(utcMonday.count(utcYear(d) - 1, d), p, 2); - } - - function formatUTCYear(d, p) { - return pad(d.getUTCFullYear() % 100, p, 2); - } - - function formatUTCFullYear(d, p) { - return pad(d.getUTCFullYear() % 10000, p, 4); - } - - function formatUTCZone() { - return "+0000"; - } - - function formatLiteralPercent() { - return "%"; - } - - function formatUnixTimestamp(d) { - return +d; - } - - function formatUnixTimestampSeconds(d) { - return Math.floor(+d / 1000); - } - - var locale$1; - var timeFormat; - var timeParse; - var utcFormat; - var utcParse; - - defaultLocale$1({ - dateTime: "%x, %X", - date: "%-m/%-d/%Y", - time: "%-I:%M:%S %p", - periods: ["AM", "PM"], - days: ["Sunday", "Monday", "Tuesday", "Wednesday", "Thursday", "Friday", "Saturday"], - shortDays: ["Sun", "Mon", "Tue", "Wed", "Thu", "Fri", "Sat"], - months: ["January", "February", "March", "April", "May", "June", "July", "August", "September", "October", "November", "December"], - shortMonths: ["Jan", "Feb", "Mar", "Apr", "May", "Jun", "Jul", "Aug", "Sep", "Oct", "Nov", "Dec"] - }); - - function defaultLocale$1(definition) { - locale$1 = formatLocale$1(definition); - timeFormat = locale$1.format; - timeParse = locale$1.parse; - utcFormat = locale$1.utcFormat; - utcParse = locale$1.utcParse; - return locale$1; - } - - var isoSpecifier = "%Y-%m-%dT%H:%M:%S.%LZ"; - - function formatIsoNative(date) { - return date.toISOString(); - } - - var formatIso = Date.prototype.toISOString - ? formatIsoNative - : utcFormat(isoSpecifier); - - function parseIsoNative(string) { - var date = new Date(string); - return isNaN(date) ? null : date; - } - - var parseIso = +new Date("2000-01-01T00:00:00.000Z") - ? parseIsoNative - : utcParse(isoSpecifier); - - var noop = {value: function() {}}; - - function dispatch() { - for (var i = 0, n = arguments.length, _ = {}, t; i < n; ++i) { - if (!(t = arguments[i] + "") || (t in _) || /[\s.]/.test(t)) throw new Error("illegal type: " + t); - _[t] = []; - } - return new Dispatch(_); - } - - function Dispatch(_) { - this._ = _; - } - - function parseTypenames(typenames, types) { - return typenames.trim().split(/^|\s+/).map(function(t) { - var name = "", i = t.indexOf("."); - if (i >= 0) name = t.slice(i + 1), t = t.slice(0, i); - if (t && !types.hasOwnProperty(t)) throw new Error("unknown type: " + t); - return {type: t, name: name}; - }); - } - - Dispatch.prototype = dispatch.prototype = { - constructor: Dispatch, - on: function(typename, callback) { - var _ = this._, - T = parseTypenames(typename + "", _), - t, - i = -1, - n = T.length; - - // If no callback was specified, return the callback of the given type and name. - if (arguments.length < 2) { - while (++i < n) if ((t = (typename = T[i]).type) && (t = get(_[t], typename.name))) return t; - return; - } - - // If a type was specified, set the callback for the given type and name. - // Otherwise, if a null callback was specified, remove callbacks of the given name. - if (callback != null && typeof callback !== "function") throw new Error("invalid callback: " + callback); - while (++i < n) { - if (t = (typename = T[i]).type) _[t] = set(_[t], typename.name, callback); - else if (callback == null) for (t in _) _[t] = set(_[t], typename.name, null); - } - - return this; - }, - copy: function() { - var copy = {}, _ = this._; - for (var t in _) copy[t] = _[t].slice(); - return new Dispatch(copy); - }, - call: function(type, that) { - if ((n = arguments.length - 2) > 0) for (var args = new Array(n), i = 0, n, t; i < n; ++i) args[i] = arguments[i + 2]; - if (!this._.hasOwnProperty(type)) throw new Error("unknown type: " + type); - for (t = this._[type], i = 0, n = t.length; i < n; ++i) t[i].value.apply(that, args); - }, - apply: function(type, that, args) { - if (!this._.hasOwnProperty(type)) throw new Error("unknown type: " + type); - for (var t = this._[type], i = 0, n = t.length; i < n; ++i) t[i].value.apply(that, args); - } - }; - - function get(type, name) { - for (var i = 0, n = type.length, c; i < n; ++i) { - if ((c = type[i]).name === name) { - return c.value; - } - } - } - - function set(type, name, callback) { - for (var i = 0, n = type.length; i < n; ++i) { - if (type[i].name === name) { - type[i] = noop, type = type.slice(0, i).concat(type.slice(i + 1)); - break; - } - } - if (callback != null) type.push({name: name, value: callback}); - return type; - } - - var xhtml = "http://www.w3.org/1999/xhtml"; - - var namespaces = { - svg: "http://www.w3.org/2000/svg", - xhtml: xhtml, - xlink: "http://www.w3.org/1999/xlink", - xml: "http://www.w3.org/XML/1998/namespace", - xmlns: "http://www.w3.org/2000/xmlns/" - }; - - function namespace(name) { - var prefix = name += "", i = prefix.indexOf(":"); - if (i >= 0 && (prefix = name.slice(0, i)) !== "xmlns") name = name.slice(i + 1); - return namespaces.hasOwnProperty(prefix) ? {space: namespaces[prefix], local: name} : name; - } - - function creatorInherit(name) { - return function() { - var document = this.ownerDocument, - uri = this.namespaceURI; - return uri === xhtml && document.documentElement.namespaceURI === xhtml - ? document.createElement(name) - : document.createElementNS(uri, name); - }; - } - - function creatorFixed(fullname) { - return function() { - return this.ownerDocument.createElementNS(fullname.space, fullname.local); - }; - } - - function creator(name) { - var fullname = namespace(name); - return (fullname.local - ? creatorFixed - : creatorInherit)(fullname); - } - - function none() {} - - function selector(selector) { - return selector == null ? none : function() { - return this.querySelector(selector); - }; - } - - function selection_select(select) { - if (typeof select !== "function") select = selector(select); - - for (var groups = this._groups, m = groups.length, subgroups = new Array(m), j = 0; j < m; ++j) { - for (var group = groups[j], n = group.length, subgroup = subgroups[j] = new Array(n), node, subnode, i = 0; i < n; ++i) { - if ((node = group[i]) && (subnode = select.call(node, node.__data__, i, group))) { - if ("__data__" in node) subnode.__data__ = node.__data__; - subgroup[i] = subnode; - } - } - } - - return new Selection(subgroups, this._parents); - } - - function empty() { - return []; - } - - function selectorAll(selector) { - return selector == null ? empty : function() { - return this.querySelectorAll(selector); - }; - } - - function selection_selectAll(select) { - if (typeof select !== "function") select = selectorAll(select); - - for (var groups = this._groups, m = groups.length, subgroups = [], parents = [], j = 0; j < m; ++j) { - for (var group = groups[j], n = group.length, node, i = 0; i < n; ++i) { - if (node = group[i]) { - subgroups.push(select.call(node, node.__data__, i, group)); - parents.push(node); - } - } - } - - return new Selection(subgroups, parents); - } - - function matcher(selector) { - return function() { - return this.matches(selector); - }; - } - - function selection_filter(match) { - if (typeof match !== "function") match = matcher(match); - - for (var groups = this._groups, m = groups.length, subgroups = new Array(m), j = 0; j < m; ++j) { - for (var group = groups[j], n = group.length, subgroup = subgroups[j] = [], node, i = 0; i < n; ++i) { - if ((node = group[i]) && match.call(node, node.__data__, i, group)) { - subgroup.push(node); - } - } - } - - return new Selection(subgroups, this._parents); - } - - function sparse(update) { - return new Array(update.length); - } - - function selection_enter() { - return new Selection(this._enter || this._groups.map(sparse), this._parents); - } - - function EnterNode(parent, datum) { - this.ownerDocument = parent.ownerDocument; - this.namespaceURI = parent.namespaceURI; - this._next = null; - this._parent = parent; - this.__data__ = datum; - } - - EnterNode.prototype = { - constructor: EnterNode, - appendChild: function(child) { return this._parent.insertBefore(child, this._next); }, - insertBefore: function(child, next) { return this._parent.insertBefore(child, next); }, - querySelector: function(selector) { return this._parent.querySelector(selector); }, - querySelectorAll: function(selector) { return this._parent.querySelectorAll(selector); } - }; - - function constant$2(x) { - return function() { - return x; - }; - } - - var keyPrefix = "$"; // Protect against keys like “__proto__”. - - function bindIndex(parent, group, enter, update, exit, data) { - var i = 0, - node, - groupLength = group.length, - dataLength = data.length; - - // Put any non-null nodes that fit into update. - // Put any null nodes into enter. - // Put any remaining data into enter. - for (; i < dataLength; ++i) { - if (node = group[i]) { - node.__data__ = data[i]; - update[i] = node; - } else { - enter[i] = new EnterNode(parent, data[i]); - } - } - - // Put any non-null nodes that don’t fit into exit. - for (; i < groupLength; ++i) { - if (node = group[i]) { - exit[i] = node; - } - } - } - - function bindKey(parent, group, enter, update, exit, data, key) { - var i, - node, - nodeByKeyValue = {}, - groupLength = group.length, - dataLength = data.length, - keyValues = new Array(groupLength), - keyValue; - - // Compute the key for each node. - // If multiple nodes have the same key, the duplicates are added to exit. - for (i = 0; i < groupLength; ++i) { - if (node = group[i]) { - keyValues[i] = keyValue = keyPrefix + key.call(node, node.__data__, i, group); - if (keyValue in nodeByKeyValue) { - exit[i] = node; - } else { - nodeByKeyValue[keyValue] = node; - } - } - } - - // Compute the key for each datum. - // If there a node associated with this key, join and add it to update. - // If there is not (or the key is a duplicate), add it to enter. - for (i = 0; i < dataLength; ++i) { - keyValue = keyPrefix + key.call(parent, data[i], i, data); - if (node = nodeByKeyValue[keyValue]) { - update[i] = node; - node.__data__ = data[i]; - nodeByKeyValue[keyValue] = null; - } else { - enter[i] = new EnterNode(parent, data[i]); - } - } - - // Add any remaining nodes that were not bound to data to exit. - for (i = 0; i < groupLength; ++i) { - if ((node = group[i]) && (nodeByKeyValue[keyValues[i]] === node)) { - exit[i] = node; - } - } - } - - function selection_data(value, key) { - if (!value) { - data = new Array(this.size()), j = -1; - this.each(function(d) { data[++j] = d; }); - return data; - } - - var bind = key ? bindKey : bindIndex, - parents = this._parents, - groups = this._groups; - - if (typeof value !== "function") value = constant$2(value); - - for (var m = groups.length, update = new Array(m), enter = new Array(m), exit = new Array(m), j = 0; j < m; ++j) { - var parent = parents[j], - group = groups[j], - groupLength = group.length, - data = value.call(parent, parent && parent.__data__, j, parents), - dataLength = data.length, - enterGroup = enter[j] = new Array(dataLength), - updateGroup = update[j] = new Array(dataLength), - exitGroup = exit[j] = new Array(groupLength); - - bind(parent, group, enterGroup, updateGroup, exitGroup, data, key); - - // Now connect the enter nodes to their following update node, such that - // appendChild can insert the materialized enter node before this node, - // rather than at the end of the parent node. - for (var i0 = 0, i1 = 0, previous, next; i0 < dataLength; ++i0) { - if (previous = enterGroup[i0]) { - if (i0 >= i1) i1 = i0 + 1; - while (!(next = updateGroup[i1]) && ++i1 < dataLength); - previous._next = next || null; - } - } - } - - update = new Selection(update, parents); - update._enter = enter; - update._exit = exit; - return update; - } - - function selection_exit() { - return new Selection(this._exit || this._groups.map(sparse), this._parents); - } - - function selection_join(onenter, onupdate, onexit) { - var enter = this.enter(), update = this, exit = this.exit(); - enter = typeof onenter === "function" ? onenter(enter) : enter.append(onenter + ""); - if (onupdate != null) update = onupdate(update); - if (onexit == null) exit.remove(); else onexit(exit); - return enter && update ? enter.merge(update).order() : update; - } - - function selection_merge(selection) { - - for (var groups0 = this._groups, groups1 = selection._groups, m0 = groups0.length, m1 = groups1.length, m = Math.min(m0, m1), merges = new Array(m0), j = 0; j < m; ++j) { - for (var group0 = groups0[j], group1 = groups1[j], n = group0.length, merge = merges[j] = new Array(n), node, i = 0; i < n; ++i) { - if (node = group0[i] || group1[i]) { - merge[i] = node; - } - } - } - - for (; j < m0; ++j) { - merges[j] = groups0[j]; - } - - return new Selection(merges, this._parents); - } - - function selection_order() { - - for (var groups = this._groups, j = -1, m = groups.length; ++j < m;) { - for (var group = groups[j], i = group.length - 1, next = group[i], node; --i >= 0;) { - if (node = group[i]) { - if (next && node.compareDocumentPosition(next) ^ 4) next.parentNode.insertBefore(node, next); - next = node; - } - } - } - - return this; - } - - function selection_sort(compare) { - if (!compare) compare = ascending$1; - - function compareNode(a, b) { - return a && b ? compare(a.__data__, b.__data__) : !a - !b; - } - - for (var groups = this._groups, m = groups.length, sortgroups = new Array(m), j = 0; j < m; ++j) { - for (var group = groups[j], n = group.length, sortgroup = sortgroups[j] = new Array(n), node, i = 0; i < n; ++i) { - if (node = group[i]) { - sortgroup[i] = node; - } - } - sortgroup.sort(compareNode); - } - - return new Selection(sortgroups, this._parents).order(); - } - - function ascending$1(a, b) { - return a < b ? -1 : a > b ? 1 : a >= b ? 0 : NaN; - } - - function selection_call() { - var callback = arguments[0]; - arguments[0] = this; - callback.apply(null, arguments); - return this; - } - - function selection_nodes() { - var nodes = new Array(this.size()), i = -1; - this.each(function() { nodes[++i] = this; }); - return nodes; - } - - function selection_node() { - - for (var groups = this._groups, j = 0, m = groups.length; j < m; ++j) { - for (var group = groups[j], i = 0, n = group.length; i < n; ++i) { - var node = group[i]; - if (node) return node; - } - } - - return null; - } - - function selection_size() { - var size = 0; - this.each(function() { ++size; }); - return size; - } - - function selection_empty() { - return !this.node(); - } - - function selection_each(callback) { - - for (var groups = this._groups, j = 0, m = groups.length; j < m; ++j) { - for (var group = groups[j], i = 0, n = group.length, node; i < n; ++i) { - if (node = group[i]) callback.call(node, node.__data__, i, group); - } - } - - return this; - } - - function attrRemove(name) { - return function() { - this.removeAttribute(name); - }; - } - - function attrRemoveNS(fullname) { - return function() { - this.removeAttributeNS(fullname.space, fullname.local); - }; - } - - function attrConstant(name, value) { - return function() { - this.setAttribute(name, value); - }; - } - - function attrConstantNS(fullname, value) { - return function() { - this.setAttributeNS(fullname.space, fullname.local, value); - }; - } - - function attrFunction(name, value) { - return function() { - var v = value.apply(this, arguments); - if (v == null) this.removeAttribute(name); - else this.setAttribute(name, v); - }; - } - - function attrFunctionNS(fullname, value) { - return function() { - var v = value.apply(this, arguments); - if (v == null) this.removeAttributeNS(fullname.space, fullname.local); - else this.setAttributeNS(fullname.space, fullname.local, v); - }; - } - - function selection_attr(name, value) { - var fullname = namespace(name); - - if (arguments.length < 2) { - var node = this.node(); - return fullname.local - ? node.getAttributeNS(fullname.space, fullname.local) - : node.getAttribute(fullname); - } - - return this.each((value == null - ? (fullname.local ? attrRemoveNS : attrRemove) : (typeof value === "function" - ? (fullname.local ? attrFunctionNS : attrFunction) - : (fullname.local ? attrConstantNS : attrConstant)))(fullname, value)); - } - - function defaultView(node) { - return (node.ownerDocument && node.ownerDocument.defaultView) // node is a Node - || (node.document && node) // node is a Window - || node.defaultView; // node is a Document - } - - function styleRemove(name) { - return function() { - this.style.removeProperty(name); - }; - } - - function styleConstant(name, value, priority) { - return function() { - this.style.setProperty(name, value, priority); - }; - } - - function styleFunction(name, value, priority) { - return function() { - var v = value.apply(this, arguments); - if (v == null) this.style.removeProperty(name); - else this.style.setProperty(name, v, priority); - }; - } - - function selection_style(name, value, priority) { - return arguments.length > 1 - ? this.each((value == null - ? styleRemove : typeof value === "function" - ? styleFunction - : styleConstant)(name, value, priority == null ? "" : priority)) - : styleValue(this.node(), name); - } - - function styleValue(node, name) { - return node.style.getPropertyValue(name) - || defaultView(node).getComputedStyle(node, null).getPropertyValue(name); - } - - function propertyRemove(name) { - return function() { - delete this[name]; - }; - } - - function propertyConstant(name, value) { - return function() { - this[name] = value; - }; - } - - function propertyFunction(name, value) { - return function() { - var v = value.apply(this, arguments); - if (v == null) delete this[name]; - else this[name] = v; - }; - } - - function selection_property(name, value) { - return arguments.length > 1 - ? this.each((value == null - ? propertyRemove : typeof value === "function" - ? propertyFunction - : propertyConstant)(name, value)) - : this.node()[name]; - } - - function classArray(string) { - return string.trim().split(/^|\s+/); - } - - function classList(node) { - return node.classList || new ClassList(node); - } - - function ClassList(node) { - this._node = node; - this._names = classArray(node.getAttribute("class") || ""); - } - - ClassList.prototype = { - add: function(name) { - var i = this._names.indexOf(name); - if (i < 0) { - this._names.push(name); - this._node.setAttribute("class", this._names.join(" ")); - } - }, - remove: function(name) { - var i = this._names.indexOf(name); - if (i >= 0) { - this._names.splice(i, 1); - this._node.setAttribute("class", this._names.join(" ")); - } - }, - contains: function(name) { - return this._names.indexOf(name) >= 0; - } - }; - - function classedAdd(node, names) { - var list = classList(node), i = -1, n = names.length; - while (++i < n) list.add(names[i]); - } - - function classedRemove(node, names) { - var list = classList(node), i = -1, n = names.length; - while (++i < n) list.remove(names[i]); - } - - function classedTrue(names) { - return function() { - classedAdd(this, names); - }; - } - - function classedFalse(names) { - return function() { - classedRemove(this, names); - }; - } - - function classedFunction(names, value) { - return function() { - (value.apply(this, arguments) ? classedAdd : classedRemove)(this, names); - }; - } - - function selection_classed(name, value) { - var names = classArray(name + ""); - - if (arguments.length < 2) { - var list = classList(this.node()), i = -1, n = names.length; - while (++i < n) if (!list.contains(names[i])) return false; - return true; - } - - return this.each((typeof value === "function" - ? classedFunction : value - ? classedTrue - : classedFalse)(names, value)); - } - - function textRemove() { - this.textContent = ""; - } - - function textConstant(value) { - return function() { - this.textContent = value; - }; - } - - function textFunction(value) { - return function() { - var v = value.apply(this, arguments); - this.textContent = v == null ? "" : v; - }; - } - - function selection_text(value) { - return arguments.length - ? this.each(value == null - ? textRemove : (typeof value === "function" - ? textFunction - : textConstant)(value)) - : this.node().textContent; - } - - function htmlRemove() { - this.innerHTML = ""; - } - - function htmlConstant(value) { - return function() { - this.innerHTML = value; - }; - } - - function htmlFunction(value) { - return function() { - var v = value.apply(this, arguments); - this.innerHTML = v == null ? "" : v; - }; - } - - function selection_html(value) { - return arguments.length - ? this.each(value == null - ? htmlRemove : (typeof value === "function" - ? htmlFunction - : htmlConstant)(value)) - : this.node().innerHTML; - } - - function raise() { - if (this.nextSibling) this.parentNode.appendChild(this); - } - - function selection_raise() { - return this.each(raise); - } - - function lower() { - if (this.previousSibling) this.parentNode.insertBefore(this, this.parentNode.firstChild); - } - - function selection_lower() { - return this.each(lower); - } - - function selection_append(name) { - var create = typeof name === "function" ? name : creator(name); - return this.select(function() { - return this.appendChild(create.apply(this, arguments)); - }); - } - - function constantNull() { - return null; - } - - function selection_insert(name, before) { - var create = typeof name === "function" ? name : creator(name), - select = before == null ? constantNull : typeof before === "function" ? before : selector(before); - return this.select(function() { - return this.insertBefore(create.apply(this, arguments), select.apply(this, arguments) || null); - }); - } - - function remove() { - var parent = this.parentNode; - if (parent) parent.removeChild(this); - } - - function selection_remove() { - return this.each(remove); - } - - function selection_cloneShallow() { - var clone = this.cloneNode(false), parent = this.parentNode; - return parent ? parent.insertBefore(clone, this.nextSibling) : clone; - } - - function selection_cloneDeep() { - var clone = this.cloneNode(true), parent = this.parentNode; - return parent ? parent.insertBefore(clone, this.nextSibling) : clone; - } - - function selection_clone(deep) { - return this.select(deep ? selection_cloneDeep : selection_cloneShallow); - } - - function selection_datum(value) { - return arguments.length - ? this.property("__data__", value) - : this.node().__data__; - } - - var filterEvents = {}; - - var event = null; - - if (typeof document !== "undefined") { - var element = document.documentElement; - if (!("onmouseenter" in element)) { - filterEvents = {mouseenter: "mouseover", mouseleave: "mouseout"}; - } - } - - function filterContextListener(listener, index, group) { - listener = contextListener(listener, index, group); - return function(event) { - var related = event.relatedTarget; - if (!related || (related !== this && !(related.compareDocumentPosition(this) & 8))) { - listener.call(this, event); - } - }; - } - - function contextListener(listener, index, group) { - return function(event1) { - var event0 = event; // Events can be reentrant (e.g., focus). - event = event1; - try { - listener.call(this, this.__data__, index, group); - } finally { - event = event0; - } - }; - } - - function parseTypenames$1(typenames) { - return typenames.trim().split(/^|\s+/).map(function(t) { - var name = "", i = t.indexOf("."); - if (i >= 0) name = t.slice(i + 1), t = t.slice(0, i); - return {type: t, name: name}; - }); - } - - function onRemove(typename) { - return function() { - var on = this.__on; - if (!on) return; - for (var j = 0, i = -1, m = on.length, o; j < m; ++j) { - if (o = on[j], (!typename.type || o.type === typename.type) && o.name === typename.name) { - this.removeEventListener(o.type, o.listener, o.capture); - } else { - on[++i] = o; - } - } - if (++i) on.length = i; - else delete this.__on; - }; - } - - function onAdd(typename, value, capture) { - var wrap = filterEvents.hasOwnProperty(typename.type) ? filterContextListener : contextListener; - return function(d, i, group) { - var on = this.__on, o, listener = wrap(value, i, group); - if (on) for (var j = 0, m = on.length; j < m; ++j) { - if ((o = on[j]).type === typename.type && o.name === typename.name) { - this.removeEventListener(o.type, o.listener, o.capture); - this.addEventListener(o.type, o.listener = listener, o.capture = capture); - o.value = value; - return; - } - } - this.addEventListener(typename.type, listener, capture); - o = {type: typename.type, name: typename.name, value: value, listener: listener, capture: capture}; - if (!on) this.__on = [o]; - else on.push(o); - }; - } - - function selection_on(typename, value, capture) { - var typenames = parseTypenames$1(typename + ""), i, n = typenames.length, t; - - if (arguments.length < 2) { - var on = this.node().__on; - if (on) for (var j = 0, m = on.length, o; j < m; ++j) { - for (i = 0, o = on[j]; i < n; ++i) { - if ((t = typenames[i]).type === o.type && t.name === o.name) { - return o.value; - } - } - } - return; - } - - on = value ? onAdd : onRemove; - if (capture == null) capture = false; - for (i = 0; i < n; ++i) this.each(on(typenames[i], value, capture)); - return this; - } - - function customEvent(event1, listener, that, args) { - var event0 = event; - event1.sourceEvent = event; - event = event1; - try { - return listener.apply(that, args); - } finally { - event = event0; - } - } - - function dispatchEvent(node, type, params) { - var window = defaultView(node), - event = window.CustomEvent; - - if (typeof event === "function") { - event = new event(type, params); - } else { - event = window.document.createEvent("Event"); - if (params) event.initEvent(type, params.bubbles, params.cancelable), event.detail = params.detail; - else event.initEvent(type, false, false); - } - - node.dispatchEvent(event); - } - - function dispatchConstant(type, params) { - return function() { - return dispatchEvent(this, type, params); - }; - } - - function dispatchFunction(type, params) { - return function() { - return dispatchEvent(this, type, params.apply(this, arguments)); - }; - } - - function selection_dispatch(type, params) { - return this.each((typeof params === "function" - ? dispatchFunction - : dispatchConstant)(type, params)); - } - - var root = [null]; - - function Selection(groups, parents) { - this._groups = groups; - this._parents = parents; - } - - function selection() { - return new Selection([[document.documentElement]], root); - } - - Selection.prototype = selection.prototype = { - constructor: Selection, - select: selection_select, - selectAll: selection_selectAll, - filter: selection_filter, - data: selection_data, - enter: selection_enter, - exit: selection_exit, - join: selection_join, - merge: selection_merge, - order: selection_order, - sort: selection_sort, - call: selection_call, - nodes: selection_nodes, - node: selection_node, - size: selection_size, - empty: selection_empty, - each: selection_each, - attr: selection_attr, - style: selection_style, - property: selection_property, - classed: selection_classed, - text: selection_text, - html: selection_html, - raise: selection_raise, - lower: selection_lower, - append: selection_append, - insert: selection_insert, - remove: selection_remove, - clone: selection_clone, - datum: selection_datum, - on: selection_on, - dispatch: selection_dispatch - }; - - function select(selector) { - return typeof selector === "string" - ? new Selection([[document.querySelector(selector)]], [document.documentElement]) - : new Selection([[selector]], root); - } - - function sourceEvent() { - var current = event, source; - while (source = current.sourceEvent) current = source; - return current; - } - - function point(node, event) { - var svg = node.ownerSVGElement || node; - - if (svg.createSVGPoint) { - var point = svg.createSVGPoint(); - point.x = event.clientX, point.y = event.clientY; - point = point.matrixTransform(node.getScreenCTM().inverse()); - return [point.x, point.y]; - } - - var rect = node.getBoundingClientRect(); - return [event.clientX - rect.left - node.clientLeft, event.clientY - rect.top - node.clientTop]; - } - - function mouse(node) { - var event = sourceEvent(); - if (event.changedTouches) event = event.changedTouches[0]; - return point(node, event); - } - - function touch(node, touches, identifier) { - if (arguments.length < 3) identifier = touches, touches = sourceEvent().changedTouches; - - for (var i = 0, n = touches ? touches.length : 0, touch; i < n; ++i) { - if ((touch = touches[i]).identifier === identifier) { - return point(node, touch); - } - } - - return null; - } - - function nopropagation() { - event.stopImmediatePropagation(); - } - - function noevent() { - event.preventDefault(); - event.stopImmediatePropagation(); - } - - function nodrag(view) { - var root = view.document.documentElement, - selection = select(view).on("dragstart.drag", noevent, true); - if ("onselectstart" in root) { - selection.on("selectstart.drag", noevent, true); - } else { - root.__noselect = root.style.MozUserSelect; - root.style.MozUserSelect = "none"; - } - } - - function yesdrag(view, noclick) { - var root = view.document.documentElement, - selection = select(view).on("dragstart.drag", null); - if (noclick) { - selection.on("click.drag", noevent, true); - setTimeout(function() { selection.on("click.drag", null); }, 0); - } - if ("onselectstart" in root) { - selection.on("selectstart.drag", null); - } else { - root.style.MozUserSelect = root.__noselect; - delete root.__noselect; - } - } - - function constant$3(x) { - return function() { - return x; - }; - } - - function DragEvent(target, type, subject, id, active, x, y, dx, dy, dispatch) { - this.target = target; - this.type = type; - this.subject = subject; - this.identifier = id; - this.active = active; - this.x = x; - this.y = y; - this.dx = dx; - this.dy = dy; - this._ = dispatch; - } - - DragEvent.prototype.on = function() { - var value = this._.on.apply(this._, arguments); - return value === this._ ? this : value; - }; - - // Ignore right-click, since that should open the context menu. - function defaultFilter() { - return !event.ctrlKey && !event.button; - } - - function defaultContainer() { - return this.parentNode; - } - - function defaultSubject(d) { - return d == null ? {x: event.x, y: event.y} : d; - } - - function defaultTouchable() { - return navigator.maxTouchPoints || ("ontouchstart" in this); - } - - function drag() { - var filter = defaultFilter, - container = defaultContainer, - subject = defaultSubject, - touchable = defaultTouchable, - gestures = {}, - listeners = dispatch("start", "drag", "end"), - active = 0, - mousedownx, - mousedowny, - mousemoving, - touchending, - clickDistance2 = 0; - - function drag(selection) { - selection - .on("mousedown.drag", mousedowned) - .filter(touchable) - .on("touchstart.drag", touchstarted) - .on("touchmove.drag", touchmoved) - .on("touchend.drag touchcancel.drag", touchended) - .style("touch-action", "none") - .style("-webkit-tap-highlight-color", "rgba(0,0,0,0)"); - } - - function mousedowned() { - if (touchending || !filter.apply(this, arguments)) return; - var gesture = beforestart("mouse", container.apply(this, arguments), mouse, this, arguments); - if (!gesture) return; - select(event.view).on("mousemove.drag", mousemoved, true).on("mouseup.drag", mouseupped, true); - nodrag(event.view); - nopropagation(); - mousemoving = false; - mousedownx = event.clientX; - mousedowny = event.clientY; - gesture("start"); - } - - function mousemoved() { - noevent(); - if (!mousemoving) { - var dx = event.clientX - mousedownx, dy = event.clientY - mousedowny; - mousemoving = dx * dx + dy * dy > clickDistance2; - } - gestures.mouse("drag"); - } - - function mouseupped() { - select(event.view).on("mousemove.drag mouseup.drag", null); - yesdrag(event.view, mousemoving); - noevent(); - gestures.mouse("end"); - } - - function touchstarted() { - if (!filter.apply(this, arguments)) return; - var touches = event.changedTouches, - c = container.apply(this, arguments), - n = touches.length, i, gesture; - - for (i = 0; i < n; ++i) { - if (gesture = beforestart(touches[i].identifier, c, touch, this, arguments)) { - nopropagation(); - gesture("start"); - } - } - } - - function touchmoved() { - var touches = event.changedTouches, - n = touches.length, i, gesture; - - for (i = 0; i < n; ++i) { - if (gesture = gestures[touches[i].identifier]) { - noevent(); - gesture("drag"); - } - } - } - - function touchended() { - var touches = event.changedTouches, - n = touches.length, i, gesture; - - if (touchending) clearTimeout(touchending); - touchending = setTimeout(function() { touchending = null; }, 500); // Ghost clicks are delayed! - for (i = 0; i < n; ++i) { - if (gesture = gestures[touches[i].identifier]) { - nopropagation(); - gesture("end"); - } - } - } - - function beforestart(id, container, point, that, args) { - var p = point(container, id), s, dx, dy, - sublisteners = listeners.copy(); - - if (!customEvent(new DragEvent(drag, "beforestart", s, id, active, p[0], p[1], 0, 0, sublisteners), function() { - if ((event.subject = s = subject.apply(that, args)) == null) return false; - dx = s.x - p[0] || 0; - dy = s.y - p[1] || 0; - return true; - })) return; - - return function gesture(type) { - var p0 = p, n; - switch (type) { - case "start": gestures[id] = gesture, n = active++; break; - case "end": delete gestures[id], --active; // nobreak - case "drag": p = point(container, id), n = active; break; - } - customEvent(new DragEvent(drag, type, s, id, n, p[0] + dx, p[1] + dy, p[0] - p0[0], p[1] - p0[1], sublisteners), sublisteners.apply, sublisteners, [type, that, args]); - }; - } - - drag.filter = function(_) { - return arguments.length ? (filter = typeof _ === "function" ? _ : constant$3(!!_), drag) : filter; - }; - - drag.container = function(_) { - return arguments.length ? (container = typeof _ === "function" ? _ : constant$3(_), drag) : container; - }; - - drag.subject = function(_) { - return arguments.length ? (subject = typeof _ === "function" ? _ : constant$3(_), drag) : subject; - }; - - drag.touchable = function(_) { - return arguments.length ? (touchable = typeof _ === "function" ? _ : constant$3(!!_), drag) : touchable; - }; - - drag.on = function() { - var value = listeners.on.apply(listeners, arguments); - return value === listeners ? drag : value; - }; - - drag.clickDistance = function(_) { - return arguments.length ? (clickDistance2 = (_ = +_) * _, drag) : Math.sqrt(clickDistance2); - }; - - return drag; - } - - // Copyright 2018 The Distill Template Authors - - const T$a = Template('d-slider', ` - - -
    -
    -
    -
    -
    -
    -
    -
    -
    -`); - - // ARIA - // If the slider has a visible label, it is referenced by aria-labelledby on the slider element. Otherwise, the slider element has a label provided by aria-label. - // If the slider is vertically oriented, it has aria-orientation set to vertical. The default value of aria-orientation for a slider is horizontal. - - const keyCodes = { - left: 37, - up: 38, - right: 39, - down: 40, - pageUp: 33, - pageDown: 34, - end: 35, - home: 36 - }; - - class Slider extends T$a(HTMLElement) { - - - connectedCallback() { - this.connected = true; - this.setAttribute('role', 'slider'); - // Makes the element tab-able. - if (!this.hasAttribute('tabindex')) { this.setAttribute('tabindex', 0); } - - // Keeps track of keyboard vs. mouse interactions for focus rings - this.mouseEvent = false; - - // Handles to shadow DOM elements - this.knob = this.root.querySelector('.knob-container'); - this.background = this.root.querySelector('.background'); - this.trackFill = this.root.querySelector('.track-fill'); - this.track = this.root.querySelector('.track'); - - // Default values for attributes - this.min = this.min ? this.min : 0; - this.max = this.max ? this.max : 100; - this.scale = linear$1().domain([this.min, this.max]).range([0, 1]).clamp(true); - - this.origin = this.origin !== undefined ? this.origin : this.min; - this.step = this.step ? this.step : 1; - this.update(this.value ? this.value : 0); - - this.ticks = this.ticks ? this.ticks : false; - this.renderTicks(); - - this.drag = drag() - .container(this.background) - .on('start', () => { - this.mouseEvent = true; - this.background.classList.add('mousedown'); - this.changeValue = this.value; - this.dragUpdate(); - }) - .on('drag', () => { - this.dragUpdate(); - }) - .on('end', () => { - this.mouseEvent = false; - this.background.classList.remove('mousedown'); - this.dragUpdate(); - if (this.changeValue !== this.value) this.dispatchChange(); - this.changeValue = this.value; - }); - this.drag(select(this.background)); - - this.addEventListener('focusin', () => { - if(!this.mouseEvent) { - this.background.classList.add('focus'); - } - }); - this.addEventListener('focusout', () => { - this.background.classList.remove('focus'); - }); - this.addEventListener('keydown', this.onKeyDown); - - } - - static get observedAttributes() {return ['min', 'max', 'value', 'step', 'ticks', 'origin', 'tickValues', 'tickLabels']; } - - attributeChangedCallback(attr, oldValue, newValue) { - if (isNaN(newValue) || newValue === undefined || newValue === null) return; - if (attr == 'min') { - this.min = +newValue; - this.setAttribute('aria-valuemin', this.min); - } - if (attr == 'max') { - this.max = +newValue; - this.setAttribute('aria-valuemax', this.max); - } - if (attr == 'value') { - this.update(+newValue); - } - if (attr == 'origin') { - this.origin = +newValue; - // this.update(this.value); - } - if (attr == 'step') { - if (newValue > 0) { - this.step = +newValue; - } - } - if (attr == 'ticks') { - this.ticks = (newValue === '' ? true : newValue); - } - } - - onKeyDown(event) { - this.changeValue = this.value; - let stopPropagation = false; - switch (event.keyCode) { - case keyCodes.left: - case keyCodes.down: - this.update(this.value - this.step); - stopPropagation = true; - break; - case keyCodes.right: - case keyCodes.up: - this.update(this.value + this.step); - stopPropagation = true; - break; - case keyCodes.pageUp: - this.update(this.value + this.step * 10); - stopPropagation = true; - break; - - case keyCodes.pageDown: - this.update(this.value + this.step * 10); - stopPropagation = true; - break; - case keyCodes.home: - this.update(this.min); - stopPropagation = true; - break; - case keyCodes.end: - this.update(this.max); - stopPropagation = true; - break; - } - if (stopPropagation) { - this.background.classList.add('focus'); - event.preventDefault(); - event.stopPropagation(); - if (this.changeValue !== this.value) this.dispatchChange(); - } - } - - validateValueRange(min, max, value) { - return Math.max(Math.min(max, value), min); - } - - quantizeValue(value, step) { - return Math.round(value / step) * step; - } - - dragUpdate() { - const bbox = this.background.getBoundingClientRect(); - const x = event.x; - const width = bbox.width; - this.update(this.scale.invert(x / width)); - } - - update(value) { - let v = value; - if (this.step !== 'any') { - v = this.quantizeValue(value, this.step); - } - v = this.validateValueRange(this.min, this.max, v); - if (this.connected) { - this.knob.style.left = this.scale(v) * 100 + '%'; - this.trackFill.style.width = this.scale(this.min + Math.abs(v - this.origin)) * 100 + '%'; - this.trackFill.style.left = this.scale(Math.min(v, this.origin)) * 100 + '%'; - } - if (this.value !== v) { - this.value = v; - this.setAttribute('aria-valuenow', this.value); - this.dispatchInput(); - } - } - - // Dispatches only on a committed change (basically only on mouseup). - dispatchChange() { - const e = new Event('change'); - this.dispatchEvent(e, {}); - } - - // Dispatches on each value change. - dispatchInput() { - const e = new Event('input'); - this.dispatchEvent(e, {}); - } - - renderTicks() { - const ticksContainer = this.root.querySelector('.ticks'); - if (this.ticks !== false) { - let tickData = []; - if (this.ticks > 0) { - tickData = this.scale.ticks(this.ticks); - } else if (this.step === 'any') { - tickData = this.scale.ticks(); - } else { - tickData = range(this.min, this.max + 1e-6, this.step); - } - tickData.forEach(d => { - const tick = document.createElement('div'); - tick.classList.add('tick'); - tick.style.left = this.scale(d) * 100 + '%'; - ticksContainer.appendChild(tick); - }); - } else { - ticksContainer.style.display = 'none'; - } - } - } - - var logo = "\n \n\n"; - - const headerTemplate = ` - -
    - - -
    -`; - - // Copyright 2018 The Distill Template Authors - - const T$b = Template('distill-header', headerTemplate, false); - - class DistillHeader extends T$b(HTMLElement) { - - } - - // Copyright 2018 The Distill Template Authors - - const styles$2 = ` - -`; - - function appendixTemplate(frontMatter) { - let html = styles$2; - - if (typeof frontMatter.githubUrl !== 'undefined') { - html += ` -

    Updates and Corrections

    -

    `; - if (frontMatter.githubCompareUpdatesUrl) { - html += `View all changes to this article since it was first published.`; - } - html += ` - If you see mistakes or want to suggest changes, please create an issue on GitHub.

    - `; - } - - const journal = frontMatter.journal; - if (typeof journal !== 'undefined' && journal.title === 'Distill') { - html += ` -

    Reuse

    -

    Diagrams and text are licensed under Creative Commons Attribution CC-BY 4.0 with the source available on GitHub, unless noted otherwise. The figures that have been reused from other sources don’t fall under this license and can be recognized by a note in their caption: “Figure from …”.

    - `; - } - - if (typeof frontMatter.publishedDate !== 'undefined') { - html += ` -

    Citation

    -

    For attribution in academic contexts, please cite this work as

    - 
    ${frontMatter.concatenatedAuthors}, "${frontMatter.title}", Distill, ${frontMatter.publishedYear}.
    -

    BibTeX citation

    - 
    ${serializeFrontmatterToBibtex(frontMatter)}
    - `; - } - - return html; - } - - class DistillAppendix extends HTMLElement { - - static get is() { return 'distill-appendix'; } - - set frontMatter(frontMatter) { - this.innerHTML = appendixTemplate(frontMatter); - } - - } - - const footerTemplate = ` - - -
    - - is dedicated to clear explanations of machine learning - -
    - About - Submit - Prize - Archive - RSS - GitHub - Twitter -      ISSN 2476-0757 -
    - -
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- return names.slice(0, names.length - 1).join(' '); - } - - // 'Olah' - get lastName() { - const names = this.name.split(' '); - return names[names.length -1]; - } - } - - function mergeFromYMLFrontmatter(target, source) { - target.title = source.title; - if (source.published) { - if (source.published instanceof Date) { - target.publishedDate = source.published; - } else if (source.published.constructor === String) { - target.publishedDate = new Date(source.published); - } - } - if (source.publishedDate) { - if (source.publishedDate instanceof Date) { - target.publishedDate = source.publishedDate; - } else if (source.publishedDate.constructor === String) { - target.publishedDate = new Date(source.publishedDate); - } else { - console.error('Don\'t know what to do with published date: ' + source.publishedDate); - } - } - target.description = source.description; - target.authors = source.authors.map( (authorObject) => new Author(authorObject)); - target.katex = source.katex; - target.password = source.password; 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- - // - // Assigned from posts.csv - // - - // publishedDate: 2016-09-08T07:00:00.000Z, - // tags: [ 'rnn' ], - // distillPath: '2016/augmented-rnns', - // githubPath: 'distillpub/post--augmented-rnns', - // doiSuffix: 1, - - // - // Assigned from journal - // - this.journal = {}; - // journal: { - // 'title': 'Distill', - // 'full_title': 'Distill', - // 'abbrev_title': 'Distill', - // 'url': 'http://distill.pub', - // 'doi': '10.23915/distill', - // 'publisherName': 'Distill Working Group', - // 'publisherEmail': 'admin@distill.pub', - // 'issn': '2476-0757', - // 'editors': [...], - // 'committee': [...] - // } - // volume: 1, - // issue: 9, - - this.katex = {}; - - // - // Assigned from publishing process - // - - // githubCompareUpdatesUrl: 'https://github.com/distillpub/post--augmented-rnns/compare/1596e094d8943d2dc0ea445d92071129c6419c59...3bd9209e0c24d020f87cf6152dcecc6017cbc193', - // updatedDate: 2017-03-21T07:13:16.000Z, - // doi: '10.23915/distill.00001', - this.doi = undefined; - this.publishedDate = undefined; - } - - // Example: - // title: Demo Title Attention and Augmented Recurrent Neural Networks - // published: Jan 10, 2017 - // authors: - // - Chris Olah: - // - Shan Carter: http://shancarter.com - // affiliations: - // - Google Brain: - // - Google Brain: http://g.co/brain - - // - // Computed Properties - // - - // 'http://distill.pub/2016/augmented-rnns', - set url(value) { - this._url = value; - } - get url() { - if (this._url) { - return this._url; - } else if (this.distillPath && this.journal.url) { - return this.journal.url + '/' + this.distillPath; - } else if (this.journal.url) { - return this.journal.url; - } - } - - // 'https://github.com/distillpub/post--augmented-rnns', - get githubUrl() { - if (this.githubPath) { - return 'https://github.com/' + this.githubPath; - } else { - return undefined; - } - } - - // TODO resolve differences in naming of URL/Url/url. - // 'http://distill.pub/2016/augmented-rnns/thumbnail.jpg', - set previewURL(value) { - this._previewURL = value; 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- } - return volume; - } - - get issue() { - return this.publishedDate.getMonth() + 1; - } - - // 'Olah & Carter', - get concatenatedAuthors() { - if (this.authors.length > 2) { - return this.authors[0].lastName + ', et al.'; - } else if (this.authors.length === 2) { - return this.authors[0].lastName + ' & ' + this.authors[1].lastName; - } else if (this.authors.length === 1) { - return this.authors[0].lastName; - } - } - - // 'Olah, Chris and Carter, Shan', - get bibtexAuthors() { - return this.authors.map(author => { - return author.lastName + ', ' + author.firstName; - }).join(' and '); - } - - // 'olah2016attention' - get slug() { - let slug = ''; - if (this.authors.length) { - slug += this.authors[0].lastName.toLowerCase(); - slug += this.publishedYear; - slug += this.title.split(' ')[0].toLowerCase(); - } - return slug || 'Untitled'; - } - - get bibliographyEntries() { - return new Map(this.citations.map( citationKey => { - const entry = this.bibliography.get(citationKey); - return [citationKey, entry]; - })); - } - - set bibliography(bibliography) { - if (bibliography instanceof Map) { - this._bibliography = bibliography; - } else if (typeof bibliography === 'object') { - this._bibliography = mapFromObject(bibliography); - } - } - - get bibliography() { - return this._bibliography; - } - - static fromObject(source) { - const frontMatter = new FrontMatter(); - Object.assign(frontMatter, source); - return frontMatter; - } - - assignToObject(target) { - Object.assign(target, this); - target.bibliography = objectFromMap(this.bibliographyEntries); - target.url = this.url; - target.doi = this.doi; - target.githubUrl = this.githubUrl; - target.previewURL = this.previewURL; - if (this.publishedDate) { - target.volume = this.volume; - target.issue = this.issue; - target.publishedDateRFC = this.publishedDateRFC; - target.publishedYear = this.publishedYear; - target.publishedMonth = this.publishedMonth; - target.publishedDay = this.publishedDay; - target.publishedMonthPadded = this.publishedMonthPadded; - target.publishedDayPadded = this.publishedDayPadded; - } - if (this.updatedDate) { - target.updatedDateRFC = this.updatedDateRFC; - } - target.concatenatedAuthors = this.concatenatedAuthors; - target.bibtexAuthors = this.bibtexAuthors; - target.slug = this.slug; - } - - } - - // Copyright 2018 The Distill Template Authors - // - // Licensed under the Apache License, Version 2.0 (the "License"); - // you may not use this file except in compliance with the License. - // You may obtain a copy of the License at - // - // http://www.apache.org/licenses/LICENSE-2.0 - // - // Unless required by applicable law or agreed to in writing, software - // distributed under the License is distributed on an "AS IS" BASIS, - // WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - // See the License for the specific language governing permissions and - // limitations under the License. - - function _moveLegacyAffiliationFormatIntoArray(frontMatter) { - // authors used to have propoerties "affiliation" and "affiliationURL". - // We now encourage using an array for affiliations containing objects with - // properties "name" and "url". - for (let author of frontMatter.authors) { - const hasOldStyle = Boolean(author.affiliation); - const hasNewStyle = Boolean(author.affiliations); - if (!hasOldStyle) continue; - if (hasNewStyle) { - console.warn(`Author ${author.author} has both old-style ("affiliation" & "affiliationURL") and new style ("affiliations") affiliation information!`); - } else { - let newAffiliation = { - "name": author.affiliation - }; - if (author.affiliationURL) newAffiliation.url = author.affiliationURL; - author.affiliations = [newAffiliation]; - } - } - return frontMatter - } - - function parseFrontmatter(element) { - const scriptTag = element.firstElementChild; - if (scriptTag) { - const type = scriptTag.getAttribute('type'); - if (type.split('/')[1] == 'json') { - const content = scriptTag.textContent; - const parsed = JSON.parse(content); - return _moveLegacyAffiliationFormatIntoArray(parsed); - } else { - console.error('Distill only supports JSON frontmatter tags anymore; no more YAML.'); - } - } else { - console.error('You added a frontmatter tag but did not provide a script tag with front matter data in it. Please take a look at our templates.'); - } - return {}; - } - - // Copyright 2018 The Distill Template Authors - - function ExtractFrontmatter(dom, data) { - const frontMatterTag = dom.querySelector('d-front-matter'); - if (!frontMatterTag) { - console.warn('No front matter tag found!'); - return; - } - const extractedData = parseFrontmatter(frontMatterTag); - mergeFromYMLFrontmatter(data, extractedData); - } - - function commonjsRequire () { - throw new Error('Dynamic requires are not currently supported by rollup-plugin-commonjs'); - } - - function unwrapExports (x) { - return x && x.__esModule && Object.prototype.hasOwnProperty.call(x, 'default') ? x['default'] : x; - } - - function createCommonjsModule(fn, module) { - return module = { exports: {} }, fn(module, module.exports), module.exports; - } - - var bibtexParse = createCommonjsModule(function (module, exports) { - /* start bibtexParse 0.0.22 */ - - //Original work by Henrik Muehe (c) 2010 - // - //CommonJS port by Mikola Lysenko 2013 - // - //Port to Browser lib by ORCID / RCPETERS - // - //Issues: - //no comment handling within strings - //no string concatenation - //no variable values yet - //Grammar implemented here: - //bibtex -> (string | preamble | comment | entry)*; - //string -> '@STRING' '{' key_equals_value '}'; - //preamble -> '@PREAMBLE' '{' value '}'; - //comment -> '@COMMENT' '{' value '}'; - //entry -> '@' key '{' key ',' key_value_list '}'; - //key_value_list -> key_equals_value (',' key_equals_value)*; - //key_equals_value -> key '=' value; - //value -> value_quotes | value_braces | key; - //value_quotes -> '"' .*? '"'; // not quite - //value_braces -> '{' .*? '"'; // not quite - (function(exports) { - - function BibtexParser() { - - this.months = ["jan", "feb", "mar", "apr", "may", "jun", "jul", "aug", "sep", "oct", "nov", "dec"]; - this.notKey = [',','{','}',' ','=']; - this.pos = 0; - this.input = ""; - this.entries = new Array(); - - this.currentEntry = ""; - - this.setInput = function(t) { - this.input = t; - }; - - this.getEntries = function() { - return this.entries; - }; - - this.isWhitespace = function(s) { - return (s == ' ' || s == '\r' || s == '\t' || s == '\n'); - }; - - this.match = function(s, canCommentOut) { - if (canCommentOut == undefined || canCommentOut == null) - canCommentOut = true; - this.skipWhitespace(canCommentOut); - if (this.input.substring(this.pos, this.pos + s.length) == s) { - this.pos += s.length; - } else { - throw "Token mismatch, expected " + s + ", found " - + this.input.substring(this.pos); - } this.skipWhitespace(canCommentOut); - }; - - this.tryMatch = function(s, canCommentOut) { - if (canCommentOut == undefined || canCommentOut == null) - canCommentOut = true; - this.skipWhitespace(canCommentOut); - if (this.input.substring(this.pos, this.pos + s.length) == s) { - return true; - } else { - return false; - } }; - - /* when search for a match all text can be ignored, not just white space */ - this.matchAt = function() { - while (this.input.length > this.pos && this.input[this.pos] != '@') { - this.pos++; - } - if (this.input[this.pos] == '@') { - return true; - } return false; - }; - - this.skipWhitespace = function(canCommentOut) { - while (this.isWhitespace(this.input[this.pos])) { - this.pos++; - } if (this.input[this.pos] == "%" && canCommentOut == true) { - while (this.input[this.pos] != "\n") { - this.pos++; - } this.skipWhitespace(canCommentOut); - } }; - - this.value_braces = function() { - var bracecount = 0; - this.match("{", false); - var start = this.pos; - var escaped = false; - while (true) { - if (!escaped) { - if (this.input[this.pos] == '}') { - if (bracecount > 0) { - bracecount--; - } else { - var end = this.pos; - this.match("}", false); - return this.input.substring(start, end); - } } else if (this.input[this.pos] == '{') { - bracecount++; - } else if (this.pos >= this.input.length - 1) { - throw "Unterminated value"; - } } if (this.input[this.pos] == '\\' && escaped == false) - escaped = true; - else - escaped = false; - this.pos++; - } }; - - this.value_comment = function() { - var str = ''; - var brcktCnt = 0; - while (!(this.tryMatch("}", false) && brcktCnt == 0)) { - str = str + this.input[this.pos]; - if (this.input[this.pos] == '{') - brcktCnt++; - if (this.input[this.pos] == '}') - brcktCnt--; - if (this.pos >= this.input.length - 1) { - throw "Unterminated value:" + this.input.substring(start); - } this.pos++; - } return str; - }; - - this.value_quotes = function() { - this.match('"', false); - var start = this.pos; - var escaped = false; - while (true) { - if (!escaped) { - if (this.input[this.pos] == '"') { - var end = this.pos; - this.match('"', false); - return this.input.substring(start, end); - } else if (this.pos >= this.input.length - 1) { - throw "Unterminated value:" + this.input.substring(start); - } } - if (this.input[this.pos] == '\\' && escaped == false) - escaped = true; - else - escaped = false; - this.pos++; - } }; - - this.single_value = function() { - var start = this.pos; - if (this.tryMatch("{")) { - return this.value_braces(); - } else if (this.tryMatch('"')) { - return this.value_quotes(); - } else { - var k = this.key(); - if (k.match("^[0-9]+$")) - return k; - else if (this.months.indexOf(k.toLowerCase()) >= 0) - return k.toLowerCase(); - else - throw "Value expected:" + this.input.substring(start) + ' for key: ' + k; - - } }; - - this.value = function() { - var values = []; - values.push(this.single_value()); - while (this.tryMatch("#")) { - this.match("#"); - values.push(this.single_value()); - } return values.join(""); - }; - - this.key = function() { - var start = this.pos; - while (true) { - if (this.pos >= this.input.length) { - throw "Runaway key"; - } // а-яА-Я is Cyrillic - //console.log(this.input[this.pos]); - if (this.notKey.indexOf(this.input[this.pos]) >= 0) { - return this.input.substring(start, this.pos); - } else { - this.pos++; - - } } }; - - this.key_equals_value = function() { - var key = this.key(); - if (this.tryMatch("=")) { - this.match("="); - var val = this.value(); - return [ key, val ]; - } else { - throw "... = value expected, equals sign missing:" - + this.input.substring(this.pos); - } }; - - this.key_value_list = function() { - var kv = this.key_equals_value(); - this.currentEntry['entryTags'] = {}; - this.currentEntry['entryTags'][kv[0]] = kv[1]; - while (this.tryMatch(",")) { - this.match(","); - // fixes problems with commas at the end of a list - if (this.tryMatch("}")) { - break; - } - kv = this.key_equals_value(); - this.currentEntry['entryTags'][kv[0]] = kv[1]; - } }; - - this.entry_body = function(d) { - this.currentEntry = {}; - this.currentEntry['citationKey'] = this.key(); - this.currentEntry['entryType'] = d.substring(1); - this.match(","); - this.key_value_list(); - this.entries.push(this.currentEntry); - }; - - this.directive = function() { - this.match("@"); - return "@" + this.key(); - }; - - this.preamble = function() { - this.currentEntry = {}; - this.currentEntry['entryType'] = 'PREAMBLE'; - this.currentEntry['entry'] = this.value_comment(); - this.entries.push(this.currentEntry); - }; - - this.comment = function() { - this.currentEntry = {}; - this.currentEntry['entryType'] = 'COMMENT'; - this.currentEntry['entry'] = this.value_comment(); - this.entries.push(this.currentEntry); - }; - - this.entry = function(d) { - this.entry_body(d); - }; - - this.bibtex = function() { - while (this.matchAt()) { - var d = this.directive(); - this.match("{"); - if (d == "@STRING") { - this.string(); - } else if (d == "@PREAMBLE") { - this.preamble(); - } else if (d == "@COMMENT") { - this.comment(); - } else { - this.entry(d); - } - this.match("}"); - } }; - } - exports.toJSON = function(bibtex) { - var b = new BibtexParser(); - b.setInput(bibtex); - b.bibtex(); - return b.entries; - }; - - /* added during hackathon don't hate on me */ - exports.toBibtex = function(json) { - var out = ''; - for ( var i in json) { - out += "@" + json[i].entryType; - out += '{'; - if (json[i].citationKey) - out += json[i].citationKey + ', '; - if (json[i].entry) - out += json[i].entry ; - if (json[i].entryTags) { - var tags = ''; - for (var jdx in json[i].entryTags) { - if (tags.length != 0) - tags += ', '; - tags += jdx + '= {' + json[i].entryTags[jdx] + '}'; - } - out += tags; - } - out += '}\n\n'; - } - return out; - - }; - - })( exports); - - /* end bibtexParse */ - }); - - // Copyright 2018 The Distill Template Authors - - function normalizeTag(string) { - return string - .replace(/[\t\n ]+/g, ' ') - .replace(/{\\["^`.'acu~Hvs]( )?([a-zA-Z])}/g, (full, x, char) => char) - .replace(/{\\([a-zA-Z])}/g, (full, char) => char); - } - - function parseBibtex(bibtex) { - const bibliography = new Map(); - const parsedEntries = bibtexParse.toJSON(bibtex); - for (const entry of parsedEntries) { - // normalize tags; note entryTags is an object, not Map - for (const [key, value] of Object.entries(entry.entryTags)) { - entry.entryTags[key.toLowerCase()] = normalizeTag(value); - } - entry.entryTags.type = entry.entryType; - // add to bibliography - bibliography.set(entry.citationKey, entry.entryTags); - } - return bibliography; - } - - function serializeFrontmatterToBibtex(frontMatter) { - return `@article{${frontMatter.slug}, - author = {${frontMatter.bibtexAuthors}}, - title = {${frontMatter.title}}, - journal = {${frontMatter.journal.title}}, - year = {${frontMatter.publishedYear}}, - note = {${frontMatter.url}}, - doi = {${frontMatter.doi}} -}`; - } - - // Copyright 2018 The Distill Template Authors - - function parseBibliography(element) { - const scriptTag = element.firstElementChild; - if (scriptTag && scriptTag.tagName === 'SCRIPT') { - if (scriptTag.type == 'text/bibtex') { - const bibtex = element.firstElementChild.textContent; - return parseBibtex(bibtex); - } else if (scriptTag.type == 'text/json') { - return new Map(JSON.parse(scriptTag.textContent)); - } else { - console.warn('Unsupported bibliography script tag type: ' + scriptTag.type); - } - } else { - console.warn('Bibliography did not have any script tag.'); - } - } - - // Copyright 2018 The Distill Template Authors - - function ExtractBibliography(dom, data) { - const bibliographyTag = dom.querySelector('d-bibliography'); - if (!bibliographyTag) { - console.warn('No bibliography tag found!'); - return; - } - - const src = bibliographyTag.getAttribute('src'); - if (src) { - const path = data.inputDirectory + '/' + src; - const text = fs.readFileSync(path, 'utf-8'); - const bibliography = parseBibtex(text); - const scriptTag = dom.createElement('script'); - scriptTag.type = 'text/json'; - scriptTag.textContent = JSON.stringify([...bibliography]); - bibliographyTag.appendChild(scriptTag); - bibliographyTag.removeAttribute('src'); - } - - data.bibliography = parseBibliography(bibliographyTag); - } - - // Copyright 2018 The Distill Template Authors - // - // Licensed under the Apache License, Version 2.0 (the "License"); - // you may not use this file except in compliance with the License. - // You may obtain a copy of the License at - // - // http://www.apache.org/licenses/LICENSE-2.0 - // - // Unless required by applicable law or agreed to in writing, software - // distributed under the License is distributed on an "AS IS" BASIS, - // WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - // See the License for the specific language governing permissions and - // limitations under the License. - - function collect_citations(dom = document) { - const citations = new Set(); - const citeTags = dom.querySelectorAll("d-cite"); - for (const tag of citeTags) { - const keyString = tag.getAttribute("key") || tag.getAttribute("bibtex-key"); - const keys = keyString.split(",").map(k => k.trim()); - for (const key of keys) { - citations.add(key); - } - } - return [...citations]; - } - - function author_string(ent, template, sep, finalSep) { - if (ent.author == null) { - return ""; - } - var names = ent.author.split(" and "); - let name_strings = names.map(name => { - name = name.trim(); - if (name.indexOf(",") != -1) { - var last = name.split(",")[0].trim(); - var firsts = name.split(",")[1]; - } else if (name.indexOf(" ") != -1) { - var last = name - .split(" ") - .slice(-1)[0] - .trim(); - var firsts = name - .split(" ") - .slice(0, -1) - .join(" "); - } else { - var last = name.trim(); - } - var initials = ""; - if (firsts != undefined) { - initials = firsts - .trim() - .split(" ") - .map(s => s.trim()[0]); - initials = initials.join(".") + "."; - } - return template - .replace("${F}", firsts) - .replace("${L}", last) - .replace("${I}", initials) - .trim(); // in case one of first or last was empty - }); - if (names.length > 1) { - var str = name_strings.slice(0, names.length - 1).join(sep); - str += (finalSep || sep) + name_strings[names.length - 1]; - return str; - } else { - return name_strings[0]; - } - } - - function venue_string(ent) { - var cite = ent.journal || ent.booktitle || ""; - if ("volume" in ent) { - var issue = ent.issue || ent.number; - issue = issue != undefined ? "(" + issue + ")" : ""; - cite += ", Vol " + ent.volume + issue; - } - if ("pages" in ent) { - cite += ", pp. " + ent.pages; - } - if (cite != "") cite += ". "; - if ("publisher" in ent) { - cite += ent.publisher; - if (cite[cite.length - 1] != ".") cite += "."; - } - return cite; - } - - function link_string(ent) { - if ("url" in ent) { - var url = ent.url; - var arxiv_match = /arxiv\.org\/abs\/([0-9\.]*)/.exec(url); - if (arxiv_match != null) { - url = `http://arxiv.org/pdf/${arxiv_match[1]}.pdf`; - } - - if (url.slice(-4) == ".pdf") { - var label = "PDF"; - } else if (url.slice(-5) == ".html") { - var label = "HTML"; - } - return `  [${label || "link"}]`; - } /* else if ("doi" in ent){ - return `  [DOI]`; - }*/ else { - return ""; - } - } - function doi_string(ent, new_line) { - if ("doi" in ent) { - return `${new_line ? "
      " : ""} DOI: ${ent.doi}`; - } else { - return ""; - } - } - - function title_string(ent) { - return '' + ent.title + " "; - } - - function bibliography_cite(ent, fancy) { - if (ent) { - var cite = title_string(ent); - cite += link_string(ent) + "
      "; - if (ent.author) { - cite += author_string(ent, "${L}, ${I}", ", ", " and "); - if (ent.year || ent.date) { - cite += ", "; - } - } - if (ent.year || ent.date) { - cite += (ent.year || ent.date) + ". "; - } else { - cite += ". "; - } - cite += venue_string(ent); - cite += doi_string(ent); - return cite; - /*var cite = author_string(ent, "${L}, ${I}", ", ", " and "); - if (ent.year || ent.date){ - cite += ", " + (ent.year || ent.date) + ". " - } else { - cite += ". " - } - cite += "" + ent.title + ". "; - cite += venue_string(ent); - cite += doi_string(ent); - cite += link_string(ent); - return cite*/ - } else { - return "?"; - } - } - - // Copyright 2018 The Distill Template Authors - - function ExtractCitations(dom, data) { - const citations = new Set(data.citations); - const newCitations = collect_citations(dom); - for (const citation of newCitations) { - citations.add(citation); - } - data.citations = Array.from(citations); - } - - // Copyright 2018 The Distill Template Authors - // - // Licensed under the Apache License, Version 2.0 (the "License"); - // you may not use this file except in compliance with the License. - // You may obtain a copy of the License at - // - // http://www.apache.org/licenses/LICENSE-2.0 - // - // Unless required by applicable law or agreed to in writing, software - // distributed under the License is distributed on an "AS IS" BASIS, - // WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - // See the License for the specific language governing permissions and - // limitations under the License. - - function HTML(dom) { - - const head = dom.querySelector('head'); - - // set language to 'en' - if (!dom.querySelector('html').getAttribute('lang')) { - dom.querySelector('html').setAttribute('lang', 'en'); - } - - // set charset to 'utf-8' - if (!dom.querySelector('meta[charset]')) { - const meta = dom.createElement('meta'); - meta.setAttribute('charset', 'utf-8'); - head.appendChild(meta); - } - - // set viewport - if (!dom.querySelector('meta[name=viewport]')) { - const meta = dom.createElement('meta'); - meta.setAttribute('name', 'viewport'); - meta.setAttribute('content', 'width=device-width, initial-scale=1'); - head.appendChild(meta); - } - } - - // Copyright 2018 The Distill Template Authors - // - // Licensed under the Apache License, Version 2.0 (the "License"); - // you may not use this file except in compliance with the License. - // You may obtain a copy of the License at - // - // http://www.apache.org/licenses/LICENSE-2.0 - // - // Unless required by applicable law or agreed to in writing, software - // distributed under the License is distributed on an "AS IS" BASIS, - // WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - // See the License for the specific language governing permissions and - // limitations under the License. - - // import style from '../styles/d-byline.css'; - - function bylineTemplate(frontMatter) { - return ` -
      -
      -

      Authors

      -

      Affiliations

      - ${frontMatter.authors.map(author => ` -

      - ${author.personalURL ? ` - ${author.name}` : ` - ${author.name}`} -

      -

      - ${author.affiliations.map(affiliation => - affiliation.url ? `${affiliation.name}` : `${affiliation.name}` - ).join(', ')} -

      - `).join('')} -
      -
      -

      Published

      - ${frontMatter.publishedDate ? ` -

      ${frontMatter.publishedMonth} ${frontMatter.publishedDay}, ${frontMatter.publishedYear}

      ` : ` -

      Not published yet.

      `} -
      -
      -`; - } - - // Copyright 2018 The Distill Template Authors - - function Byline(dom, data) { - const byline = dom.querySelector('d-byline'); - if (byline) { - byline.innerHTML = bylineTemplate(data); - } - } - - // Copyright 2018 The Distill Template Authors - // - // Licensed under the Apache License, Version 2.0 (the "License"); - // you may not use this file except in compliance with the License. - // You may obtain a copy of the License at - // - // http://www.apache.org/licenses/LICENSE-2.0 - // - // Unless required by applicable law or agreed to in writing, software - // distributed under the License is distributed on an "AS IS" BASIS, - // WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - // See the License for the specific language governing permissions and - // limitations under the License. - - // no appendix -> add appendix - // title in front, no h1 -> add it - // no title in front, h1 -> read and put into frontMatter - // footnote -> footnote list - // break up bib - // if citation, no bib-list -> add citation-list - - // if authors, no byline -> add byline - - function OptionalComponents(dom, data) { - const body = dom.body; - const article = body.querySelector('d-article'); - - // If we don't have an article tag, something weird is going on—giving up. - if (!article) { - console.warn('No d-article tag found; skipping adding optional components!'); - return; - } - - let byline = dom.querySelector('d-byline'); - if (!byline) { - if (data.authors) { - byline = dom.createElement('d-byline'); - body.insertBefore(byline, article); - } else { - console.warn('No authors found in front matter; please add them before submission!'); - } - } - - let title = dom.querySelector('d-title'); - if (!title) { - title = dom.createElement('d-title'); - body.insertBefore(title, byline); - } - - let h1 = title.querySelector('h1'); - if (!h1) { - h1 = dom.createElement('h1'); - h1.textContent = data.title; - title.insertBefore(h1, title.firstChild); - } - - const hasPassword = typeof data.password !== 'undefined'; - let interstitial = body.querySelector('d-interstitial'); - if (hasPassword && !interstitial) { - const inBrowser = typeof window !== 'undefined'; - const onLocalhost = inBrowser && window.location.hostname.includes('localhost'); - if (!inBrowser || !onLocalhost) { - interstitial = dom.createElement('d-interstitial'); - interstitial.password = data.password; - body.insertBefore(interstitial, body.firstChild); - } - } else if (!hasPassword && interstitial) { - interstitial.parentElement.removeChild(this); - } - - let appendix = dom.querySelector('d-appendix'); - if (!appendix) { - appendix = dom.createElement('d-appendix'); - dom.body.appendChild(appendix); - } - - let footnoteList = dom.querySelector('d-footnote-list'); - if (!footnoteList) { - footnoteList = dom.createElement('d-footnote-list'); - appendix.appendChild(footnoteList); - } - - let citationList = dom.querySelector('d-citation-list'); - if (!citationList) { - citationList = dom.createElement('d-citation-list'); - appendix.appendChild(citationList); - } - - } - - var katex$1 = createCommonjsModule(function (module, exports) { - (function(f){{module.exports=f();}})(function(){return (function e(t,n,r){function s(o,u){if(!n[o]){if(!t[o]){var a=typeof commonjsRequire=="function"&&commonjsRequire;if(!u&&a)return a(o,!0);if(i)return i(o,!0);var f=new Error("Cannot find module '"+o+"'");throw f.code="MODULE_NOT_FOUND",f}var l=n[o]={exports:{}};t[o][0].call(l.exports,function(e){var n=t[o][1][e];return s(n?n:e)},l,l.exports,e,t,n,r);}return n[o].exports}var i=typeof commonjsRequire=="function"&&commonjsRequire;for(var o=0;o= 0; --i) { - tok = expansion[i]; - if (tok.text === "#") { - if (i === 0) { - throw new _ParseError2.default("Incomplete placeholder at end of macro body", tok); - } - tok = expansion[--i]; // next token on stack - if (tok.text === "#") { - // ## → # - expansion.splice(i + 1, 1); // drop first # - } else if (/^[1-9]$/.test(tok.text)) { - // expansion.splice(i, 2, arg[0], arg[1], …) - // to replace placeholder with the indicated argument. - // TODO: use spread once we move to ES2015 - expansion.splice.apply(expansion, [i, 2].concat(args[tok.text - 1])); - } else { - throw new _ParseError2.default("Not a valid argument number", tok); - } - } - } - } - this.stack = this.stack.concat(expansion); - } - } - }, { - key: "get", - value: function get(ignoreSpace) { - this.discardedWhiteSpace = []; - var token = this.nextToken(); - if (ignoreSpace) { - while (token.text === " ") { - this.discardedWhiteSpace.push(token); - token = this.nextToken(); - } - } - return token; - } - - /** - * Undo the effect of the preceding call to the get method. - * A call to this method MUST be immediately preceded and immediately followed - * by a call to get. Only used during mode switching, i.e. after one token - * was got in the old mode but should get got again in a new mode - * with possibly different whitespace handling. - */ - - }, { - key: "unget", - value: function unget(token) { - this.stack.push(token); - while (this.discardedWhiteSpace.length !== 0) { - this.stack.push(this.discardedWhiteSpace.pop()); - } - } - }]); - return MacroExpander; - }(); - - module.exports = MacroExpander; - - },{"./Lexer":26,"./ParseError":29,"./macros":44,"babel-runtime/helpers/classCallCheck":4,"babel-runtime/helpers/createClass":5,"object-assign":25}],28:[function(require,module,exports){ - - var _classCallCheck2 = require("babel-runtime/helpers/classCallCheck"); - - var _classCallCheck3 = _interopRequireDefault(_classCallCheck2); - - var _createClass2 = require("babel-runtime/helpers/createClass"); - - var _createClass3 = _interopRequireDefault(_createClass2); - - var _fontMetrics2 = require("./fontMetrics"); - - var _fontMetrics3 = _interopRequireDefault(_fontMetrics2); - - function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { default: obj }; } - - var BASESIZE = 6; /** - * This file contains information about the options that the Parser carries - * around with it while parsing. Data is held in an `Options` object, and when - * recursing, a new `Options` object can be created with the `.with*` and - * `.reset` functions. - */ - - var sizeStyleMap = [ - // Each element contains [textsize, scriptsize, scriptscriptsize]. - // The size mappings are taken from TeX with \normalsize=10pt. - [1, 1, 1], // size1: [5, 5, 5] \tiny - [2, 1, 1], // size2: [6, 5, 5] - [3, 1, 1], // size3: [7, 5, 5] \scriptsize - [4, 2, 1], // size4: [8, 6, 5] \footnotesize - [5, 2, 1], // size5: [9, 6, 5] \small - [6, 3, 1], // size6: [10, 7, 5] \normalsize - [7, 4, 2], // size7: [12, 8, 6] \large - [8, 6, 3], // size8: [14.4, 10, 7] \Large - [9, 7, 6], // size9: [17.28, 12, 10] \LARGE - [10, 8, 7], // size10: [20.74, 14.4, 12] \huge - [11, 10, 9]]; - - var sizeMultipliers = [ - // fontMetrics.js:getFontMetrics also uses size indexes, so if - // you change size indexes, change that function. - 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 1.2, 1.44, 1.728, 2.074, 2.488]; - - var sizeAtStyle = function sizeAtStyle(size, style) { - return style.size < 2 ? size : sizeStyleMap[size - 1][style.size - 1]; - }; - - /** - * This is the main options class. It contains the current style, size, color, - * and font. - * - * Options objects should not be modified. To create a new Options with - * different properties, call a `.having*` method. - */ - - var Options = function () { - function Options(data) { - (0, _classCallCheck3.default)(this, Options); - - this.style = data.style; - this.color = data.color; - this.size = data.size || BASESIZE; - this.textSize = data.textSize || this.size; - this.phantom = data.phantom; - this.font = data.font; - this.sizeMultiplier = sizeMultipliers[this.size - 1]; - this._fontMetrics = null; - } - - /** - * Returns a new options object with the same properties as "this". Properties - * from "extension" will be copied to the new options object. - */ - - - (0, _createClass3.default)(Options, [{ - key: "extend", - value: function extend(extension) { - var data = { - style: this.style, - size: this.size, - textSize: this.textSize, - color: this.color, - phantom: this.phantom, - font: this.font - }; - - for (var key in extension) { - if (extension.hasOwnProperty(key)) { - data[key] = extension[key]; - } - } - - return new Options(data); - } - - /** - * Return an options object with the given style. If `this.style === style`, - * returns `this`. - */ - - }, { - key: "havingStyle", - value: function havingStyle(style) { - if (this.style === style) { - return this; - } else { - return this.extend({ - style: style, - size: sizeAtStyle(this.textSize, style) - }); - } - } - - /** - * Return an options object with a cramped version of the current style. If - * the current style is cramped, returns `this`. - */ - - }, { - key: "havingCrampedStyle", - value: function havingCrampedStyle() { - return this.havingStyle(this.style.cramp()); - } - - /** - * Return an options object with the given size and in at least `\textstyle`. - * Returns `this` if appropriate. - */ - - }, { - key: "havingSize", - value: function havingSize(size) { - if (this.size === size && this.textSize === size) { - return this; - } else { - return this.extend({ - style: this.style.text(), - size: size, - textSize: size - }); - } - } - - /** - * Like `this.havingSize(BASESIZE).havingStyle(style)`. If `style` is omitted, - * changes to at least `\textstyle`. - */ - - }, { - key: "havingBaseStyle", - value: function havingBaseStyle(style) { - style = style || this.style.text(); - var wantSize = sizeAtStyle(BASESIZE, style); - if (this.size === wantSize && this.textSize === BASESIZE && this.style === style) { - return this; - } else { - return this.extend({ - style: style, - size: wantSize, - baseSize: BASESIZE - }); - } - } - - /** - * Create a new options object with the given color. - */ - - }, { - key: "withColor", - value: function withColor(color) { - return this.extend({ - color: color - }); - } - - /** - * Create a new options object with "phantom" set to true. - */ - - }, { - key: "withPhantom", - value: function withPhantom() { - return this.extend({ - phantom: true - }); - } - - /** - * Create a new options objects with the give font. - */ - - }, { - key: "withFont", - value: function withFont(font) { - return this.extend({ - font: font || this.font - }); - } - - /** - * Return the CSS sizing classes required to switch from enclosing options - * `oldOptions` to `this`. Returns an array of classes. - */ - - }, { - key: "sizingClasses", - value: function sizingClasses(oldOptions) { - if (oldOptions.size !== this.size) { - return ["sizing", "reset-size" + oldOptions.size, "size" + this.size]; - } else { - return []; - } - } - - /** - * Return the CSS sizing classes required to switch to the base size. Like - * `this.havingSize(BASESIZE).sizingClasses(this)`. - */ - - }, { - key: "baseSizingClasses", - value: function baseSizingClasses() { - if (this.size !== BASESIZE) { - return ["sizing", "reset-size" + this.size, "size" + BASESIZE]; - } else { - return []; - } - } - - /** - * Return the font metrics for this size. - */ - - }, { - key: "fontMetrics", - value: function fontMetrics() { - if (!this._fontMetrics) { - this._fontMetrics = _fontMetrics3.default.getFontMetrics(this.size); - } - return this._fontMetrics; - } - - /** - * A map of color names to CSS colors. - * TODO(emily): Remove this when we have real macros - */ - - }, { - key: "getColor", - - - /** - * Gets the CSS color of the current options object, accounting for the - * `colorMap`. - */ - value: function getColor() { - if (this.phantom) { - return "transparent"; - } else { - return Options.colorMap[this.color] || this.color; - } - } - }]); - return Options; - }(); - - /** - * The base size index. - */ - - - Options.colorMap = { - "katex-blue": "#6495ed", - "katex-orange": "#ffa500", - "katex-pink": "#ff00af", - "katex-red": "#df0030", - "katex-green": "#28ae7b", - "katex-gray": "gray", - "katex-purple": "#9d38bd", - "katex-blueA": "#ccfaff", - "katex-blueB": "#80f6ff", - "katex-blueC": "#63d9ea", - "katex-blueD": "#11accd", - "katex-blueE": "#0c7f99", - "katex-tealA": "#94fff5", - "katex-tealB": "#26edd5", - "katex-tealC": "#01d1c1", - "katex-tealD": "#01a995", - "katex-tealE": "#208170", - "katex-greenA": "#b6ffb0", - "katex-greenB": "#8af281", - "katex-greenC": "#74cf70", - "katex-greenD": "#1fab54", - "katex-greenE": "#0d923f", - "katex-goldA": "#ffd0a9", - "katex-goldB": "#ffbb71", - "katex-goldC": "#ff9c39", - "katex-goldD": "#e07d10", - "katex-goldE": "#a75a05", - "katex-redA": "#fca9a9", - "katex-redB": "#ff8482", - "katex-redC": "#f9685d", - "katex-redD": "#e84d39", - "katex-redE": "#bc2612", - "katex-maroonA": "#ffbde0", - "katex-maroonB": "#ff92c6", - "katex-maroonC": "#ed5fa6", - "katex-maroonD": "#ca337c", - "katex-maroonE": "#9e034e", - "katex-purpleA": "#ddd7ff", - "katex-purpleB": "#c6b9fc", - "katex-purpleC": "#aa87ff", - "katex-purpleD": "#7854ab", - "katex-purpleE": "#543b78", - "katex-mintA": "#f5f9e8", - "katex-mintB": "#edf2df", - "katex-mintC": "#e0e5cc", - "katex-grayA": "#f6f7f7", - "katex-grayB": "#f0f1f2", - "katex-grayC": "#e3e5e6", - "katex-grayD": "#d6d8da", - "katex-grayE": "#babec2", - "katex-grayF": "#888d93", - "katex-grayG": "#626569", - "katex-grayH": "#3b3e40", - "katex-grayI": "#21242c", - "katex-kaBlue": "#314453", - "katex-kaGreen": "#71B307" - }; - Options.BASESIZE = BASESIZE; - - module.exports = Options; - - },{"./fontMetrics":41,"babel-runtime/helpers/classCallCheck":4,"babel-runtime/helpers/createClass":5}],29:[function(require,module,exports){ - - var _classCallCheck2 = require("babel-runtime/helpers/classCallCheck"); - - var _classCallCheck3 = _interopRequireDefault(_classCallCheck2); - - function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { default: obj }; } - - /** - * This is the ParseError class, which is the main error thrown by KaTeX - * functions when something has gone wrong. This is used to distinguish internal - * errors from errors in the expression that the user provided. - * - * If possible, a caller should provide a Token or ParseNode with information - * about where in the source string the problem occurred. - * - * @param {string} message The error message - * @param {(Token|ParseNode)=} token An object providing position information - */ - var ParseError = function ParseError(message, token) { - (0, _classCallCheck3.default)(this, ParseError); - - var error = "KaTeX parse error: " + message; - var start = void 0; - var end = void 0; - - if (token && token.lexer && token.start <= token.end) { - // If we have the input and a position, make the error a bit fancier - - // Get the input - var input = token.lexer.input; - - // Prepend some information - start = token.start; - end = token.end; - if (start === input.length) { - error += " at end of input: "; - } else { - error += " at position " + (start + 1) + ": "; - } - - // Underline token in question using combining underscores - var underlined = input.slice(start, end).replace(/[^]/g, "$&\u0332"); - - // Extract some context from the input and add it to the error - var left = void 0; - if (start > 15) { - left = "…" + input.slice(start - 15, start); - } else { - left = input.slice(0, start); - } - var right = void 0; - if (end + 15 < input.length) { - right = input.slice(end, end + 15) + "…"; - } else { - right = input.slice(end); - } - error += left + underlined + right; - } - - // Some hackery to make ParseError a prototype of Error - // See http://stackoverflow.com/a/8460753 - var self = new Error(error); - self.name = "ParseError"; - self.__proto__ = ParseError.prototype; - - self.position = start; - return self; - }; - - // More hackery - - - ParseError.prototype.__proto__ = Error.prototype; - - module.exports = ParseError; - - },{"babel-runtime/helpers/classCallCheck":4}],30:[function(require,module,exports){ - - Object.defineProperty(exports, "__esModule", { - value: true - }); - - var _classCallCheck2 = require("babel-runtime/helpers/classCallCheck"); - - var _classCallCheck3 = _interopRequireDefault(_classCallCheck2); - - function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { default: obj }; } - - /** - * The resulting parse tree nodes of the parse tree. - * - * It is possible to provide position information, so that a ParseNode can - * fulfil a role similar to a Token in error reporting. - * For details on the corresponding properties see Token constructor. - * Providing such information can lead to better error reporting. - * - * @param {string} type type of node, like e.g. "ordgroup" - * @param {?object} value type-specific representation of the node - * @param {string} mode parse mode in action for this node, - * "math" or "text" - * @param {Token=} firstToken first token of the input for this node, - * will omit position information if unset - * @param {Token=} lastToken last token of the input for this node, - * will default to firstToken if unset - */ - var ParseNode = function ParseNode(type, value, mode, firstToken, lastToken) { - (0, _classCallCheck3.default)(this, ParseNode); - - this.type = type; - this.value = value; - this.mode = mode; - if (firstToken && (!lastToken || lastToken.lexer === firstToken.lexer)) { - this.lexer = firstToken.lexer; - this.start = firstToken.start; - this.end = (lastToken || firstToken).end; - } - }; - - exports.default = ParseNode; - - },{"babel-runtime/helpers/classCallCheck":4}],31:[function(require,module,exports){ - - var _classCallCheck2 = require("babel-runtime/helpers/classCallCheck"); - - var _classCallCheck3 = _interopRequireDefault(_classCallCheck2); - - var _createClass2 = require("babel-runtime/helpers/createClass"); - - var _createClass3 = _interopRequireDefault(_createClass2); - - var _functions = require("./functions"); - - var _functions2 = _interopRequireDefault(_functions); - - var _environments = require("./environments"); - - var _environments2 = _interopRequireDefault(_environments); - - var _MacroExpander = require("./MacroExpander"); - - var _MacroExpander2 = _interopRequireDefault(_MacroExpander); - - var _symbols = require("./symbols"); - - var _symbols2 = _interopRequireDefault(_symbols); - - var _utils = require("./utils"); - - var _utils2 = _interopRequireDefault(_utils); - - var _units = require("./units"); - - var _units2 = _interopRequireDefault(_units); - - var _unicodeRegexes = require("./unicodeRegexes"); - - var _ParseNode = require("./ParseNode"); - - var _ParseNode2 = _interopRequireDefault(_ParseNode); - - var _ParseError = require("./ParseError"); - - var _ParseError2 = _interopRequireDefault(_ParseError); - - function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { default: obj }; } - - /** - * This file contains the parser used to parse out a TeX expression from the - * input. Since TeX isn't context-free, standard parsers don't work particularly - * well. - * - * The strategy of this parser is as such: - * - * The main functions (the `.parse...` ones) take a position in the current - * parse string to parse tokens from. The lexer (found in Lexer.js, stored at - * this.lexer) also supports pulling out tokens at arbitrary places. When - * individual tokens are needed at a position, the lexer is called to pull out a - * token, which is then used. - * - * The parser has a property called "mode" indicating the mode that - * the parser is currently in. Currently it has to be one of "math" or - * "text", which denotes whether the current environment is a math-y - * one or a text-y one (e.g. inside \text). Currently, this serves to - * limit the functions which can be used in text mode. - * - * The main functions then return an object which contains the useful data that - * was parsed at its given point, and a new position at the end of the parsed - * data. The main functions can call each other and continue the parsing by - * using the returned position as a new starting point. - * - * There are also extra `.handle...` functions, which pull out some reused - * functionality into self-contained functions. - * - * The earlier functions return ParseNodes. - * The later functions (which are called deeper in the parse) sometimes return - * ParseFuncOrArgument, which contain a ParseNode as well as some data about - * whether the parsed object is a function which is missing some arguments, or a - * standalone object which can be used as an argument to another function. - */ - - /** - * An initial function (without its arguments), or an argument to a function. - * The `result` argument should be a ParseNode. - */ - function ParseFuncOrArgument(result, isFunction, token) { - this.result = result; - // Is this a function (i.e. is it something defined in functions.js)? - this.isFunction = isFunction; - this.token = token; - } /* eslint no-constant-condition:0 */ - - var Parser = function () { - function Parser(input, settings) { - (0, _classCallCheck3.default)(this, Parser); - - // Create a new macro expander (gullet) and (indirectly via that) also a - // new lexer (mouth) for this parser (stomach, in the language of TeX) - this.gullet = new _MacroExpander2.default(input, settings.macros); - // Use old \color behavior (same as LaTeX's \textcolor) if requested. - // We do this after the macros object has been copied by MacroExpander. - if (settings.colorIsTextColor) { - this.gullet.macros["\\color"] = "\\textcolor"; - } - // Store the settings for use in parsing - this.settings = settings; - // Count leftright depth (for \middle errors) - this.leftrightDepth = 0; - } - - /** - * Checks a result to make sure it has the right type, and throws an - * appropriate error otherwise. - * - * @param {boolean=} consume whether to consume the expected token, - * defaults to true - */ - - - (0, _createClass3.default)(Parser, [{ - key: "expect", - value: function expect(text, consume) { - if (this.nextToken.text !== text) { - throw new _ParseError2.default("Expected '" + text + "', got '" + this.nextToken.text + "'", this.nextToken); - } - if (consume !== false) { - this.consume(); - } - } - - /** - * Considers the current look ahead token as consumed, - * and fetches the one after that as the new look ahead. - */ - - }, { - key: "consume", - value: function consume() { - this.nextToken = this.gullet.get(this.mode === "math"); - } - }, { - key: "switchMode", - value: function switchMode(newMode) { - this.gullet.unget(this.nextToken); - this.mode = newMode; - this.consume(); - } - - /** - * Main parsing function, which parses an entire input. - * - * @return {?Array.} - */ - - }, { - key: "parse", - value: function parse() { - // Try to parse the input - this.mode = "math"; - this.consume(); - var parse = this.parseInput(); - return parse; - } - - /** - * Parses an entire input tree. - */ - - }, { - key: "parseInput", - value: function parseInput() { - // Parse an expression - var expression = this.parseExpression(false); - // If we succeeded, make sure there's an EOF at the end - this.expect("EOF", false); - return expression; - } - }, { - key: "parseExpression", - - - /** - * Parses an "expression", which is a list of atoms. - * - * @param {boolean} breakOnInfix Should the parsing stop when we hit infix - * nodes? This happens when functions have higher precendence - * than infix nodes in implicit parses. - * - * @param {?string} breakOnTokenText The text of the token that the expression - * should end with, or `null` if something else should end the - * expression. - * - * @return {ParseNode} - */ - value: function parseExpression(breakOnInfix, breakOnTokenText) { - var body = []; - // Keep adding atoms to the body until we can't parse any more atoms (either - // we reached the end, a }, or a \right) - while (true) { - var lex = this.nextToken; - if (Parser.endOfExpression.indexOf(lex.text) !== -1) { - break; - } - if (breakOnTokenText && lex.text === breakOnTokenText) { - break; - } - if (breakOnInfix && _functions2.default[lex.text] && _functions2.default[lex.text].infix) { - break; - } - var atom = this.parseAtom(); - if (!atom) { - if (!this.settings.throwOnError && lex.text[0] === "\\") { - var errorNode = this.handleUnsupportedCmd(); - body.push(errorNode); - continue; - } - - break; - } - body.push(atom); - } - return this.handleInfixNodes(body); - } - - /** - * Rewrites infix operators such as \over with corresponding commands such - * as \frac. - * - * There can only be one infix operator per group. If there's more than one - * then the expression is ambiguous. This can be resolved by adding {}. - * - * @returns {Array} - */ - - }, { - key: "handleInfixNodes", - value: function handleInfixNodes(body) { - var overIndex = -1; - var funcName = void 0; - - for (var i = 0; i < body.length; i++) { - var node = body[i]; - if (node.type === "infix") { - if (overIndex !== -1) { - throw new _ParseError2.default("only one infix operator per group", node.value.token); - } - overIndex = i; - funcName = node.value.replaceWith; - } - } - - if (overIndex !== -1) { - var numerNode = void 0; - var denomNode = void 0; - - var numerBody = body.slice(0, overIndex); - var denomBody = body.slice(overIndex + 1); - - if (numerBody.length === 1 && numerBody[0].type === "ordgroup") { - numerNode = numerBody[0]; - } else { - numerNode = new _ParseNode2.default("ordgroup", numerBody, this.mode); - } - - if (denomBody.length === 1 && denomBody[0].type === "ordgroup") { - denomNode = denomBody[0]; - } else { - denomNode = new _ParseNode2.default("ordgroup", denomBody, this.mode); - } - - var value = this.callFunction(funcName, [numerNode, denomNode], null); - return [new _ParseNode2.default(value.type, value, this.mode)]; - } else { - return body; - } - } - - // The greediness of a superscript or subscript - - }, { - key: "handleSupSubscript", - - - /** - * Handle a subscript or superscript with nice errors. - */ - value: function handleSupSubscript(name) { - var symbolToken = this.nextToken; - var symbol = symbolToken.text; - this.consume(); - var group = this.parseGroup(); - - if (!group) { - if (!this.settings.throwOnError && this.nextToken.text[0] === "\\") { - return this.handleUnsupportedCmd(); - } else { - throw new _ParseError2.default("Expected group after '" + symbol + "'", symbolToken); - } - } else if (group.isFunction) { - // ^ and _ have a greediness, so handle interactions with functions' - // greediness - var funcGreediness = _functions2.default[group.result].greediness; - if (funcGreediness > Parser.SUPSUB_GREEDINESS) { - return this.parseFunction(group); - } else { - throw new _ParseError2.default("Got function '" + group.result + "' with no arguments " + "as " + name, symbolToken); - } - } else { - return group.result; - } - } - - /** - * Converts the textual input of an unsupported command into a text node - * contained within a color node whose color is determined by errorColor - */ - - }, { - key: "handleUnsupportedCmd", - value: function handleUnsupportedCmd() { - var text = this.nextToken.text; - var textordArray = []; - - for (var i = 0; i < text.length; i++) { - textordArray.push(new _ParseNode2.default("textord", text[i], "text")); - } - - var textNode = new _ParseNode2.default("text", { - body: textordArray, - type: "text" - }, this.mode); - - var colorNode = new _ParseNode2.default("color", { - color: this.settings.errorColor, - value: [textNode], - type: "color" - }, this.mode); - - this.consume(); - return colorNode; - } - - /** - * Parses a group with optional super/subscripts. - * - * @return {?ParseNode} - */ - - }, { - key: "parseAtom", - value: function parseAtom() { - // The body of an atom is an implicit group, so that things like - // \left(x\right)^2 work correctly. - var base = this.parseImplicitGroup(); - - // In text mode, we don't have superscripts or subscripts - if (this.mode === "text") { - return base; - } - - // Note that base may be empty (i.e. null) at this point. - - var superscript = void 0; - var subscript = void 0; - while (true) { - // Lex the first token - var lex = this.nextToken; - - if (lex.text === "\\limits" || lex.text === "\\nolimits") { - // We got a limit control - if (!base || base.type !== "op") { - throw new _ParseError2.default("Limit controls must follow a math operator", lex); - } else { - var limits = lex.text === "\\limits"; - base.value.limits = limits; - base.value.alwaysHandleSupSub = true; - } - this.consume(); - } else if (lex.text === "^") { - // We got a superscript start - if (superscript) { - throw new _ParseError2.default("Double superscript", lex); - } - superscript = this.handleSupSubscript("superscript"); - } else if (lex.text === "_") { - // We got a subscript start - if (subscript) { - throw new _ParseError2.default("Double subscript", lex); - } - subscript = this.handleSupSubscript("subscript"); - } else if (lex.text === "'") { - // We got a prime - if (superscript) { - throw new _ParseError2.default("Double superscript", lex); - } - var prime = new _ParseNode2.default("textord", "\\prime", this.mode); - - // Many primes can be grouped together, so we handle this here - var primes = [prime]; - this.consume(); - // Keep lexing tokens until we get something that's not a prime - while (this.nextToken.text === "'") { - // For each one, add another prime to the list - primes.push(prime); - this.consume(); - } - // If there's a superscript following the primes, combine that - // superscript in with the primes. - if (this.nextToken.text === "^") { - primes.push(this.handleSupSubscript("superscript")); - } - // Put everything into an ordgroup as the superscript - superscript = new _ParseNode2.default("ordgroup", primes, this.mode); - } else { - // If it wasn't ^, _, or ', stop parsing super/subscripts - break; - } - } - - if (superscript || subscript) { - // If we got either a superscript or subscript, create a supsub - return new _ParseNode2.default("supsub", { - base: base, - sup: superscript, - sub: subscript - }, this.mode); - } else { - // Otherwise return the original body - return base; - } - } - - // A list of the size-changing functions, for use in parseImplicitGroup - - - // A list of the style-changing functions, for use in parseImplicitGroup - - - // Old font functions - - }, { - key: "parseImplicitGroup", - - - /** - * Parses an implicit group, which is a group that starts at the end of a - * specified, and ends right before a higher explicit group ends, or at EOL. It - * is used for functions that appear to affect the current style, like \Large or - * \textrm, where instead of keeping a style we just pretend that there is an - * implicit grouping after it until the end of the group. E.g. - * small text {\Large large text} small text again - * It is also used for \left and \right to get the correct grouping. - * - * @return {?ParseNode} - */ - value: function parseImplicitGroup() { - var start = this.parseSymbol(); - - if (start == null) { - // If we didn't get anything we handle, fall back to parseFunction - return this.parseFunction(); - } - - var func = start.result; - - if (func === "\\left") { - // If we see a left: - // Parse the entire left function (including the delimiter) - var left = this.parseFunction(start); - // Parse out the implicit body - ++this.leftrightDepth; - var body = this.parseExpression(false); - --this.leftrightDepth; - // Check the next token - this.expect("\\right", false); - var right = this.parseFunction(); - return new _ParseNode2.default("leftright", { - body: body, - left: left.value.value, - right: right.value.value - }, this.mode); - } else if (func === "\\begin") { - // begin...end is similar to left...right - var begin = this.parseFunction(start); - var envName = begin.value.name; - if (!_environments2.default.hasOwnProperty(envName)) { - throw new _ParseError2.default("No such environment: " + envName, begin.value.nameGroup); - } - // Build the environment object. Arguments and other information will - // be made available to the begin and end methods using properties. - var env = _environments2.default[envName]; - var args = this.parseArguments("\\begin{" + envName + "}", env); - var context = { - mode: this.mode, - envName: envName, - parser: this, - positions: args.pop() - }; - var result = env.handler(context, args); - this.expect("\\end", false); - var endNameToken = this.nextToken; - var end = this.parseFunction(); - if (end.value.name !== envName) { - throw new _ParseError2.default("Mismatch: \\begin{" + envName + "} matched " + "by \\end{" + end.value.name + "}", endNameToken); - } - result.position = end.position; - return result; - } else if (_utils2.default.contains(Parser.sizeFuncs, func)) { - // If we see a sizing function, parse out the implicit body - this.consumeSpaces(); - var _body = this.parseExpression(false); - return new _ParseNode2.default("sizing", { - // Figure out what size to use based on the list of functions above - size: _utils2.default.indexOf(Parser.sizeFuncs, func) + 1, - value: _body - }, this.mode); - } else if (_utils2.default.contains(Parser.styleFuncs, func)) { - // If we see a styling function, parse out the implicit body - this.consumeSpaces(); - var _body2 = this.parseExpression(true); - return new _ParseNode2.default("styling", { - // Figure out what style to use by pulling out the style from - // the function name - style: func.slice(1, func.length - 5), - value: _body2 - }, this.mode); - } else if (func in Parser.oldFontFuncs) { - var style = Parser.oldFontFuncs[func]; - // If we see an old font function, parse out the implicit body - this.consumeSpaces(); - var _body3 = this.parseExpression(true); - if (style.slice(0, 4) === 'text') { - return new _ParseNode2.default("text", { - style: style, - body: new _ParseNode2.default("ordgroup", _body3, this.mode) - }, this.mode); - } else { - return new _ParseNode2.default("font", { - font: style, - body: new _ParseNode2.default("ordgroup", _body3, this.mode) - }, this.mode); - } - } else if (func === "\\color") { - // If we see a styling function, parse out the implicit body - var color = this.parseColorGroup(false); - if (!color) { - throw new _ParseError2.default("\\color not followed by color"); - } - var _body4 = this.parseExpression(true); - return new _ParseNode2.default("color", { - type: "color", - color: color.result.value, - value: _body4 - }, this.mode); - } else if (func === "$") { - if (this.mode === "math") { - throw new _ParseError2.default("$ within math mode"); - } - this.consume(); - var outerMode = this.mode; - this.switchMode("math"); - var _body5 = this.parseExpression(false, "$"); - this.expect("$", true); - this.switchMode(outerMode); - return new _ParseNode2.default("styling", { - style: "text", - value: _body5 - }, "math"); - } else { - // Defer to parseFunction if it's not a function we handle - return this.parseFunction(start); - } - } - - /** - * Parses an entire function, including its base and all of its arguments. - * The base might either have been parsed already, in which case - * it is provided as an argument, or it's the next group in the input. - * - * @param {ParseFuncOrArgument=} baseGroup optional as described above - * @return {?ParseNode} - */ - - }, { - key: "parseFunction", - value: function parseFunction(baseGroup) { - if (!baseGroup) { - baseGroup = this.parseGroup(); - } - - if (baseGroup) { - if (baseGroup.isFunction) { - var func = baseGroup.result; - var funcData = _functions2.default[func]; - if (this.mode === "text" && !funcData.allowedInText) { - throw new _ParseError2.default("Can't use function '" + func + "' in text mode", baseGroup.token); - } else if (this.mode === "math" && funcData.allowedInMath === false) { - throw new _ParseError2.default("Can't use function '" + func + "' in math mode", baseGroup.token); - } - - var args = this.parseArguments(func, funcData); - var token = baseGroup.token; - var result = this.callFunction(func, args, args.pop(), token); - return new _ParseNode2.default(result.type, result, this.mode); - } else { - return baseGroup.result; - } - } else { - return null; - } - } - - /** - * Call a function handler with a suitable context and arguments. - */ - - }, { - key: "callFunction", - value: function callFunction(name, args, positions, token) { - var context = { - funcName: name, - parser: this, - positions: positions, - token: token - }; - return _functions2.default[name].handler(context, args); - } - - /** - * Parses the arguments of a function or environment - * - * @param {string} func "\name" or "\begin{name}" - * @param {{numArgs:number,numOptionalArgs:number|undefined}} funcData - * @return the array of arguments, with the list of positions as last element - */ - - }, { - key: "parseArguments", - value: function parseArguments(func, funcData) { - var totalArgs = funcData.numArgs + funcData.numOptionalArgs; - if (totalArgs === 0) { - return [[this.pos]]; - } - - var baseGreediness = funcData.greediness; - var positions = [this.pos]; - var args = []; - - for (var i = 0; i < totalArgs; i++) { - var nextToken = this.nextToken; - var argType = funcData.argTypes && funcData.argTypes[i]; - var arg = void 0; - if (i < funcData.numOptionalArgs) { - if (argType) { - arg = this.parseGroupOfType(argType, true); - } else { - arg = this.parseGroup(true); - } - if (!arg) { - args.push(null); - positions.push(this.pos); - continue; - } - } else { - if (argType) { - arg = this.parseGroupOfType(argType); - } else { - arg = this.parseGroup(); - } - if (!arg) { - if (!this.settings.throwOnError && this.nextToken.text[0] === "\\") { - arg = new ParseFuncOrArgument(this.handleUnsupportedCmd(this.nextToken.text), false); - } else { - throw new _ParseError2.default("Expected group after '" + func + "'", nextToken); - } - } - } - var argNode = void 0; - if (arg.isFunction) { - var argGreediness = _functions2.default[arg.result].greediness; - if (argGreediness > baseGreediness) { - argNode = this.parseFunction(arg); - } else { - throw new _ParseError2.default("Got function '" + arg.result + "' as " + "argument to '" + func + "'", nextToken); - } - } else { - argNode = arg.result; - } - args.push(argNode); - positions.push(this.pos); - } - - args.push(positions); - - return args; - } - - /** - * Parses a group when the mode is changing. - * - * @return {?ParseFuncOrArgument} - */ - - }, { - key: "parseGroupOfType", - value: function parseGroupOfType(innerMode, optional) { - var outerMode = this.mode; - // Handle `original` argTypes - if (innerMode === "original") { - innerMode = outerMode; - } - - if (innerMode === "color") { - return this.parseColorGroup(optional); - } - if (innerMode === "size") { - return this.parseSizeGroup(optional); - } - - this.switchMode(innerMode); - if (innerMode === "text") { - // text mode is special because it should ignore the whitespace before - // it - this.consumeSpaces(); - } - // By the time we get here, innerMode is one of "text" or "math". - // We switch the mode of the parser, recurse, then restore the old mode. - var res = this.parseGroup(optional); - this.switchMode(outerMode); - return res; - } - }, { - key: "consumeSpaces", - value: function consumeSpaces() { - while (this.nextToken.text === " ") { - this.consume(); - } - } - - /** - * Parses a group, essentially returning the string formed by the - * brace-enclosed tokens plus some position information. - * - * @param {string} modeName Used to describe the mode in error messages - * @param {boolean=} optional Whether the group is optional or required - */ - - }, { - key: "parseStringGroup", - value: function parseStringGroup(modeName, optional) { - if (optional && this.nextToken.text !== "[") { - return null; - } - var outerMode = this.mode; - this.mode = "text"; - this.expect(optional ? "[" : "{"); - var str = ""; - var firstToken = this.nextToken; - var lastToken = firstToken; - while (this.nextToken.text !== (optional ? "]" : "}")) { - if (this.nextToken.text === "EOF") { - throw new _ParseError2.default("Unexpected end of input in " + modeName, firstToken.range(this.nextToken, str)); - } - lastToken = this.nextToken; - str += lastToken.text; - this.consume(); - } - this.mode = outerMode; - this.expect(optional ? "]" : "}"); - return firstToken.range(lastToken, str); - } - - /** - * Parses a regex-delimited group: the largest sequence of tokens - * whose concatenated strings match `regex`. Returns the string - * formed by the tokens plus some position information. - * - * @param {RegExp} regex - * @param {string} modeName Used to describe the mode in error messages - */ - - }, { - key: "parseRegexGroup", - value: function parseRegexGroup(regex, modeName) { - var outerMode = this.mode; - this.mode = "text"; - var firstToken = this.nextToken; - var lastToken = firstToken; - var str = ""; - while (this.nextToken.text !== "EOF" && regex.test(str + this.nextToken.text)) { - lastToken = this.nextToken; - str += lastToken.text; - this.consume(); - } - if (str === "") { - throw new _ParseError2.default("Invalid " + modeName + ": '" + firstToken.text + "'", firstToken); - } - this.mode = outerMode; - return firstToken.range(lastToken, str); - } - - /** - * Parses a color description. - */ - - }, { - key: "parseColorGroup", - value: function parseColorGroup(optional) { - var res = this.parseStringGroup("color", optional); - if (!res) { - return null; - } - var match = /^(#[a-z0-9]+|[a-z]+)$/i.exec(res.text); - if (!match) { - throw new _ParseError2.default("Invalid color: '" + res.text + "'", res); - } - return new ParseFuncOrArgument(new _ParseNode2.default("color", match[0], this.mode), false); - } - - /** - * Parses a size specification, consisting of magnitude and unit. - */ - - }, { - key: "parseSizeGroup", - value: function parseSizeGroup(optional) { - var res = void 0; - if (!optional && this.nextToken.text !== "{") { - res = this.parseRegexGroup(/^[-+]? *(?:$|\d+|\d+\.\d*|\.\d*) *[a-z]{0,2} *$/, "size"); - } else { - res = this.parseStringGroup("size", optional); - } - if (!res) { - return null; - } - var match = /([-+]?) *(\d+(?:\.\d*)?|\.\d+) *([a-z]{2})/.exec(res.text); - if (!match) { - throw new _ParseError2.default("Invalid size: '" + res.text + "'", res); - } - var data = { - number: +(match[1] + match[2]), // sign + magnitude, cast to number - unit: match[3] - }; - if (!_units2.default.validUnit(data)) { - throw new _ParseError2.default("Invalid unit: '" + data.unit + "'", res); - } - return new ParseFuncOrArgument(new _ParseNode2.default("size", data, this.mode), false); - } - - /** - * If the argument is false or absent, this parses an ordinary group, - * which is either a single nucleus (like "x") or an expression - * in braces (like "{x+y}"). - * If the argument is true, it parses either a bracket-delimited expression - * (like "[x+y]") or returns null to indicate the absence of a - * bracket-enclosed group. - * - * @param {boolean=} optional Whether the group is optional or required - * @return {?ParseFuncOrArgument} - */ - - }, { - key: "parseGroup", - value: function parseGroup(optional) { - var firstToken = this.nextToken; - // Try to parse an open brace - if (this.nextToken.text === (optional ? "[" : "{")) { - // If we get a brace, parse an expression - this.consume(); - var expression = this.parseExpression(false, optional ? "]" : null); - var lastToken = this.nextToken; - // Make sure we get a close brace - this.expect(optional ? "]" : "}"); - if (this.mode === "text") { - this.formLigatures(expression); - } - return new ParseFuncOrArgument(new _ParseNode2.default("ordgroup", expression, this.mode, firstToken, lastToken), false); - } else { - // Otherwise, just return a nucleus, or nothing for an optional group - return optional ? null : this.parseSymbol(); - } - } - - /** - * Form ligature-like combinations of characters for text mode. - * This includes inputs like "--", "---", "``" and "''". - * The result will simply replace multiple textord nodes with a single - * character in each value by a single textord node having multiple - * characters in its value. The representation is still ASCII source. - * - * @param {Array.} group the nodes of this group, - * list will be moified in place - */ - - }, { - key: "formLigatures", - value: function formLigatures(group) { - var n = group.length - 1; - for (var i = 0; i < n; ++i) { - var a = group[i]; - var v = a.value; - if (v === "-" && group[i + 1].value === "-") { - if (i + 1 < n && group[i + 2].value === "-") { - group.splice(i, 3, new _ParseNode2.default("textord", "---", "text", a, group[i + 2])); - n -= 2; - } else { - group.splice(i, 2, new _ParseNode2.default("textord", "--", "text", a, group[i + 1])); - n -= 1; - } - } - if ((v === "'" || v === "`") && group[i + 1].value === v) { - group.splice(i, 2, new _ParseNode2.default("textord", v + v, "text", a, group[i + 1])); - n -= 1; - } - } - } - - /** - * Parse a single symbol out of the string. Here, we handle both the functions - * we have defined, as well as the single character symbols - * - * @return {?ParseFuncOrArgument} - */ - - }, { - key: "parseSymbol", - value: function parseSymbol() { - var nucleus = this.nextToken; - - if (_functions2.default[nucleus.text]) { - this.consume(); - // If there exists a function with this name, we return the function and - // say that it is a function. - return new ParseFuncOrArgument(nucleus.text, true, nucleus); - } else if (_symbols2.default[this.mode][nucleus.text]) { - this.consume(); - // Otherwise if this is a no-argument function, find the type it - // corresponds to in the symbols map - return new ParseFuncOrArgument(new _ParseNode2.default(_symbols2.default[this.mode][nucleus.text].group, nucleus.text, this.mode, nucleus), false, nucleus); - } else if (this.mode === "text" && _unicodeRegexes.cjkRegex.test(nucleus.text)) { - this.consume(); - return new ParseFuncOrArgument(new _ParseNode2.default("textord", nucleus.text, this.mode, nucleus), false, nucleus); - } else if (nucleus.text === "$") { - return new ParseFuncOrArgument(nucleus.text, false, nucleus); - } else { - return null; - } - } - }]); - return Parser; - }(); - - Parser.endOfExpression = ["}", "\\end", "\\right", "&", "\\\\", "\\cr"]; - Parser.SUPSUB_GREEDINESS = 1; - Parser.sizeFuncs = ["\\tiny", "\\sixptsize", "\\scriptsize", "\\footnotesize", "\\small", "\\normalsize", "\\large", "\\Large", "\\LARGE", "\\huge", "\\Huge"]; - Parser.styleFuncs = ["\\displaystyle", "\\textstyle", "\\scriptstyle", "\\scriptscriptstyle"]; - Parser.oldFontFuncs = { - "\\rm": "mathrm", - "\\sf": "mathsf", - "\\tt": "mathtt", - "\\bf": "mathbf", - "\\it": "mathit" - }; - - - Parser.prototype.ParseNode = _ParseNode2.default; - - module.exports = Parser; - - },{"./MacroExpander":27,"./ParseError":29,"./ParseNode":30,"./environments":40,"./functions":43,"./symbols":48,"./unicodeRegexes":49,"./units":50,"./utils":51,"babel-runtime/helpers/classCallCheck":4,"babel-runtime/helpers/createClass":5}],32:[function(require,module,exports){ - - var _classCallCheck2 = require("babel-runtime/helpers/classCallCheck"); - - var _classCallCheck3 = _interopRequireDefault(_classCallCheck2); - - var _utils = require("./utils"); - - var _utils2 = _interopRequireDefault(_utils); - - function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { default: obj }; } - - /** - * The main Settings object - * - * The current options stored are: - * - displayMode: Whether the expression should be typeset as inline math - * (false, the default), meaning that the math starts in - * \textstyle and is placed in an inline-block); or as display - * math (true), meaning that the math starts in \displaystyle - * and is placed in a block with vertical margin. - */ - var Settings = function Settings(options) { - (0, _classCallCheck3.default)(this, Settings); - - // allow null options - options = options || {}; - this.displayMode = _utils2.default.deflt(options.displayMode, false); - this.throwOnError = _utils2.default.deflt(options.throwOnError, true); - this.errorColor = _utils2.default.deflt(options.errorColor, "#cc0000"); - this.macros = options.macros || {}; - this.colorIsTextColor = _utils2.default.deflt(options.colorIsTextColor, false); - }; /** - * This is a module for storing settings passed into KaTeX. It correctly handles - * default settings. - */ - - module.exports = Settings; - - },{"./utils":51,"babel-runtime/helpers/classCallCheck":4}],33:[function(require,module,exports){ - - var _classCallCheck2 = require("babel-runtime/helpers/classCallCheck"); - - var _classCallCheck3 = _interopRequireDefault(_classCallCheck2); - - var _createClass2 = require("babel-runtime/helpers/createClass"); - - var _createClass3 = _interopRequireDefault(_createClass2); - - function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { default: obj }; } - - /** - * This file contains information and classes for the various kinds of styles - * used in TeX. It provides a generic `Style` class, which holds information - * about a specific style. It then provides instances of all the different kinds - * of styles possible, and provides functions to move between them and get - * information about them. - */ - - /** - * The main style class. Contains a unique id for the style, a size (which is - * the same for cramped and uncramped version of a style), and a cramped flag. - */ - var Style = function () { - function Style(id, size, cramped) { - (0, _classCallCheck3.default)(this, Style); - - this.id = id; - this.size = size; - this.cramped = cramped; - } - - /** - * Get the style of a superscript given a base in the current style. - */ - - - (0, _createClass3.default)(Style, [{ - key: "sup", - value: function sup() { - return styles[_sup[this.id]]; - } - - /** - * Get the style of a subscript given a base in the current style. - */ - - }, { - key: "sub", - value: function sub() { - return styles[_sub[this.id]]; - } - - /** - * Get the style of a fraction numerator given the fraction in the current - * style. - */ - - }, { - key: "fracNum", - value: function fracNum() { - return styles[_fracNum[this.id]]; - } - - /** - * Get the style of a fraction denominator given the fraction in the current - * style. - */ - - }, { - key: "fracDen", - value: function fracDen() { - return styles[_fracDen[this.id]]; - } - - /** - * Get the cramped version of a style (in particular, cramping a cramped style - * doesn't change the style). - */ - - }, { - key: "cramp", - value: function cramp() { - return styles[_cramp[this.id]]; - } - - /** - * Get a text or display version of this style. - */ - - }, { - key: "text", - value: function text() { - return styles[_text[this.id]]; - } - - /** - * Return if this style is tightly spaced (scriptstyle/scriptscriptstyle) - */ - - }, { - key: "isTight", - value: function isTight() { - return this.size >= 2; - } - }]); - return Style; - }(); - - // IDs of the different styles - - - var D = 0; - var Dc = 1; - var T = 2; - var Tc = 3; - var S = 4; - var Sc = 5; - var SS = 6; - var SSc = 7; - - // Instances of the different styles - var styles = [new Style(D, 0, false), new Style(Dc, 0, true), new Style(T, 1, false), new Style(Tc, 1, true), new Style(S, 2, false), new Style(Sc, 2, true), new Style(SS, 3, false), new Style(SSc, 3, true)]; - - // Lookup tables for switching from one style to another - var _sup = [S, Sc, S, Sc, SS, SSc, SS, SSc]; - var _sub = [Sc, Sc, Sc, Sc, SSc, SSc, SSc, SSc]; - var _fracNum = [T, Tc, S, Sc, SS, SSc, SS, SSc]; - var _fracDen = [Tc, Tc, Sc, Sc, SSc, SSc, SSc, SSc]; - var _cramp = [Dc, Dc, Tc, Tc, Sc, Sc, SSc, SSc]; - var _text = [D, Dc, T, Tc, T, Tc, T, Tc]; - - // We only export some of the styles. Also, we don't export the `Style` class so - // no more styles can be generated. - module.exports = { - DISPLAY: styles[D], - TEXT: styles[T], - SCRIPT: styles[S], - SCRIPTSCRIPT: styles[SS] - }; - - },{"babel-runtime/helpers/classCallCheck":4,"babel-runtime/helpers/createClass":5}],34:[function(require,module,exports){ - - var _domTree = require("./domTree"); - - var _domTree2 = _interopRequireDefault(_domTree); - - var _fontMetrics = require("./fontMetrics"); - - var _fontMetrics2 = _interopRequireDefault(_fontMetrics); - - var _symbols = require("./symbols"); - - var _symbols2 = _interopRequireDefault(_symbols); - - var _utils = require("./utils"); - - var _utils2 = _interopRequireDefault(_utils); - - function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { default: obj }; } - - // The following have to be loaded from Main-Italic font, using class mainit - /* eslint no-console:0 */ - /** - * This module contains general functions that can be used for building - * different kinds of domTree nodes in a consistent manner. - */ - - var mainitLetters = ["\\imath", // dotless i - "\\jmath", // dotless j - "\\pounds"]; - - /** - * Looks up the given symbol in fontMetrics, after applying any symbol - * replacements defined in symbol.js - */ - var lookupSymbol = function lookupSymbol(value, fontFamily, mode) { - // Replace the value with its replaced value from symbol.js - if (_symbols2.default[mode][value] && _symbols2.default[mode][value].replace) { - value = _symbols2.default[mode][value].replace; - } - return { - value: value, - metrics: _fontMetrics2.default.getCharacterMetrics(value, fontFamily) - }; - }; - - /** - * Makes a symbolNode after translation via the list of symbols in symbols.js. - * Correctly pulls out metrics for the character, and optionally takes a list of - * classes to be attached to the node. - * - * TODO: make argument order closer to makeSpan - * TODO: add a separate argument for math class (e.g. `mop`, `mbin`), which - * should if present come first in `classes`. - */ - var makeSymbol = function makeSymbol(value, fontFamily, mode, options, classes) { - var lookup = lookupSymbol(value, fontFamily, mode); - var metrics = lookup.metrics; - value = lookup.value; - - var symbolNode = void 0; - if (metrics) { - var italic = metrics.italic; - if (mode === "text") { - italic = 0; - } - symbolNode = new _domTree2.default.symbolNode(value, metrics.height, metrics.depth, italic, metrics.skew, classes); - } else { - // TODO(emily): Figure out a good way to only print this in development - typeof console !== "undefined" && console.warn("No character metrics for '" + value + "' in style '" + fontFamily + "'"); - symbolNode = new _domTree2.default.symbolNode(value, 0, 0, 0, 0, classes); - } - - if (options) { - symbolNode.maxFontSize = options.sizeMultiplier; - if (options.style.isTight()) { - symbolNode.classes.push("mtight"); - } - if (options.getColor()) { - symbolNode.style.color = options.getColor(); - } - } - - return symbolNode; - }; - - /** - * Makes a symbol in Main-Regular or AMS-Regular. - * Used for rel, bin, open, close, inner, and punct. - */ - var mathsym = function mathsym(value, mode, options, classes) { - // Decide what font to render the symbol in by its entry in the symbols - // table. - // Have a special case for when the value = \ because the \ is used as a - // textord in unsupported command errors but cannot be parsed as a regular - // text ordinal and is therefore not present as a symbol in the symbols - // table for text - if (value === "\\" || _symbols2.default[mode][value].font === "main") { - return makeSymbol(value, "Main-Regular", mode, options, classes); - } else { - return makeSymbol(value, "AMS-Regular", mode, options, classes.concat(["amsrm"])); - } - }; - - /** - * Makes a symbol in the default font for mathords and textords. - */ - var mathDefault = function mathDefault(value, mode, options, classes, type) { - if (type === "mathord") { - var fontLookup = mathit(value); - return makeSymbol(value, fontLookup.fontName, mode, options, classes.concat([fontLookup.fontClass])); - } else if (type === "textord") { - var font = _symbols2.default[mode][value] && _symbols2.default[mode][value].font; - if (font === "ams") { - return makeSymbol(value, "AMS-Regular", mode, options, classes.concat(["amsrm"])); - } else { - // if (font === "main") { - return makeSymbol(value, "Main-Regular", mode, options, classes.concat(["mathrm"])); - } - } else { - throw new Error("unexpected type: " + type + " in mathDefault"); - } - }; - - /** - * Determines which of the two font names (Main-Italic and Math-Italic) and - * corresponding style tags (mainit or mathit) to use for font "mathit", - * depending on the symbol. Use this function instead of fontMap for font - * "mathit". - */ - var mathit = function mathit(value, mode, options, classes) { - if (/[0-9]/.test(value.charAt(0)) || - // glyphs for \imath and \jmath do not exist in Math-Italic so we - // need to use Main-Italic instead - _utils2.default.contains(mainitLetters, value)) { - return { - fontName: "Main-Italic", - fontClass: "mainit" - }; - } else { - return { - fontName: "Math-Italic", - fontClass: "mathit" - }; - } - }; - - /** - * Makes either a mathord or textord in the correct font and color. - */ - var makeOrd = function makeOrd(group, options, type) { - var mode = group.mode; - var value = group.value; - - var classes = ["mord"]; - - var font = options.font; - if (font) { - var fontLookup = void 0; - if (font === "mathit" || _utils2.default.contains(mainitLetters, value)) { - fontLookup = mathit(value); - } else { - fontLookup = fontMap[font]; - } - if (lookupSymbol(value, fontLookup.fontName, mode).metrics) { - return makeSymbol(value, fontLookup.fontName, mode, options, classes.concat([fontLookup.fontClass || font])); - } else { - return mathDefault(value, mode, options, classes, type); - } - } else { - return mathDefault(value, mode, options, classes, type); - } - }; - - /** - * Calculate the height, depth, and maxFontSize of an element based on its - * children. - */ - var sizeElementFromChildren = function sizeElementFromChildren(elem) { - var height = 0; - var depth = 0; - var maxFontSize = 0; - - if (elem.children) { - for (var i = 0; i < elem.children.length; i++) { - if (elem.children[i].height > height) { - height = elem.children[i].height; - } - if (elem.children[i].depth > depth) { - depth = elem.children[i].depth; - } - if (elem.children[i].maxFontSize > maxFontSize) { - maxFontSize = elem.children[i].maxFontSize; - } - } - } - - elem.height = height; - elem.depth = depth; - elem.maxFontSize = maxFontSize; - }; - - /** - * Makes a span with the given list of classes, list of children, and options. - * - * TODO: Ensure that `options` is always provided (currently some call sites - * don't pass it). - * TODO: add a separate argument for math class (e.g. `mop`, `mbin`), which - * should if present come first in `classes`. - */ - var makeSpan = function makeSpan(classes, children, options) { - var span = new _domTree2.default.span(classes, children, options); - - sizeElementFromChildren(span); - - return span; - }; - - /** - * Prepends the given children to the given span, updating height, depth, and - * maxFontSize. - */ - var prependChildren = function prependChildren(span, children) { - span.children = children.concat(span.children); - - sizeElementFromChildren(span); - }; - - /** - * Makes a document fragment with the given list of children. - */ - var makeFragment = function makeFragment(children) { - var fragment = new _domTree2.default.documentFragment(children); - - sizeElementFromChildren(fragment); - - return fragment; - }; - - /** - * Makes a vertical list by stacking elements and kerns on top of each other. - * Allows for many different ways of specifying the positioning method. - * - * Arguments: - * - children: A list of child or kern nodes to be stacked on top of each other - * (i.e. the first element will be at the bottom, and the last at - * the top). Element nodes are specified as - * {type: "elem", elem: node} - * while kern nodes are specified as - * {type: "kern", size: size} - * - positionType: The method by which the vlist should be positioned. Valid - * values are: - * - "individualShift": The children list only contains elem - * nodes, and each node contains an extra - * "shift" value of how much it should be - * shifted (note that shifting is always - * moving downwards). positionData is - * ignored. - * - "top": The positionData specifies the topmost point of - * the vlist (note this is expected to be a height, - * so positive values move up) - * - "bottom": The positionData specifies the bottommost point - * of the vlist (note this is expected to be a - * depth, so positive values move down - * - "shift": The vlist will be positioned such that its - * baseline is positionData away from the baseline - * of the first child. Positive values move - * downwards. - * - "firstBaseline": The vlist will be positioned such that - * its baseline is aligned with the - * baseline of the first child. - * positionData is ignored. (this is - * equivalent to "shift" with - * positionData=0) - * - positionData: Data used in different ways depending on positionType - * - options: An Options object - * - */ - var makeVList = function makeVList(children, positionType, positionData, options) { - var depth = void 0; - var currPos = void 0; - var i = void 0; - if (positionType === "individualShift") { - var oldChildren = children; - children = [oldChildren[0]]; - - // Add in kerns to the list of children to get each element to be - // shifted to the correct specified shift - depth = -oldChildren[0].shift - oldChildren[0].elem.depth; - currPos = depth; - for (i = 1; i < oldChildren.length; i++) { - var diff = -oldChildren[i].shift - currPos - oldChildren[i].elem.depth; - var size = diff - (oldChildren[i - 1].elem.height + oldChildren[i - 1].elem.depth); - - currPos = currPos + diff; - - children.push({ type: "kern", size: size }); - children.push(oldChildren[i]); - } - } else if (positionType === "top") { - // We always start at the bottom, so calculate the bottom by adding up - // all the sizes - var bottom = positionData; - for (i = 0; i < children.length; i++) { - if (children[i].type === "kern") { - bottom -= children[i].size; - } else { - bottom -= children[i].elem.height + children[i].elem.depth; - } - } - depth = bottom; - } else if (positionType === "bottom") { - depth = -positionData; - } else if (positionType === "shift") { - depth = -children[0].elem.depth - positionData; - } else if (positionType === "firstBaseline") { - depth = -children[0].elem.depth; - } else { - depth = 0; - } - - // Create a strut that is taller than any list item. The strut is added to - // each item, where it will determine the item's baseline. Since it has - // `overflow:hidden`, the strut's top edge will sit on the item's line box's - // top edge and the strut's bottom edge will sit on the item's baseline, - // with no additional line-height spacing. This allows the item baseline to - // be positioned precisely without worrying about font ascent and - // line-height. - var pstrutSize = 0; - for (i = 0; i < children.length; i++) { - if (children[i].type === "elem") { - var child = children[i].elem; - pstrutSize = Math.max(pstrutSize, child.maxFontSize, child.height); - } - } - pstrutSize += 2; - var pstrut = makeSpan(["pstrut"], []); - pstrut.style.height = pstrutSize + "em"; - - // Create a new list of actual children at the correct offsets - var realChildren = []; - var minPos = depth; - var maxPos = depth; - currPos = depth; - for (i = 0; i < children.length; i++) { - if (children[i].type === "kern") { - currPos += children[i].size; - } else { - var _child = children[i].elem; - - var childWrap = makeSpan([], [pstrut, _child]); - childWrap.style.top = -pstrutSize - currPos - _child.depth + "em"; - if (children[i].marginLeft) { - childWrap.style.marginLeft = children[i].marginLeft; - } - if (children[i].marginRight) { - childWrap.style.marginRight = children[i].marginRight; - } - - realChildren.push(childWrap); - currPos += _child.height + _child.depth; - } - minPos = Math.min(minPos, currPos); - maxPos = Math.max(maxPos, currPos); - } - - // The vlist contents go in a table-cell with `vertical-align:bottom`. - // This cell's bottom edge will determine the containing table's baseline - // without overly expanding the containing line-box. - var vlist = makeSpan(["vlist"], realChildren); - vlist.style.height = maxPos + "em"; - - // A second row is used if necessary to represent the vlist's depth. - var rows = void 0; - if (minPos < 0) { - var depthStrut = makeSpan(["vlist"], []); - depthStrut.style.height = -minPos + "em"; - - // Safari wants the first row to have inline content; otherwise it - // puts the bottom of the *second* row on the baseline. - var topStrut = makeSpan(["vlist-s"], [new _domTree2.default.symbolNode("\u200B")]); - - rows = [makeSpan(["vlist-r"], [vlist, topStrut]), makeSpan(["vlist-r"], [depthStrut])]; - } else { - rows = [makeSpan(["vlist-r"], [vlist])]; - } - - var vtable = makeSpan(["vlist-t"], rows); - if (rows.length === 2) { - vtable.classes.push("vlist-t2"); - } - vtable.height = maxPos; - vtable.depth = -minPos; - return vtable; - }; - - // A map of spacing functions to their attributes, like size and corresponding - // CSS class - var spacingFunctions = { - "\\qquad": { - size: "2em", - className: "qquad" - }, - "\\quad": { - size: "1em", - className: "quad" - }, - "\\enspace": { - size: "0.5em", - className: "enspace" - }, - "\\;": { - size: "0.277778em", - className: "thickspace" - }, - "\\:": { - size: "0.22222em", - className: "mediumspace" - }, - "\\,": { - size: "0.16667em", - className: "thinspace" - }, - "\\!": { - size: "-0.16667em", - className: "negativethinspace" - } - }; - - /** - * Maps TeX font commands to objects containing: - * - variant: string used for "mathvariant" attribute in buildMathML.js - * - fontName: the "style" parameter to fontMetrics.getCharacterMetrics - */ - // A map between tex font commands an MathML mathvariant attribute values - var fontMap = { - // styles - "mathbf": { - variant: "bold", - fontName: "Main-Bold" - }, - "mathrm": { - variant: "normal", - fontName: "Main-Regular" - }, - "textit": { - variant: "italic", - fontName: "Main-Italic" - }, - - // "mathit" is missing because it requires the use of two fonts: Main-Italic - // and Math-Italic. This is handled by a special case in makeOrd which ends - // up calling mathit. - - // families - "mathbb": { - variant: "double-struck", - fontName: "AMS-Regular" - }, - "mathcal": { - variant: "script", - fontName: "Caligraphic-Regular" - }, - "mathfrak": { - variant: "fraktur", - fontName: "Fraktur-Regular" - }, - "mathscr": { - variant: "script", - fontName: "Script-Regular" - }, - "mathsf": { - variant: "sans-serif", - fontName: "SansSerif-Regular" - }, - "mathtt": { - variant: "monospace", - fontName: "Typewriter-Regular" - } - }; - - module.exports = { - fontMap: fontMap, - makeSymbol: makeSymbol, - mathsym: mathsym, - makeSpan: makeSpan, - makeFragment: makeFragment, - makeVList: makeVList, - makeOrd: makeOrd, - prependChildren: prependChildren, - spacingFunctions: spacingFunctions - }; - - },{"./domTree":39,"./fontMetrics":41,"./symbols":48,"./utils":51}],35:[function(require,module,exports){ - - var _stringify = require("babel-runtime/core-js/json/stringify"); - - var _stringify2 = _interopRequireDefault(_stringify); - - var _ParseError = require("./ParseError"); - - var _ParseError2 = _interopRequireDefault(_ParseError); - - var _Style = require("./Style"); - - var _Style2 = _interopRequireDefault(_Style); - - var _buildCommon = require("./buildCommon"); - - var _buildCommon2 = _interopRequireDefault(_buildCommon); - - var _delimiter = require("./delimiter"); - - var _delimiter2 = _interopRequireDefault(_delimiter); - - var _domTree = require("./domTree"); - - var _domTree2 = _interopRequireDefault(_domTree); - - var _units = require("./units"); - - var _units2 = _interopRequireDefault(_units); - - var _utils = require("./utils"); - - var _utils2 = _interopRequireDefault(_utils); - - var _stretchy = require("./stretchy"); - - var _stretchy2 = _interopRequireDefault(_stretchy); - - function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { default: obj }; } - - /* eslint no-console:0 */ - /** - * This file does the main work of building a domTree structure from a parse - * tree. The entry point is the `buildHTML` function, which takes a parse tree. - * Then, the buildExpression, buildGroup, and various groupTypes functions are - * called, to produce a final HTML tree. - */ - - var isSpace = function isSpace(node) { - return node instanceof _domTree2.default.span && node.classes[0] === "mspace"; - }; - - // Binary atoms (first class `mbin`) change into ordinary atoms (`mord`) - // depending on their surroundings. See TeXbook pg. 442-446, Rules 5 and 6, - // and the text before Rule 19. - var isBin = function isBin(node) { - return node && node.classes[0] === "mbin"; - }; - - var isBinLeftCanceller = function isBinLeftCanceller(node, isRealGroup) { - // TODO: This code assumes that a node's math class is the first element - // of its `classes` array. A later cleanup should ensure this, for - // instance by changing the signature of `makeSpan`. - if (node) { - return _utils2.default.contains(["mbin", "mopen", "mrel", "mop", "mpunct"], node.classes[0]); - } else { - return isRealGroup; - } - }; - - var isBinRightCanceller = function isBinRightCanceller(node, isRealGroup) { - if (node) { - return _utils2.default.contains(["mrel", "mclose", "mpunct"], node.classes[0]); - } else { - return isRealGroup; - } - }; - - /** - * Splice out any spaces from `children` starting at position `i`, and return - * the spliced-out array. Returns null if `children[i]` does not exist or is not - * a space. - */ - var spliceSpaces = function spliceSpaces(children, i) { - var j = i; - while (j < children.length && isSpace(children[j])) { - j++; - } - if (j === i) { - return null; - } else { - return children.splice(i, j - i); - } - }; - - /** - * Take a list of nodes, build them in order, and return a list of the built - * nodes. documentFragments are flattened into their contents, so the - * returned list contains no fragments. `isRealGroup` is true if `expression` - * is a real group (no atoms will be added on either side), as opposed to - * a partial group (e.g. one created by \color). - */ - var buildExpression = function buildExpression(expression, options, isRealGroup) { - // Parse expressions into `groups`. - var groups = []; - for (var i = 0; i < expression.length; i++) { - var group = expression[i]; - var output = buildGroup(group, options); - if (output instanceof _domTree2.default.documentFragment) { - Array.prototype.push.apply(groups, output.children); - } else { - groups.push(output); - } - } - // At this point `groups` consists entirely of `symbolNode`s and `span`s. - - // Explicit spaces (e.g., \;, \,) should be ignored with respect to atom - // spacing (e.g., "add thick space between mord and mrel"). Since CSS - // adjacency rules implement atom spacing, spaces should be invisible to - // CSS. So we splice them out of `groups` and into the atoms themselves. - for (var _i = 0; _i < groups.length; _i++) { - var spaces = spliceSpaces(groups, _i); - if (spaces) { - // Splicing of spaces may have removed all remaining groups. - if (_i < groups.length) { - // If there is a following group, move space within it. - if (groups[_i] instanceof _domTree2.default.symbolNode) { - groups[_i] = (0, _buildCommon.makeSpan)([].concat(groups[_i].classes), [groups[_i]]); - } - _buildCommon2.default.prependChildren(groups[_i], spaces); - } else { - // Otherwise, put any spaces back at the end of the groups. - Array.prototype.push.apply(groups, spaces); - break; - } - } - } - - // Binary operators change to ordinary symbols in some contexts. - for (var _i2 = 0; _i2 < groups.length; _i2++) { - if (isBin(groups[_i2]) && (isBinLeftCanceller(groups[_i2 - 1], isRealGroup) || isBinRightCanceller(groups[_i2 + 1], isRealGroup))) { - groups[_i2].classes[0] = "mord"; - } - } - - // Process \\not commands within the group. - // TODO(kevinb): Handle multiple \\not commands in a row. - // TODO(kevinb): Handle \\not{abc} correctly. The \\not should appear over - // the 'a' instead of the 'c'. - for (var _i3 = 0; _i3 < groups.length; _i3++) { - if (groups[_i3].value === "\u0338" && _i3 + 1 < groups.length) { - var children = groups.slice(_i3, _i3 + 2); - - children[0].classes = ["mainrm"]; - // \u0338 is a combining glyph so we could reorder the children so - // that it comes after the other glyph. This works correctly on - // most browsers except for Safari. Instead we absolutely position - // the glyph and set its right side to match that of the other - // glyph which is visually equivalent. - children[0].style.position = "absolute"; - children[0].style.right = "0"; - - // Copy the classes from the second glyph to the new container. - // This is so it behaves the same as though there was no \\not. - var classes = groups[_i3 + 1].classes; - var container = (0, _buildCommon.makeSpan)(classes, children); - - // LaTeX adds a space between ords separated by a \\not. - if (classes.indexOf("mord") !== -1) { - // \glue(\thickmuskip) 2.77771 plus 2.77771 - container.style.paddingLeft = "0.277771em"; - } - - // Ensure that the \u0338 is positioned relative to the container. - container.style.position = "relative"; - groups.splice(_i3, 2, container); - } - } - - return groups; - }; - - // Return math atom class (mclass) of a domTree. - var getTypeOfDomTree = function getTypeOfDomTree(node) { - if (node instanceof _domTree2.default.documentFragment) { - if (node.children.length) { - return getTypeOfDomTree(node.children[node.children.length - 1]); - } - } else { - if (_utils2.default.contains(["mord", "mop", "mbin", "mrel", "mopen", "mclose", "mpunct", "minner"], node.classes[0])) { - return node.classes[0]; - } - } - return null; - }; - - /** - * Sometimes, groups perform special rules when they have superscripts or - * subscripts attached to them. This function lets the `supsub` group know that - * its inner element should handle the superscripts and subscripts instead of - * handling them itself. - */ - var shouldHandleSupSub = function shouldHandleSupSub(group, options) { - if (!group.value.base) { - return false; - } else { - var base = group.value.base; - if (base.type === "op") { - // Operators handle supsubs differently when they have limits - // (e.g. `\displaystyle\sum_2^3`) - return base.value.limits && (options.style.size === _Style2.default.DISPLAY.size || base.value.alwaysHandleSupSub); - } else if (base.type === "accent") { - return isCharacterBox(base.value.base); - } else if (base.type === "horizBrace") { - var isSup = group.value.sub ? false : true; - return isSup === base.value.isOver; - } else { - return null; - } - } - }; - - /** - * Sometimes we want to pull out the innermost element of a group. In most - * cases, this will just be the group itself, but when ordgroups and colors have - * a single element, we want to pull that out. - */ - var getBaseElem = function getBaseElem(group) { - if (!group) { - return false; - } else if (group.type === "ordgroup") { - if (group.value.length === 1) { - return getBaseElem(group.value[0]); - } else { - return group; - } - } else if (group.type === "color") { - if (group.value.value.length === 1) { - return getBaseElem(group.value.value[0]); - } else { - return group; - } - } else if (group.type === "font") { - return getBaseElem(group.value.body); - } else { - return group; - } - }; - - /** - * TeXbook algorithms often reference "character boxes", which are simply groups - * with a single character in them. To decide if something is a character box, - * we find its innermost group, and see if it is a single character. - */ - var isCharacterBox = function isCharacterBox(group) { - var baseElem = getBaseElem(group); - - // These are all they types of groups which hold single characters - return baseElem.type === "mathord" || baseElem.type === "textord" || baseElem.type === "bin" || baseElem.type === "rel" || baseElem.type === "inner" || baseElem.type === "open" || baseElem.type === "close" || baseElem.type === "punct"; - }; - - var makeNullDelimiter = function makeNullDelimiter(options, classes) { - var moreClasses = ["nulldelimiter"].concat(options.baseSizingClasses()); - return (0, _buildCommon.makeSpan)(classes.concat(moreClasses)); - }; - - /** - * This is a map of group types to the function used to handle that type. - * Simpler types come at the beginning, while complicated types come afterwards. - */ - var groupTypes = {}; - - groupTypes.mathord = function (group, options) { - return _buildCommon2.default.makeOrd(group, options, "mathord"); - }; - - groupTypes.textord = function (group, options) { - return _buildCommon2.default.makeOrd(group, options, "textord"); - }; - - groupTypes.bin = function (group, options) { - return _buildCommon2.default.mathsym(group.value, group.mode, options, ["mbin"]); - }; - - groupTypes.rel = function (group, options) { - return _buildCommon2.default.mathsym(group.value, group.mode, options, ["mrel"]); - }; - - groupTypes.open = function (group, options) { - return _buildCommon2.default.mathsym(group.value, group.mode, options, ["mopen"]); - }; - - groupTypes.close = function (group, options) { - return _buildCommon2.default.mathsym(group.value, group.mode, options, ["mclose"]); - }; - - groupTypes.inner = function (group, options) { - return _buildCommon2.default.mathsym(group.value, group.mode, options, ["minner"]); - }; - - groupTypes.punct = function (group, options) { - return _buildCommon2.default.mathsym(group.value, group.mode, options, ["mpunct"]); - }; - - groupTypes.ordgroup = function (group, options) { - return (0, _buildCommon.makeSpan)(["mord"], buildExpression(group.value, options, true), options); - }; - - groupTypes.text = function (group, options) { - var newOptions = options.withFont(group.value.style); - var inner = buildExpression(group.value.body, newOptions, true); - for (var i = 0; i < inner.length - 1; i++) { - if (inner[i].tryCombine(inner[i + 1])) { - inner.splice(i + 1, 1); - i--; - } - } - return (0, _buildCommon.makeSpan)(["mord", "text"], inner, newOptions); - }; - - groupTypes.color = function (group, options) { - var elements = buildExpression(group.value.value, options.withColor(group.value.color), false); - - // \color isn't supposed to affect the type of the elements it contains. - // To accomplish this, we wrap the results in a fragment, so the inner - // elements will be able to directly interact with their neighbors. For - // example, `\color{red}{2 +} 3` has the same spacing as `2 + 3` - return new _buildCommon2.default.makeFragment(elements); - }; - - groupTypes.supsub = function (group, options) { - // Superscript and subscripts are handled in the TeXbook on page - // 445-446, rules 18(a-f). - - // Here is where we defer to the inner group if it should handle - // superscripts and subscripts itself. - if (shouldHandleSupSub(group, options)) { - return groupTypes[group.value.base.type](group, options); - } - - var base = buildGroup(group.value.base, options); - var supm = void 0; - var subm = void 0; - - var metrics = options.fontMetrics(); - var newOptions = void 0; - - // Rule 18a - var supShift = 0; - var subShift = 0; - - if (group.value.sup) { - newOptions = options.havingStyle(options.style.sup()); - supm = buildGroup(group.value.sup, newOptions, options); - if (!isCharacterBox(group.value.base)) { - supShift = base.height - newOptions.fontMetrics().supDrop * newOptions.sizeMultiplier / options.sizeMultiplier; - } - } - - if (group.value.sub) { - newOptions = options.havingStyle(options.style.sub()); - subm = buildGroup(group.value.sub, newOptions, options); - if (!isCharacterBox(group.value.base)) { - subShift = base.depth + newOptions.fontMetrics().subDrop * newOptions.sizeMultiplier / options.sizeMultiplier; - } - } - - // Rule 18c - var minSupShift = void 0; - if (options.style === _Style2.default.DISPLAY) { - minSupShift = metrics.sup1; - } else if (options.style.cramped) { - minSupShift = metrics.sup3; - } else { - minSupShift = metrics.sup2; - } - - // scriptspace is a font-size-independent size, so scale it - // appropriately - var multiplier = options.sizeMultiplier; - var scriptspace = 0.5 / metrics.ptPerEm / multiplier + "em"; - - var supsub = void 0; - if (!group.value.sup) { - // Rule 18b - subShift = Math.max(subShift, metrics.sub1, subm.height - 0.8 * metrics.xHeight); - - var vlistElem = [{ type: "elem", elem: subm, marginRight: scriptspace }]; - // Subscripts shouldn't be shifted by the base's italic correction. - // Account for that by shifting the subscript back the appropriate - // amount. Note we only do this when the base is a single symbol. - if (base instanceof _domTree2.default.symbolNode) { - vlistElem[0].marginLeft = -base.italic + "em"; - } - - supsub = _buildCommon2.default.makeVList(vlistElem, "shift", subShift, options); - } else if (!group.value.sub) { - // Rule 18c, d - supShift = Math.max(supShift, minSupShift, supm.depth + 0.25 * metrics.xHeight); - - supsub = _buildCommon2.default.makeVList([{ type: "elem", elem: supm, marginRight: scriptspace }], "shift", -supShift, options); - } else { - supShift = Math.max(supShift, minSupShift, supm.depth + 0.25 * metrics.xHeight); - subShift = Math.max(subShift, metrics.sub2); - - var ruleWidth = metrics.defaultRuleThickness; - - // Rule 18e - if (supShift - supm.depth - (subm.height - subShift) < 4 * ruleWidth) { - subShift = 4 * ruleWidth - (supShift - supm.depth) + subm.height; - var psi = 0.8 * metrics.xHeight - (supShift - supm.depth); - if (psi > 0) { - supShift += psi; - subShift -= psi; - } - } - - var _vlistElem = [{ type: "elem", elem: subm, shift: subShift, marginRight: scriptspace }, { type: "elem", elem: supm, shift: -supShift, marginRight: scriptspace }]; - // See comment above about subscripts not being shifted - if (base instanceof _domTree2.default.symbolNode) { - _vlistElem[0].marginLeft = -base.italic + "em"; - } - - supsub = _buildCommon2.default.makeVList(_vlistElem, "individualShift", null, options); - } - - // We ensure to wrap the supsub vlist in a span.msupsub to reset text-align - var mclass = getTypeOfDomTree(base) || "mord"; - return (0, _buildCommon.makeSpan)([mclass], [base, (0, _buildCommon.makeSpan)(["msupsub"], [supsub])], options); - }; - - groupTypes.genfrac = function (group, options) { - // Fractions are handled in the TeXbook on pages 444-445, rules 15(a-e). - // Figure out what style this fraction should be in based on the - // function used - var style = options.style; - if (group.value.size === "display") { - style = _Style2.default.DISPLAY; - } else if (group.value.size === "text") { - style = _Style2.default.TEXT; - } - - var nstyle = style.fracNum(); - var dstyle = style.fracDen(); - var newOptions = void 0; - - newOptions = options.havingStyle(nstyle); - var numerm = buildGroup(group.value.numer, newOptions, options); - - newOptions = options.havingStyle(dstyle); - var denomm = buildGroup(group.value.denom, newOptions, options); - - var rule = void 0; - var ruleWidth = void 0; - var ruleSpacing = void 0; - if (group.value.hasBarLine) { - rule = makeLineSpan("frac-line", options); - ruleWidth = rule.height; - ruleSpacing = rule.height; - } else { - rule = null; - ruleWidth = 0; - ruleSpacing = options.fontMetrics().defaultRuleThickness; - } - - // Rule 15b - var numShift = void 0; - var clearance = void 0; - var denomShift = void 0; - if (style.size === _Style2.default.DISPLAY.size) { - numShift = options.fontMetrics().num1; - if (ruleWidth > 0) { - clearance = 3 * ruleSpacing; - } else { - clearance = 7 * ruleSpacing; - } - denomShift = options.fontMetrics().denom1; - } else { - if (ruleWidth > 0) { - numShift = options.fontMetrics().num2; - clearance = ruleSpacing; - } else { - numShift = options.fontMetrics().num3; - clearance = 3 * ruleSpacing; - } - denomShift = options.fontMetrics().denom2; - } - - var frac = void 0; - if (ruleWidth === 0) { - // Rule 15c - var candidateClearance = numShift - numerm.depth - (denomm.height - denomShift); - if (candidateClearance < clearance) { - numShift += 0.5 * (clearance - candidateClearance); - denomShift += 0.5 * (clearance - candidateClearance); - } - - frac = _buildCommon2.default.makeVList([{ type: "elem", elem: denomm, shift: denomShift }, { type: "elem", elem: numerm, shift: -numShift }], "individualShift", null, options); - } else { - // Rule 15d - var axisHeight = options.fontMetrics().axisHeight; - - if (numShift - numerm.depth - (axisHeight + 0.5 * ruleWidth) < clearance) { - numShift += clearance - (numShift - numerm.depth - (axisHeight + 0.5 * ruleWidth)); - } - - if (axisHeight - 0.5 * ruleWidth - (denomm.height - denomShift) < clearance) { - denomShift += clearance - (axisHeight - 0.5 * ruleWidth - (denomm.height - denomShift)); - } - - var midShift = -(axisHeight - 0.5 * ruleWidth); - - frac = _buildCommon2.default.makeVList([{ type: "elem", elem: denomm, shift: denomShift }, { type: "elem", elem: rule, shift: midShift }, { type: "elem", elem: numerm, shift: -numShift }], "individualShift", null, options); - } - - // Since we manually change the style sometimes (with \dfrac or \tfrac), - // account for the possible size change here. - newOptions = options.havingStyle(style); - frac.height *= newOptions.sizeMultiplier / options.sizeMultiplier; - frac.depth *= newOptions.sizeMultiplier / options.sizeMultiplier; - - // Rule 15e - var delimSize = void 0; - if (style.size === _Style2.default.DISPLAY.size) { - delimSize = options.fontMetrics().delim1; - } else { - delimSize = options.fontMetrics().delim2; - } - - var leftDelim = void 0; - var rightDelim = void 0; - if (group.value.leftDelim == null) { - leftDelim = makeNullDelimiter(options, ["mopen"]); - } else { - leftDelim = _delimiter2.default.customSizedDelim(group.value.leftDelim, delimSize, true, options.havingStyle(style), group.mode, ["mopen"]); - } - if (group.value.rightDelim == null) { - rightDelim = makeNullDelimiter(options, ["mclose"]); - } else { - rightDelim = _delimiter2.default.customSizedDelim(group.value.rightDelim, delimSize, true, options.havingStyle(style), group.mode, ["mclose"]); - } - - return (0, _buildCommon.makeSpan)(["mord"].concat(newOptions.sizingClasses(options)), [leftDelim, (0, _buildCommon.makeSpan)(["mfrac"], [frac]), rightDelim], options); - }; - - groupTypes.array = function (group, options) { - var r = void 0; - var c = void 0; - var nr = group.value.body.length; - var nc = 0; - var body = new Array(nr); - - // Horizontal spacing - var pt = 1 / options.fontMetrics().ptPerEm; - var arraycolsep = 5 * pt; // \arraycolsep in article.cls - - // Vertical spacing - var baselineskip = 12 * pt; // see size10.clo - // Default \jot from ltmath.dtx - // TODO(edemaine): allow overriding \jot via \setlength (#687) - var jot = 3 * pt; - // Default \arraystretch from lttab.dtx - // TODO(gagern): may get redefined once we have user-defined macros - var arraystretch = _utils2.default.deflt(group.value.arraystretch, 1); - var arrayskip = arraystretch * baselineskip; - var arstrutHeight = 0.7 * arrayskip; // \strutbox in ltfsstrc.dtx and - var arstrutDepth = 0.3 * arrayskip; // \@arstrutbox in lttab.dtx - - var totalHeight = 0; - for (r = 0; r < group.value.body.length; ++r) { - var inrow = group.value.body[r]; - var height = arstrutHeight; // \@array adds an \@arstrut - var depth = arstrutDepth; // to each tow (via the template) - - if (nc < inrow.length) { - nc = inrow.length; - } - - var outrow = new Array(inrow.length); - for (c = 0; c < inrow.length; ++c) { - var elt = buildGroup(inrow[c], options); - if (depth < elt.depth) { - depth = elt.depth; - } - if (height < elt.height) { - height = elt.height; - } - outrow[c] = elt; - } - - var gap = 0; - if (group.value.rowGaps[r]) { - gap = _units2.default.calculateSize(group.value.rowGaps[r].value, options); - if (gap > 0) { - // \@argarraycr - gap += arstrutDepth; - if (depth < gap) { - depth = gap; // \@xargarraycr - } - gap = 0; - } - } - // In AMS multiline environments such as aligned and gathered, rows - // correspond to lines that have additional \jot added to the - // \baselineskip via \openup. - if (group.value.addJot) { - depth += jot; - } - - outrow.height = height; - outrow.depth = depth; - totalHeight += height; - outrow.pos = totalHeight; - totalHeight += depth + gap; // \@yargarraycr - body[r] = outrow; - } - - var offset = totalHeight / 2 + options.fontMetrics().axisHeight; - var colDescriptions = group.value.cols || []; - var cols = []; - var colSep = void 0; - var colDescrNum = void 0; - for (c = 0, colDescrNum = 0; - // Continue while either there are more columns or more column - // descriptions, so trailing separators don't get lost. - c < nc || colDescrNum < colDescriptions.length; ++c, ++colDescrNum) { - - var colDescr = colDescriptions[colDescrNum] || {}; - - var firstSeparator = true; - while (colDescr.type === "separator") { - // If there is more than one separator in a row, add a space - // between them. - if (!firstSeparator) { - colSep = (0, _buildCommon.makeSpan)(["arraycolsep"], []); - colSep.style.width = options.fontMetrics().doubleRuleSep + "em"; - cols.push(colSep); - } - - if (colDescr.separator === "|") { - var separator = (0, _buildCommon.makeSpan)(["vertical-separator"], []); - separator.style.height = totalHeight + "em"; - separator.style.verticalAlign = -(totalHeight - offset) + "em"; - - cols.push(separator); - } else { - throw new _ParseError2.default("Invalid separator type: " + colDescr.separator); - } - - colDescrNum++; - colDescr = colDescriptions[colDescrNum] || {}; - firstSeparator = false; - } - - if (c >= nc) { - continue; - } - - var sepwidth = void 0; - if (c > 0 || group.value.hskipBeforeAndAfter) { - sepwidth = _utils2.default.deflt(colDescr.pregap, arraycolsep); - if (sepwidth !== 0) { - colSep = (0, _buildCommon.makeSpan)(["arraycolsep"], []); - colSep.style.width = sepwidth + "em"; - cols.push(colSep); - } - } - - var col = []; - for (r = 0; r < nr; ++r) { - var row = body[r]; - var elem = row[c]; - if (!elem) { - continue; - } - var shift = row.pos - offset; - elem.depth = row.depth; - elem.height = row.height; - col.push({ type: "elem", elem: elem, shift: shift }); - } - - col = _buildCommon2.default.makeVList(col, "individualShift", null, options); - col = (0, _buildCommon.makeSpan)(["col-align-" + (colDescr.align || "c")], [col]); - cols.push(col); - - if (c < nc - 1 || group.value.hskipBeforeAndAfter) { - sepwidth = _utils2.default.deflt(colDescr.postgap, arraycolsep); - if (sepwidth !== 0) { - colSep = (0, _buildCommon.makeSpan)(["arraycolsep"], []); - colSep.style.width = sepwidth + "em"; - cols.push(colSep); - } - } - } - body = (0, _buildCommon.makeSpan)(["mtable"], cols); - return (0, _buildCommon.makeSpan)(["mord"], [body], options); - }; - - groupTypes.spacing = function (group, options) { - if (group.value === "\\ " || group.value === "\\space" || group.value === " " || group.value === "~") { - // Spaces are generated by adding an actual space. Each of these - // things has an entry in the symbols table, so these will be turned - // into appropriate outputs. - if (group.mode === "text") { - return _buildCommon2.default.makeOrd(group, options, "textord"); - } else { - return (0, _buildCommon.makeSpan)(["mspace"], [_buildCommon2.default.mathsym(group.value, group.mode, options)], options); - } - } else { - // Other kinds of spaces are of arbitrary width. We use CSS to - // generate these. - return (0, _buildCommon.makeSpan)(["mspace", _buildCommon2.default.spacingFunctions[group.value].className], [], options); - } - }; - - groupTypes.llap = function (group, options) { - var inner = (0, _buildCommon.makeSpan)(["inner"], [buildGroup(group.value.body, options)]); - var fix = (0, _buildCommon.makeSpan)(["fix"], []); - return (0, _buildCommon.makeSpan)(["mord", "llap"], [inner, fix], options); - }; - - groupTypes.rlap = function (group, options) { - var inner = (0, _buildCommon.makeSpan)(["inner"], [buildGroup(group.value.body, options)]); - var fix = (0, _buildCommon.makeSpan)(["fix"], []); - return (0, _buildCommon.makeSpan)(["mord", "rlap"], [inner, fix], options); - }; - - groupTypes.op = function (group, options) { - // Operators are handled in the TeXbook pg. 443-444, rule 13(a). - var supGroup = void 0; - var subGroup = void 0; - var hasLimits = false; - if (group.type === "supsub") { - // If we have limits, supsub will pass us its group to handle. Pull - // out the superscript and subscript and set the group to the op in - // its base. - supGroup = group.value.sup; - subGroup = group.value.sub; - group = group.value.base; - hasLimits = true; - } - - var style = options.style; - - // Most operators have a large successor symbol, but these don't. - var noSuccessor = ["\\smallint"]; - - var large = false; - if (style.size === _Style2.default.DISPLAY.size && group.value.symbol && !_utils2.default.contains(noSuccessor, group.value.body)) { - - // Most symbol operators get larger in displaystyle (rule 13) - large = true; - } - - var base = void 0; - if (group.value.symbol) { - // If this is a symbol, create the symbol. - var fontName = large ? "Size2-Regular" : "Size1-Regular"; - base = _buildCommon2.default.makeSymbol(group.value.body, fontName, "math", options, ["mop", "op-symbol", large ? "large-op" : "small-op"]); - } else if (group.value.value) { - // If this is a list, compose that list. - var inner = buildExpression(group.value.value, options, true); - if (inner.length === 1 && inner[0] instanceof _domTree2.default.symbolNode) { - base = inner[0]; - base.classes[0] = "mop"; // replace old mclass - } else { - base = (0, _buildCommon.makeSpan)(["mop"], inner, options); - } - } else { - // Otherwise, this is a text operator. Build the text from the - // operator's name. - // TODO(emily): Add a space in the middle of some of these - // operators, like \limsup - var output = []; - for (var i = 1; i < group.value.body.length; i++) { - output.push(_buildCommon2.default.mathsym(group.value.body[i], group.mode)); - } - base = (0, _buildCommon.makeSpan)(["mop"], output, options); - } - - // If content of op is a single symbol, shift it vertically. - var baseShift = 0; - var slant = 0; - if (base instanceof _domTree2.default.symbolNode) { - // Shift the symbol so its center lies on the axis (rule 13). It - // appears that our fonts have the centers of the symbols already - // almost on the axis, so these numbers are very small. Note we - // don't actually apply this here, but instead it is used either in - // the vlist creation or separately when there are no limits. - baseShift = (base.height - base.depth) / 2 - options.fontMetrics().axisHeight; - - // The slant of the symbol is just its italic correction. - slant = base.italic; - } - - if (hasLimits) { - // IE 8 clips \int if it is in a display: inline-block. We wrap it - // in a new span so it is an inline, and works. - base = (0, _buildCommon.makeSpan)([], [base]); - - var supm = void 0; - var supKern = void 0; - var subm = void 0; - var subKern = void 0; - var newOptions = void 0; - // We manually have to handle the superscripts and subscripts. This, - // aside from the kern calculations, is copied from supsub. - if (supGroup) { - newOptions = options.havingStyle(style.sup()); - supm = buildGroup(supGroup, newOptions, options); - - supKern = Math.max(options.fontMetrics().bigOpSpacing1, options.fontMetrics().bigOpSpacing3 - supm.depth); - } - - if (subGroup) { - newOptions = options.havingStyle(style.sub()); - subm = buildGroup(subGroup, newOptions, options); - - subKern = Math.max(options.fontMetrics().bigOpSpacing2, options.fontMetrics().bigOpSpacing4 - subm.height); - } - - // Build the final group as a vlist of the possible subscript, base, - // and possible superscript. - var finalGroup = void 0; - var top = void 0; - var bottom = void 0; - if (!supGroup) { - top = base.height - baseShift; - - // Shift the limits by the slant of the symbol. Note - // that we are supposed to shift the limits by 1/2 of the slant, - // but since we are centering the limits adding a full slant of - // margin will shift by 1/2 that. - finalGroup = _buildCommon2.default.makeVList([{ type: "kern", size: options.fontMetrics().bigOpSpacing5 }, { type: "elem", elem: subm, marginLeft: -slant + "em" }, { type: "kern", size: subKern }, { type: "elem", elem: base }], "top", top, options); - } else if (!subGroup) { - bottom = base.depth + baseShift; - - finalGroup = _buildCommon2.default.makeVList([{ type: "elem", elem: base }, { type: "kern", size: supKern }, { type: "elem", elem: supm, marginLeft: slant + "em" }, { type: "kern", size: options.fontMetrics().bigOpSpacing5 }], "bottom", bottom, options); - } else if (!supGroup && !subGroup) { - // This case probably shouldn't occur (this would mean the - // supsub was sending us a group with no superscript or - // subscript) but be safe. - return base; - } else { - bottom = options.fontMetrics().bigOpSpacing5 + subm.height + subm.depth + subKern + base.depth + baseShift; - - finalGroup = _buildCommon2.default.makeVList([{ type: "kern", size: options.fontMetrics().bigOpSpacing5 }, { type: "elem", elem: subm, marginLeft: -slant + "em" }, { type: "kern", size: subKern }, { type: "elem", elem: base }, { type: "kern", size: supKern }, { type: "elem", elem: supm, marginLeft: slant + "em" }, { type: "kern", size: options.fontMetrics().bigOpSpacing5 }], "bottom", bottom, options); - } - - return (0, _buildCommon.makeSpan)(["mop", "op-limits"], [finalGroup], options); - } else { - if (baseShift) { - base.style.position = "relative"; - base.style.top = baseShift + "em"; - } - - return base; - } - }; - - groupTypes.mod = function (group, options) { - var inner = []; - - if (group.value.modType === "bmod") { - // “\nonscript\mskip-\medmuskip\mkern5mu” - if (!options.style.isTight()) { - inner.push((0, _buildCommon.makeSpan)(["mspace", "negativemediumspace"], [], options)); - } - inner.push((0, _buildCommon.makeSpan)(["mspace", "thickspace"], [], options)); - } else if (options.style.size === _Style2.default.DISPLAY.size) { - inner.push((0, _buildCommon.makeSpan)(["mspace", "quad"], [], options)); - } else if (group.value.modType === "mod") { - inner.push((0, _buildCommon.makeSpan)(["mspace", "twelvemuspace"], [], options)); - } else { - inner.push((0, _buildCommon.makeSpan)(["mspace", "eightmuspace"], [], options)); - } - - if (group.value.modType === "pod" || group.value.modType === "pmod") { - inner.push(_buildCommon2.default.mathsym("(", group.mode)); - } - - if (group.value.modType !== "pod") { - var modInner = [_buildCommon2.default.mathsym("m", group.mode), _buildCommon2.default.mathsym("o", group.mode), _buildCommon2.default.mathsym("d", group.mode)]; - if (group.value.modType === "bmod") { - inner.push((0, _buildCommon.makeSpan)(["mbin"], modInner, options)); - // “\mkern5mu\nonscript\mskip-\medmuskip” - inner.push((0, _buildCommon.makeSpan)(["mspace", "thickspace"], [], options)); - if (!options.style.isTight()) { - inner.push((0, _buildCommon.makeSpan)(["mspace", "negativemediumspace"], [], options)); - } - } else { - Array.prototype.push.apply(inner, modInner); - inner.push((0, _buildCommon.makeSpan)(["mspace", "sixmuspace"], [], options)); - } - } - - if (group.value.value) { - Array.prototype.push.apply(inner, buildExpression(group.value.value, options, false)); - } - - if (group.value.modType === "pod" || group.value.modType === "pmod") { - inner.push(_buildCommon2.default.mathsym(")", group.mode)); - } - - return _buildCommon2.default.makeFragment(inner); - }; - - groupTypes.katex = function (group, options) { - // The KaTeX logo. The offsets for the K and a were chosen to look - // good, but the offsets for the T, E, and X were taken from the - // definition of \TeX in TeX (see TeXbook pg. 356) - var k = (0, _buildCommon.makeSpan)(["k"], [_buildCommon2.default.mathsym("K", group.mode)], options); - var a = (0, _buildCommon.makeSpan)(["a"], [_buildCommon2.default.mathsym("A", group.mode)], options); - - a.height = (a.height + 0.2) * 0.75; - a.depth = (a.height - 0.2) * 0.75; - - var t = (0, _buildCommon.makeSpan)(["t"], [_buildCommon2.default.mathsym("T", group.mode)], options); - var e = (0, _buildCommon.makeSpan)(["e"], [_buildCommon2.default.mathsym("E", group.mode)], options); - - e.height = e.height - 0.2155; - e.depth = e.depth + 0.2155; - - var x = (0, _buildCommon.makeSpan)(["x"], [_buildCommon2.default.mathsym("X", group.mode)], options); - - return (0, _buildCommon.makeSpan)(["mord", "katex-logo"], [k, a, t, e, x], options); - }; - - var makeLineSpan = function makeLineSpan(className, options, thickness) { - var line = (0, _buildCommon.makeSpan)([className], [], options); - line.height = thickness || options.fontMetrics().defaultRuleThickness; - line.style.borderBottomWidth = line.height + "em"; - line.maxFontSize = 1.0; - return line; - }; - - groupTypes.overline = function (group, options) { - // Overlines are handled in the TeXbook pg 443, Rule 9. - - // Build the inner group in the cramped style. - var innerGroup = buildGroup(group.value.body, options.havingCrampedStyle()); - - // Create the line above the body - var line = makeLineSpan("overline-line", options); - - // Generate the vlist, with the appropriate kerns - var vlist = _buildCommon2.default.makeVList([{ type: "elem", elem: innerGroup }, { type: "kern", size: 3 * line.height }, { type: "elem", elem: line }, { type: "kern", size: line.height }], "firstBaseline", null, options); - - return (0, _buildCommon.makeSpan)(["mord", "overline"], [vlist], options); - }; - - groupTypes.underline = function (group, options) { - // Underlines are handled in the TeXbook pg 443, Rule 10. - // Build the inner group. - var innerGroup = buildGroup(group.value.body, options); - - // Create the line above the body - var line = makeLineSpan("underline-line", options); - - // Generate the vlist, with the appropriate kerns - var vlist = _buildCommon2.default.makeVList([{ type: "kern", size: line.height }, { type: "elem", elem: line }, { type: "kern", size: 3 * line.height }, { type: "elem", elem: innerGroup }], "top", innerGroup.height, options); - - return (0, _buildCommon.makeSpan)(["mord", "underline"], [vlist], options); - }; - - groupTypes.sqrt = function (group, options) { - // Square roots are handled in the TeXbook pg. 443, Rule 11. - - // First, we do the same steps as in overline to build the inner group - // and line - var inner = buildGroup(group.value.body, options.havingCrampedStyle()); - - // Some groups can return document fragments. Handle those by wrapping - // them in a span. - if (inner instanceof _domTree2.default.documentFragment) { - inner = (0, _buildCommon.makeSpan)([], [inner], options); - } - - // Calculate the minimum size for the \surd delimiter - var metrics = options.fontMetrics(); - var theta = metrics.defaultRuleThickness; - - var phi = theta; - if (options.style.id < _Style2.default.TEXT.id) { - phi = options.fontMetrics().xHeight; - } - - // Calculate the clearance between the body and line - var lineClearance = theta + phi / 4; - - var minDelimiterHeight = (inner.height + inner.depth + lineClearance + theta) * options.sizeMultiplier; - - // Create a sqrt SVG of the required minimum size - var img = _delimiter2.default.customSizedDelim("\\surd", minDelimiterHeight, false, options, group.mode); - - // Calculate the actual line width. - // This actually should depend on the chosen font -- e.g. \boldmath - // should use the thicker surd symbols from e.g. KaTeX_Main-Bold, and - // have thicker rules. - var ruleWidth = options.fontMetrics().sqrtRuleThickness * img.sizeMultiplier; - - var delimDepth = img.height - ruleWidth; - - // Adjust the clearance based on the delimiter size - if (delimDepth > inner.height + inner.depth + lineClearance) { - lineClearance = (lineClearance + delimDepth - inner.height - inner.depth) / 2; - } - - // Shift the sqrt image - var imgShift = img.height - inner.height - lineClearance - ruleWidth; - - // We add a special case here, because even when `inner` is empty, we - // still get a line. So, we use a simple heuristic to decide if we - // should omit the body entirely. (note this doesn't work for something - // like `\sqrt{\rlap{x}}`, but if someone is doing that they deserve for - // it not to work. - var body = void 0; - if (inner.height === 0 && inner.depth === 0) { - body = (0, _buildCommon.makeSpan)(); - } else { - inner.style.paddingLeft = img.surdWidth + "em"; - - // Overlay the image and the argument. - body = _buildCommon2.default.makeVList([{ type: "elem", elem: inner }, { type: "kern", size: -(inner.height + imgShift) }, { type: "elem", elem: img }, { type: "kern", size: ruleWidth }], "firstBaseline", null, options); - body.children[0].children[0].classes.push("svg-align"); - } - - if (!group.value.index) { - return (0, _buildCommon.makeSpan)(["mord", "sqrt"], [body], options); - } else { - // Handle the optional root index - - // The index is always in scriptscript style - var newOptions = options.havingStyle(_Style2.default.SCRIPTSCRIPT); - var rootm = buildGroup(group.value.index, newOptions, options); - - // The amount the index is shifted by. This is taken from the TeX - // source, in the definition of `\r@@t`. - var toShift = 0.6 * (body.height - body.depth); - - // Build a VList with the superscript shifted up correctly - var rootVList = _buildCommon2.default.makeVList([{ type: "elem", elem: rootm }], "shift", -toShift, options); - // Add a class surrounding it so we can add on the appropriate - // kerning - var rootVListWrap = (0, _buildCommon.makeSpan)(["root"], [rootVList]); - - return (0, _buildCommon.makeSpan)(["mord", "sqrt"], [rootVListWrap, body], options); - } - }; - - function sizingGroup(value, options, baseOptions) { - var inner = buildExpression(value, options, false); - var multiplier = options.sizeMultiplier / baseOptions.sizeMultiplier; - - // Add size-resetting classes to the inner list and set maxFontSize - // manually. Handle nested size changes. - for (var i = 0; i < inner.length; i++) { - var pos = _utils2.default.indexOf(inner[i].classes, "sizing"); - if (pos < 0) { - Array.prototype.push.apply(inner[i].classes, options.sizingClasses(baseOptions)); - } else if (inner[i].classes[pos + 1] === "reset-size" + options.size) { - // This is a nested size change: e.g., inner[i] is the "b" in - // `\Huge a \small b`. Override the old size (the `reset-` class) - // but not the new size. - inner[i].classes[pos + 1] = "reset-size" + baseOptions.size; - } - - inner[i].height *= multiplier; - inner[i].depth *= multiplier; - } - - return _buildCommon2.default.makeFragment(inner); - } - - groupTypes.sizing = function (group, options) { - // Handle sizing operators like \Huge. Real TeX doesn't actually allow - // these functions inside of math expressions, so we do some special - // handling. - var newOptions = options.havingSize(group.value.size); - return sizingGroup(group.value.value, newOptions, options); - }; - - groupTypes.styling = function (group, options) { - // Style changes are handled in the TeXbook on pg. 442, Rule 3. - - // Figure out what style we're changing to. - var styleMap = { - "display": _Style2.default.DISPLAY, - "text": _Style2.default.TEXT, - "script": _Style2.default.SCRIPT, - "scriptscript": _Style2.default.SCRIPTSCRIPT - }; - - var newStyle = styleMap[group.value.style]; - var newOptions = options.havingStyle(newStyle); - return sizingGroup(group.value.value, newOptions, options); - }; - - groupTypes.font = function (group, options) { - var font = group.value.font; - return buildGroup(group.value.body, options.withFont(font)); - }; - - groupTypes.delimsizing = function (group, options) { - var delim = group.value.value; - - if (delim === ".") { - // Empty delimiters still count as elements, even though they don't - // show anything. - return (0, _buildCommon.makeSpan)([group.value.mclass]); - } - - // Use delimiter.sizedDelim to generate the delimiter. - return _delimiter2.default.sizedDelim(delim, group.value.size, options, group.mode, [group.value.mclass]); - }; - - groupTypes.leftright = function (group, options) { - // Build the inner expression - var inner = buildExpression(group.value.body, options, true); - - var innerHeight = 0; - var innerDepth = 0; - var hadMiddle = false; - - // Calculate its height and depth - for (var i = 0; i < inner.length; i++) { - if (inner[i].isMiddle) { - hadMiddle = true; - } else { - innerHeight = Math.max(inner[i].height, innerHeight); - innerDepth = Math.max(inner[i].depth, innerDepth); - } - } - - // The size of delimiters is the same, regardless of what style we are - // in. Thus, to correctly calculate the size of delimiter we need around - // a group, we scale down the inner size based on the size. - innerHeight *= options.sizeMultiplier; - innerDepth *= options.sizeMultiplier; - - var leftDelim = void 0; - if (group.value.left === ".") { - // Empty delimiters in \left and \right make null delimiter spaces. - leftDelim = makeNullDelimiter(options, ["mopen"]); - } else { - // Otherwise, use leftRightDelim to generate the correct sized - // delimiter. - leftDelim = _delimiter2.default.leftRightDelim(group.value.left, innerHeight, innerDepth, options, group.mode, ["mopen"]); - } - // Add it to the beginning of the expression - inner.unshift(leftDelim); - - // Handle middle delimiters - if (hadMiddle) { - for (var _i4 = 1; _i4 < inner.length; _i4++) { - var middleDelim = inner[_i4]; - if (middleDelim.isMiddle) { - // Apply the options that were active when \middle was called - inner[_i4] = _delimiter2.default.leftRightDelim(middleDelim.isMiddle.value, innerHeight, innerDepth, middleDelim.isMiddle.options, group.mode, []); - // Add back spaces shifted into the delimiter - var spaces = spliceSpaces(middleDelim.children, 0); - if (spaces) { - _buildCommon2.default.prependChildren(inner[_i4], spaces); - } - } - } - } - - var rightDelim = void 0; - // Same for the right delimiter - if (group.value.right === ".") { - rightDelim = makeNullDelimiter(options, ["mclose"]); - } else { - rightDelim = _delimiter2.default.leftRightDelim(group.value.right, innerHeight, innerDepth, options, group.mode, ["mclose"]); - } - // Add it to the end of the expression. - inner.push(rightDelim); - - return (0, _buildCommon.makeSpan)(["minner"], inner, options); - }; - - groupTypes.middle = function (group, options) { - var middleDelim = void 0; - if (group.value.value === ".") { - middleDelim = makeNullDelimiter(options, []); - } else { - middleDelim = _delimiter2.default.sizedDelim(group.value.value, 1, options, group.mode, []); - middleDelim.isMiddle = { value: group.value.value, options: options }; - } - return middleDelim; - }; - - groupTypes.rule = function (group, options) { - // Make an empty span for the rule - var rule = (0, _buildCommon.makeSpan)(["mord", "rule"], [], options); - - // Calculate the shift, width, and height of the rule, and account for units - var shift = 0; - if (group.value.shift) { - shift = _units2.default.calculateSize(group.value.shift, options); - } - - var width = _units2.default.calculateSize(group.value.width, options); - var height = _units2.default.calculateSize(group.value.height, options); - - // Style the rule to the right size - rule.style.borderRightWidth = width + "em"; - rule.style.borderTopWidth = height + "em"; - rule.style.bottom = shift + "em"; - - // Record the height and width - rule.width = width; - rule.height = height + shift; - rule.depth = -shift; - // Font size is the number large enough that the browser will - // reserve at least `absHeight` space above the baseline. - // The 1.125 factor was empirically determined - rule.maxFontSize = height * 1.125 * options.sizeMultiplier; - - return rule; - }; - - groupTypes.kern = function (group, options) { - // Make an empty span for the rule - var rule = (0, _buildCommon.makeSpan)(["mord", "rule"], [], options); - - if (group.value.dimension) { - var dimension = _units2.default.calculateSize(group.value.dimension, options); - rule.style.marginLeft = dimension + "em"; - } - - return rule; - }; - - groupTypes.accent = function (group, options) { - // Accents are handled in the TeXbook pg. 443, rule 12. - var base = group.value.base; - - var supsubGroup = void 0; - if (group.type === "supsub") { - // If our base is a character box, and we have superscripts and - // subscripts, the supsub will defer to us. In particular, we want - // to attach the superscripts and subscripts to the inner body (so - // that the position of the superscripts and subscripts won't be - // affected by the height of the accent). We accomplish this by - // sticking the base of the accent into the base of the supsub, and - // rendering that, while keeping track of where the accent is. - - // The supsub group is the group that was passed in - var supsub = group; - // The real accent group is the base of the supsub group - group = supsub.value.base; - // The character box is the base of the accent group - base = group.value.base; - // Stick the character box into the base of the supsub group - supsub.value.base = base; - - // Rerender the supsub group with its new base, and store that - // result. - supsubGroup = buildGroup(supsub, options); - } - - // Build the base group - var body = buildGroup(base, options.havingCrampedStyle()); - - // Does the accent need to shift for the skew of a character? - var mustShift = group.value.isShifty && isCharacterBox(base); - - // Calculate the skew of the accent. This is based on the line "If the - // nucleus is not a single character, let s = 0; otherwise set s to the - // kern amount for the nucleus followed by the \skewchar of its font." - // Note that our skew metrics are just the kern between each character - // and the skewchar. - var skew = 0; - if (mustShift) { - // If the base is a character box, then we want the skew of the - // innermost character. To do that, we find the innermost character: - var baseChar = getBaseElem(base); - // Then, we render its group to get the symbol inside it - var baseGroup = buildGroup(baseChar, options.havingCrampedStyle()); - // Finally, we pull the skew off of the symbol. - skew = baseGroup.skew; - // Note that we now throw away baseGroup, because the layers we - // removed with getBaseElem might contain things like \color which - // we can't get rid of. - // TODO(emily): Find a better way to get the skew - } - - // calculate the amount of space between the body and the accent - var clearance = Math.min(body.height, options.fontMetrics().xHeight); - - // Build the accent - var accentBody = void 0; - if (!group.value.isStretchy) { - var accent = _buildCommon2.default.makeSymbol(group.value.label, "Main-Regular", group.mode, options); - // Remove the italic correction of the accent, because it only serves to - // shift the accent over to a place we don't want. - accent.italic = 0; - - // The \vec character that the fonts use is a combining character, and - // thus shows up much too far to the left. To account for this, we add a - // specific class which shifts the accent over to where we want it. - // TODO(emily): Fix this in a better way, like by changing the font - // Similarly, text accent \H is a combining character and - // requires a different adjustment. - var accentClass = null; - if (group.value.label === "\\vec") { - accentClass = "accent-vec"; - } else if (group.value.label === '\\H') { - accentClass = "accent-hungarian"; - } - - accentBody = (0, _buildCommon.makeSpan)([], [accent]); - accentBody = (0, _buildCommon.makeSpan)(["accent-body", accentClass], [accentBody]); - - // Shift the accent over by the skew. Note we shift by twice the skew - // because we are centering the accent, so by adding 2*skew to the left, - // we shift it to the right by 1*skew. - accentBody.style.marginLeft = 2 * skew + "em"; - - accentBody = _buildCommon2.default.makeVList([{ type: "elem", elem: body }, { type: "kern", size: -clearance }, { type: "elem", elem: accentBody }], "firstBaseline", null, options); - } else { - accentBody = _stretchy2.default.svgSpan(group, options); - - accentBody = _buildCommon2.default.makeVList([{ type: "elem", elem: body }, { type: "elem", elem: accentBody }], "firstBaseline", null, options); - - var styleSpan = accentBody.children[0].children[0].children[1]; - styleSpan.classes.push("svg-align"); // text-align: left; - if (skew > 0) { - // Shorten the accent and nudge it to the right. - styleSpan.style.width = "calc(100% - " + 2 * skew + "em)"; - styleSpan.style.marginLeft = 2 * skew + "em"; - } - } - - var accentWrap = (0, _buildCommon.makeSpan)(["mord", "accent"], [accentBody], options); - - if (supsubGroup) { - // Here, we replace the "base" child of the supsub with our newly - // generated accent. - supsubGroup.children[0] = accentWrap; - - // Since we don't rerun the height calculation after replacing the - // accent, we manually recalculate height. - supsubGroup.height = Math.max(accentWrap.height, supsubGroup.height); - - // Accents should always be ords, even when their innards are not. - supsubGroup.classes[0] = "mord"; - - return supsubGroup; - } else { - return accentWrap; - } - }; - - groupTypes.horizBrace = function (group, options) { - var style = options.style; - - var hasSupSub = group.type === "supsub"; - var supSubGroup = void 0; - var newOptions = void 0; - if (hasSupSub) { - // Ref: LaTeX source2e: }}}}\limits} - // i.e. LaTeX treats the brace similar to an op and passes it - // with \limits, so we need to assign supsub style. - if (group.value.sup) { - newOptions = options.havingStyle(style.sup()); - supSubGroup = buildGroup(group.value.sup, newOptions, options); - } else { - newOptions = options.havingStyle(style.sub()); - supSubGroup = buildGroup(group.value.sub, newOptions, options); - } - group = group.value.base; - } - - // Build the base group - var body = buildGroup(group.value.base, options.havingBaseStyle(_Style2.default.DISPLAY)); - - // Create the stretchy element - var braceBody = _stretchy2.default.svgSpan(group, options); - - // Generate the vlist, with the appropriate kerns ┏━━━━━━━━┓ - // This first vlist contains the subject matter and the brace: equation - var vlist = void 0; - if (group.value.isOver) { - vlist = _buildCommon2.default.makeVList([{ type: "elem", elem: body }, { type: "kern", size: 0.1 }, { type: "elem", elem: braceBody }], "firstBaseline", null, options); - vlist.children[0].children[0].children[1].classes.push("svg-align"); - } else { - vlist = _buildCommon2.default.makeVList([{ type: "elem", elem: braceBody }, { type: "kern", size: 0.1 }, { type: "elem", elem: body }], "bottom", body.depth + 0.1 + braceBody.height, options); - vlist.children[0].children[0].children[0].classes.push("svg-align"); - } - - if (hasSupSub) { - // In order to write the supsub, wrap the first vlist in another vlist: - // They can't all go in the same vlist, because the note might be wider - // than the equation. We want the equation to control the brace width. - - // note long note long note - // ┏━━━━━━━━┓ or ┏━━━┓ not ┏━━━━━━━━━┓ - // equation eqn eqn - - var vSpan = (0, _buildCommon.makeSpan)(["mord", group.value.isOver ? "mover" : "munder"], [vlist], options); - - if (group.value.isOver) { - vlist = _buildCommon2.default.makeVList([{ type: "elem", elem: vSpan }, { type: "kern", size: 0.2 }, { type: "elem", elem: supSubGroup }], "firstBaseline", null, options); - } else { - vlist = _buildCommon2.default.makeVList([{ type: "elem", elem: supSubGroup }, { type: "kern", size: 0.2 }, { type: "elem", elem: vSpan }], "bottom", vSpan.depth + 0.2 + supSubGroup.height, options); - } - } - - return (0, _buildCommon.makeSpan)(["mord", group.value.isOver ? "mover" : "munder"], [vlist], options); - }; - - groupTypes.accentUnder = function (group, options) { - // Treat under accents much like underlines. - var innerGroup = buildGroup(group.value.body, options); - - var accentBody = _stretchy2.default.svgSpan(group, options); - var kern = /tilde/.test(group.value.label) ? 0.12 : 0; - - // Generate the vlist, with the appropriate kerns - var vlist = _buildCommon2.default.makeVList([{ type: "elem", elem: accentBody }, { type: "kern", size: kern }, { type: "elem", elem: innerGroup }], "bottom", accentBody.height + kern, options); - - vlist.children[0].children[0].children[0].classes.push("svg-align"); - - return (0, _buildCommon.makeSpan)(["mord", "accentunder"], [vlist], options); - }; - - groupTypes.enclose = function (group, options) { - // \cancel, \bcancel, \xcancel, \sout, \fbox - var inner = buildGroup(group.value.body, options); - - var label = group.value.label.substr(1); - var scale = options.sizeMultiplier; - var img = void 0; - var pad = 0; - var imgShift = 0; - - if (label === "sout") { - img = (0, _buildCommon.makeSpan)(["stretchy", "sout"]); - img.height = options.fontMetrics().defaultRuleThickness / scale; - imgShift = -0.5 * options.fontMetrics().xHeight; - } else { - // Add horizontal padding - inner.classes.push(label === "fbox" ? "boxpad" : "cancel-pad"); - - // Add vertical padding - var isCharBox = isCharacterBox(group.value.body); - // ref: LaTeX source2e: \fboxsep = 3pt; \fboxrule = .4pt - // ref: cancel package: \advance\totalheight2\p@ % "+2" - pad = label === "fbox" ? 0.34 : isCharBox ? 0.2 : 0; - imgShift = inner.depth + pad; - - img = _stretchy2.default.encloseSpan(inner, label, pad, options); - } - - var vlist = _buildCommon2.default.makeVList([{ type: "elem", elem: inner, shift: 0 }, { type: "elem", elem: img, shift: imgShift }], "individualShift", null, options); - - if (label !== "fbox") { - vlist.children[0].children[0].children[1].classes.push("svg-align"); - } - - if (/cancel/.test(label)) { - // cancel does not create horiz space for its line extension. - // That is, not when adjacent to a mord. - return (0, _buildCommon.makeSpan)(["mord", "cancel-lap"], [vlist], options); - } else { - return (0, _buildCommon.makeSpan)(["mord"], [vlist], options); - } - }; - - groupTypes.xArrow = function (group, options) { - var style = options.style; - - // Build the argument groups in the appropriate style. - // Ref: amsmath.dtx: \hbox{$\scriptstyle\mkern#3mu{#6}\mkern#4mu$}% - - var newOptions = options.havingStyle(style.sup()); - var upperGroup = buildGroup(group.value.body, newOptions, options); - upperGroup.classes.push("x-arrow-pad"); - - var lowerGroup = void 0; - if (group.value.below) { - // Build the lower group - newOptions = options.havingStyle(style.sub()); - lowerGroup = buildGroup(group.value.below, newOptions, options); - lowerGroup.classes.push("x-arrow-pad"); - } - - var arrowBody = _stretchy2.default.svgSpan(group, options); - - var arrowShift = -options.fontMetrics().axisHeight + arrowBody.depth; - var upperShift = -options.fontMetrics().axisHeight - arrowBody.height - 0.111; // 2 mu. Ref: amsmath.dtx: #7\if0#2\else\mkern#2mu\fi - - // Generate the vlist - var vlist = void 0; - if (group.value.below) { - var lowerShift = -options.fontMetrics().axisHeight + lowerGroup.height + arrowBody.height + 0.111; - vlist = _buildCommon2.default.makeVList([{ type: "elem", elem: upperGroup, shift: upperShift }, { type: "elem", elem: arrowBody, shift: arrowShift }, { type: "elem", elem: lowerGroup, shift: lowerShift }], "individualShift", null, options); - } else { - vlist = _buildCommon2.default.makeVList([{ type: "elem", elem: upperGroup, shift: upperShift }, { type: "elem", elem: arrowBody, shift: arrowShift }], "individualShift", null, options); - } - - vlist.children[0].children[0].children[1].classes.push("svg-align"); - - return (0, _buildCommon.makeSpan)(["mrel", "x-arrow"], [vlist], options); - }; - - groupTypes.phantom = function (group, options) { - var elements = buildExpression(group.value.value, options.withPhantom(), false); - - // \phantom isn't supposed to affect the elements it contains. - // See "color" for more details. - return new _buildCommon2.default.makeFragment(elements); - }; - - groupTypes.mclass = function (group, options) { - var elements = buildExpression(group.value.value, options, true); - - return (0, _buildCommon.makeSpan)([group.value.mclass], elements, options); - }; - - /** - * buildGroup is the function that takes a group and calls the correct groupType - * function for it. It also handles the interaction of size and style changes - * between parents and children. - */ - var buildGroup = function buildGroup(group, options, baseOptions) { - if (!group) { - return (0, _buildCommon.makeSpan)(); - } - - if (groupTypes[group.type]) { - // Call the groupTypes function - var groupNode = groupTypes[group.type](group, options); - - // If the size changed between the parent and the current group, account - // for that size difference. - if (baseOptions && options.size !== baseOptions.size) { - groupNode = (0, _buildCommon.makeSpan)(options.sizingClasses(baseOptions), [groupNode], options); - - var multiplier = options.sizeMultiplier / baseOptions.sizeMultiplier; - - groupNode.height *= multiplier; - groupNode.depth *= multiplier; - } - - return groupNode; - } else { - throw new _ParseError2.default("Got group of unknown type: '" + group.type + "'"); - } - }; - - /** - * Take an entire parse tree, and build it into an appropriate set of HTML - * nodes. - */ - var buildHTML = function buildHTML(tree, options) { - // buildExpression is destructive, so we need to make a clone - // of the incoming tree so that it isn't accidentally changed - tree = JSON.parse((0, _stringify2.default)(tree)); - - // Build the expression contained in the tree - var expression = buildExpression(tree, options, true); - var body = (0, _buildCommon.makeSpan)(["base"], expression, options); - - // Add struts, which ensure that the top of the HTML element falls at the - // height of the expression, and the bottom of the HTML element falls at the - // depth of the expression. - var topStrut = (0, _buildCommon.makeSpan)(["strut"]); - var bottomStrut = (0, _buildCommon.makeSpan)(["strut", "bottom"]); - - topStrut.style.height = body.height + "em"; - bottomStrut.style.height = body.height + body.depth + "em"; - // We'd like to use `vertical-align: top` but in IE 9 this lowers the - // baseline of the box to the bottom of this strut (instead staying in the - // normal place) so we use an absolute value for vertical-align instead - bottomStrut.style.verticalAlign = -body.depth + "em"; - - // Wrap the struts and body together - var htmlNode = (0, _buildCommon.makeSpan)(["katex-html"], [topStrut, bottomStrut, body]); - - htmlNode.setAttribute("aria-hidden", "true"); - - return htmlNode; - }; - - module.exports = buildHTML; - - },{"./ParseError":29,"./Style":33,"./buildCommon":34,"./delimiter":38,"./domTree":39,"./stretchy":47,"./units":50,"./utils":51,"babel-runtime/core-js/json/stringify":2}],36:[function(require,module,exports){ - - var _buildCommon = require("./buildCommon"); - - var _buildCommon2 = _interopRequireDefault(_buildCommon); - - var _fontMetrics = require("./fontMetrics"); - - var _fontMetrics2 = _interopRequireDefault(_fontMetrics); - - var _mathMLTree = require("./mathMLTree"); - - var _mathMLTree2 = _interopRequireDefault(_mathMLTree); - - var _ParseError = require("./ParseError"); - - var _ParseError2 = _interopRequireDefault(_ParseError); - - var _Style = require("./Style"); - - var _Style2 = _interopRequireDefault(_Style); - - var _symbols = require("./symbols"); - - var _symbols2 = _interopRequireDefault(_symbols); - - var _utils = require("./utils"); - - var _utils2 = _interopRequireDefault(_utils); - - var _stretchy = require("./stretchy"); - - var _stretchy2 = _interopRequireDefault(_stretchy); - - function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { default: obj }; } - - /** - * Takes a symbol and converts it into a MathML text node after performing - * optional replacement from symbols.js. - */ - /** - * This file converts a parse tree into a cooresponding MathML tree. The main - * entry point is the `buildMathML` function, which takes a parse tree from the - * parser. - */ - - var makeText = function makeText(text, mode) { - if (_symbols2.default[mode][text] && _symbols2.default[mode][text].replace) { - text = _symbols2.default[mode][text].replace; - } - - return new _mathMLTree2.default.TextNode(text); - }; - - /** - * Returns the math variant as a string or null if none is required. - */ - var getVariant = function getVariant(group, options) { - var font = options.font; - if (!font) { - return null; - } - - var mode = group.mode; - if (font === "mathit") { - return "italic"; - } - - var value = group.value; - if (_utils2.default.contains(["\\imath", "\\jmath"], value)) { - return null; - } - - if (_symbols2.default[mode][value] && _symbols2.default[mode][value].replace) { - value = _symbols2.default[mode][value].replace; - } - - var fontName = _buildCommon.fontMap[font].fontName; - if (_fontMetrics2.default.getCharacterMetrics(value, fontName)) { - return _buildCommon.fontMap[options.font].variant; - } - - return null; - }; - - /** - * Functions for handling the different types of groups found in the parse - * tree. Each function should take a parse group and return a MathML node. - */ - var groupTypes = {}; - - var defaultVariant = { - "mi": "italic", - "mn": "normal", - "mtext": "normal" - }; - - groupTypes.mathord = function (group, options) { - var node = new _mathMLTree2.default.MathNode("mi", [makeText(group.value, group.mode)]); - - var variant = getVariant(group, options) || "italic"; - if (variant !== defaultVariant[node.type]) { - node.setAttribute("mathvariant", variant); - } - return node; - }; - - groupTypes.textord = function (group, options) { - var text = makeText(group.value, group.mode); - - var variant = getVariant(group, options) || "normal"; - - var node = void 0; - if (group.mode === 'text') { - node = new _mathMLTree2.default.MathNode("mtext", [text]); - } else if (/[0-9]/.test(group.value)) { - // TODO(kevinb) merge adjacent nodes - // do it as a post processing step - node = new _mathMLTree2.default.MathNode("mn", [text]); - } else if (group.value === "\\prime") { - node = new _mathMLTree2.default.MathNode("mo", [text]); - } else { - node = new _mathMLTree2.default.MathNode("mi", [text]); - } - if (variant !== defaultVariant[node.type]) { - node.setAttribute("mathvariant", variant); - } - - return node; - }; - - groupTypes.bin = function (group) { - var node = new _mathMLTree2.default.MathNode("mo", [makeText(group.value, group.mode)]); - - return node; - }; - - groupTypes.rel = function (group) { - var node = new _mathMLTree2.default.MathNode("mo", [makeText(group.value, group.mode)]); - - return node; - }; - - groupTypes.open = function (group) { - var node = new _mathMLTree2.default.MathNode("mo", [makeText(group.value, group.mode)]); - - return node; - }; - - groupTypes.close = function (group) { - var node = new _mathMLTree2.default.MathNode("mo", [makeText(group.value, group.mode)]); - - return node; - }; - - groupTypes.inner = function (group) { - var node = new _mathMLTree2.default.MathNode("mo", [makeText(group.value, group.mode)]); - - return node; - }; - - groupTypes.punct = function (group) { - var node = new _mathMLTree2.default.MathNode("mo", [makeText(group.value, group.mode)]); - - node.setAttribute("separator", "true"); - - return node; - }; - - groupTypes.ordgroup = function (group, options) { - var inner = buildExpression(group.value, options); - - var node = new _mathMLTree2.default.MathNode("mrow", inner); - - return node; - }; - - groupTypes.text = function (group, options) { - var body = group.value.body; - - // Convert each element of the body into MathML, and combine consecutive - // outputs into a single tag. In this way, we don't - // nest non-text items (e.g., $nested-math$) within an . - var inner = []; - var currentText = null; - for (var i = 0; i < body.length; i++) { - var _group = buildGroup(body[i], options); - if (_group.type === 'mtext' && currentText != null) { - Array.prototype.push.apply(currentText.children, _group.children); - } else { - inner.push(_group); - if (_group.type === 'mtext') { - currentText = _group; - } - } - } - - // If there is a single tag in the end (presumably ), - // just return it. Otherwise, wrap them in an . - if (inner.length === 1) { - return inner[0]; - } else { - return new _mathMLTree2.default.MathNode("mrow", inner); - } - }; - - groupTypes.color = function (group, options) { - var inner = buildExpression(group.value.value, options); - - var node = new _mathMLTree2.default.MathNode("mstyle", inner); - - node.setAttribute("mathcolor", group.value.color); - - return node; - }; - - groupTypes.supsub = function (group, options) { - // Is the inner group a relevant horizonal brace? - var isBrace = false; - var isOver = void 0; - var isSup = void 0; - if (group.value.base) { - if (group.value.base.value.type === "horizBrace") { - isSup = group.value.sup ? true : false; - if (isSup === group.value.base.value.isOver) { - isBrace = true; - isOver = group.value.base.value.isOver; - } - } - } - - var removeUnnecessaryRow = true; - var children = [buildGroup(group.value.base, options, removeUnnecessaryRow)]; - - if (group.value.sub) { - children.push(buildGroup(group.value.sub, options, removeUnnecessaryRow)); - } - - if (group.value.sup) { - children.push(buildGroup(group.value.sup, options, removeUnnecessaryRow)); - } - - var nodeType = void 0; - if (isBrace) { - nodeType = isOver ? "mover" : "munder"; - } else if (!group.value.sub) { - nodeType = "msup"; - } else if (!group.value.sup) { - nodeType = "msub"; - } else { - var base = group.value.base; - if (base && base.value.limits && options.style === _Style2.default.DISPLAY) { - nodeType = "munderover"; - } else { - nodeType = "msubsup"; - } - } - - var node = new _mathMLTree2.default.MathNode(nodeType, children); - - return node; - }; - - groupTypes.genfrac = function (group, options) { - var node = new _mathMLTree2.default.MathNode("mfrac", [buildGroup(group.value.numer, options), buildGroup(group.value.denom, options)]); - - if (!group.value.hasBarLine) { - node.setAttribute("linethickness", "0px"); - } - - if (group.value.leftDelim != null || group.value.rightDelim != null) { - var withDelims = []; - - if (group.value.leftDelim != null) { - var leftOp = new _mathMLTree2.default.MathNode("mo", [new _mathMLTree2.default.TextNode(group.value.leftDelim)]); - - leftOp.setAttribute("fence", "true"); - - withDelims.push(leftOp); - } - - withDelims.push(node); - - if (group.value.rightDelim != null) { - var rightOp = new _mathMLTree2.default.MathNode("mo", [new _mathMLTree2.default.TextNode(group.value.rightDelim)]); - - rightOp.setAttribute("fence", "true"); - - withDelims.push(rightOp); - } - - var outerNode = new _mathMLTree2.default.MathNode("mrow", withDelims); - - return outerNode; - } - - return node; - }; - - groupTypes.array = function (group, options) { - return new _mathMLTree2.default.MathNode("mtable", group.value.body.map(function (row) { - return new _mathMLTree2.default.MathNode("mtr", row.map(function (cell) { - return new _mathMLTree2.default.MathNode("mtd", [buildGroup(cell, options)]); - })); - })); - }; - - groupTypes.sqrt = function (group, options) { - var node = void 0; - if (group.value.index) { - node = new _mathMLTree2.default.MathNode("mroot", [buildGroup(group.value.body, options), buildGroup(group.value.index, options)]); - } else { - node = new _mathMLTree2.default.MathNode("msqrt", [buildGroup(group.value.body, options)]); - } - - return node; - }; - - groupTypes.leftright = function (group, options) { - var inner = buildExpression(group.value.body, options); - - if (group.value.left !== ".") { - var leftNode = new _mathMLTree2.default.MathNode("mo", [makeText(group.value.left, group.mode)]); - - leftNode.setAttribute("fence", "true"); - - inner.unshift(leftNode); - } - - if (group.value.right !== ".") { - var rightNode = new _mathMLTree2.default.MathNode("mo", [makeText(group.value.right, group.mode)]); - - rightNode.setAttribute("fence", "true"); - - inner.push(rightNode); - } - - var outerNode = new _mathMLTree2.default.MathNode("mrow", inner); - - return outerNode; - }; - - groupTypes.middle = function (group, options) { - var middleNode = new _mathMLTree2.default.MathNode("mo", [makeText(group.value.middle, group.mode)]); - middleNode.setAttribute("fence", "true"); - return middleNode; - }; - - groupTypes.accent = function (group, options) { - var accentNode = void 0; - if (group.value.isStretchy) { - accentNode = _stretchy2.default.mathMLnode(group.value.label); - } else { - accentNode = new _mathMLTree2.default.MathNode("mo", [makeText(group.value.label, group.mode)]); - } - - var node = new _mathMLTree2.default.MathNode("mover", [buildGroup(group.value.base, options), accentNode]); - - node.setAttribute("accent", "true"); - - return node; - }; - - groupTypes.spacing = function (group) { - var node = void 0; - - if (group.value === "\\ " || group.value === "\\space" || group.value === " " || group.value === "~") { - node = new _mathMLTree2.default.MathNode("mtext", [new _mathMLTree2.default.TextNode("\xA0")]); - } else { - node = new _mathMLTree2.default.MathNode("mspace"); - - node.setAttribute("width", _buildCommon2.default.spacingFunctions[group.value].size); - } - - return node; - }; - - groupTypes.op = function (group, options) { - var node = void 0; - - // TODO(emily): handle big operators using the `largeop` attribute - - if (group.value.symbol) { - // This is a symbol. Just add the symbol. - node = new _mathMLTree2.default.MathNode("mo", [makeText(group.value.body, group.mode)]); - } else if (group.value.value) { - // This is an operator with children. Add them. - node = new _mathMLTree2.default.MathNode("mo", buildExpression(group.value.value, options)); - } else { - // This is a text operator. Add all of the characters from the - // operator's name. - // TODO(emily): Add a space in the middle of some of these - // operators, like \limsup. - node = new _mathMLTree2.default.MathNode("mi", [new _mathMLTree2.default.TextNode(group.value.body.slice(1))]); - } - - return node; - }; - - groupTypes.mod = function (group, options) { - var inner = []; - - if (group.value.modType === "pod" || group.value.modType === "pmod") { - inner.push(new _mathMLTree2.default.MathNode("mo", [makeText("(", group.mode)])); - } - if (group.value.modType !== "pod") { - inner.push(new _mathMLTree2.default.MathNode("mo", [makeText("mod", group.mode)])); - } - if (group.value.value) { - var space = new _mathMLTree2.default.MathNode("mspace"); - space.setAttribute("width", "0.333333em"); - inner.push(space); - inner = inner.concat(buildExpression(group.value.value, options)); - } - if (group.value.modType === "pod" || group.value.modType === "pmod") { - inner.push(new _mathMLTree2.default.MathNode("mo", [makeText(")", group.mode)])); - } - - return new _mathMLTree2.default.MathNode("mo", inner); - }; - - groupTypes.katex = function (group) { - var node = new _mathMLTree2.default.MathNode("mtext", [new _mathMLTree2.default.TextNode("KaTeX")]); - - return node; - }; - - groupTypes.font = function (group, options) { - var font = group.value.font; - return buildGroup(group.value.body, options.withFont(font)); - }; - - groupTypes.delimsizing = function (group) { - var children = []; - - if (group.value.value !== ".") { - children.push(makeText(group.value.value, group.mode)); - } - - var node = new _mathMLTree2.default.MathNode("mo", children); - - if (group.value.mclass === "mopen" || group.value.mclass === "mclose") { - // Only some of the delimsizing functions act as fences, and they - // return "mopen" or "mclose" mclass. - node.setAttribute("fence", "true"); - } else { - // Explicitly disable fencing if it's not a fence, to override the - // defaults. - node.setAttribute("fence", "false"); - } - - return node; - }; - - groupTypes.styling = function (group, options) { - // Figure out what style we're changing to. - // TODO(kevinb): dedupe this with buildHTML.js - // This will be easier of handling of styling nodes is in the same file. - var styleMap = { - "display": _Style2.default.DISPLAY, - "text": _Style2.default.TEXT, - "script": _Style2.default.SCRIPT, - "scriptscript": _Style2.default.SCRIPTSCRIPT - }; - - var newStyle = styleMap[group.value.style]; - var newOptions = options.havingStyle(newStyle); - - var inner = buildExpression(group.value.value, newOptions); - - var node = new _mathMLTree2.default.MathNode("mstyle", inner); - - var styleAttributes = { - "display": ["0", "true"], - "text": ["0", "false"], - "script": ["1", "false"], - "scriptscript": ["2", "false"] - }; - - var attr = styleAttributes[group.value.style]; - - node.setAttribute("scriptlevel", attr[0]); - node.setAttribute("displaystyle", attr[1]); - - return node; - }; - - groupTypes.sizing = function (group, options) { - var newOptions = options.havingSize(group.value.size); - var inner = buildExpression(group.value.value, newOptions); - - var node = new _mathMLTree2.default.MathNode("mstyle", inner); - - // TODO(emily): This doesn't produce the correct size for nested size - // changes, because we don't keep state of what style we're currently - // in, so we can't reset the size to normal before changing it. Now - // that we're passing an options parameter we should be able to fix - // this. - node.setAttribute("mathsize", newOptions.sizeMultiplier + "em"); - - return node; - }; - - groupTypes.overline = function (group, options) { - var operator = new _mathMLTree2.default.MathNode("mo", [new _mathMLTree2.default.TextNode("\u203E")]); - operator.setAttribute("stretchy", "true"); - - var node = new _mathMLTree2.default.MathNode("mover", [buildGroup(group.value.body, options), operator]); - node.setAttribute("accent", "true"); - - return node; - }; - - groupTypes.underline = function (group, options) { - var operator = new _mathMLTree2.default.MathNode("mo", [new _mathMLTree2.default.TextNode("\u203E")]); - operator.setAttribute("stretchy", "true"); - - var node = new _mathMLTree2.default.MathNode("munder", [buildGroup(group.value.body, options), operator]); - node.setAttribute("accentunder", "true"); - - return node; - }; - - groupTypes.accentUnder = function (group, options) { - var accentNode = _stretchy2.default.mathMLnode(group.value.label); - var node = new _mathMLTree2.default.MathNode("munder", [buildGroup(group.value.body, options), accentNode]); - node.setAttribute("accentunder", "true"); - return node; - }; - - groupTypes.enclose = function (group, options) { - var node = new _mathMLTree2.default.MathNode("menclose", [buildGroup(group.value.body, options)]); - var notation = ""; - switch (group.value.label) { - case "\\bcancel": - notation = "downdiagonalstrike"; - break; - case "\\sout": - notation = "horizontalstrike"; - break; - case "\\fbox": - notation = "box"; - break; - default: - notation = "updiagonalstrike"; - } - node.setAttribute("notation", notation); - return node; - }; - - groupTypes.horizBrace = function (group, options) { - var accentNode = _stretchy2.default.mathMLnode(group.value.label); - return new _mathMLTree2.default.MathNode(group.value.isOver ? "mover" : "munder", [buildGroup(group.value.base, options), accentNode]); - }; - - groupTypes.xArrow = function (group, options) { - var arrowNode = _stretchy2.default.mathMLnode(group.value.label); - var node = void 0; - var lowerNode = void 0; - - if (group.value.body) { - var upperNode = buildGroup(group.value.body, options); - if (group.value.below) { - lowerNode = buildGroup(group.value.below, options); - node = new _mathMLTree2.default.MathNode("munderover", [arrowNode, lowerNode, upperNode]); - } else { - node = new _mathMLTree2.default.MathNode("mover", [arrowNode, upperNode]); - } - } else if (group.value.below) { - lowerNode = buildGroup(group.value.below, options); - node = new _mathMLTree2.default.MathNode("munder", [arrowNode, lowerNode]); - } else { - node = new _mathMLTree2.default.MathNode("mover", [arrowNode]); - } - return node; - }; - - groupTypes.rule = function (group) { - // TODO(emily): Figure out if there's an actual way to draw black boxes - // in MathML. - var node = new _mathMLTree2.default.MathNode("mrow"); - - return node; - }; - - groupTypes.kern = function (group) { - // TODO(kevin): Figure out if there's a way to add space in MathML - var node = new _mathMLTree2.default.MathNode("mrow"); - - return node; - }; - - groupTypes.llap = function (group, options) { - var node = new _mathMLTree2.default.MathNode("mpadded", [buildGroup(group.value.body, options)]); - - node.setAttribute("lspace", "-1width"); - node.setAttribute("width", "0px"); - - return node; - }; - - groupTypes.rlap = function (group, options) { - var node = new _mathMLTree2.default.MathNode("mpadded", [buildGroup(group.value.body, options)]); - - node.setAttribute("width", "0px"); - - return node; - }; - - groupTypes.phantom = function (group, options) { - var inner = buildExpression(group.value.value, options); - return new _mathMLTree2.default.MathNode("mphantom", inner); - }; - - groupTypes.mclass = function (group, options) { - var inner = buildExpression(group.value.value, options); - return new _mathMLTree2.default.MathNode("mstyle", inner); - }; - - /** - * Takes a list of nodes, builds them, and returns a list of the generated - * MathML nodes. A little simpler than the HTML version because we don't do any - * previous-node handling. - */ - var buildExpression = function buildExpression(expression, options) { - var groups = []; - for (var i = 0; i < expression.length; i++) { - var group = expression[i]; - groups.push(buildGroup(group, options)); - } - - // TODO(kevinb): combine \\not with mrels and mords - - return groups; - }; - - /** - * Takes a group from the parser and calls the appropriate groupTypes function - * on it to produce a MathML node. - */ - // TODO(kevinb): determine if removeUnnecessaryRow should always be true - var buildGroup = function buildGroup(group, options) { - var removeUnnecessaryRow = arguments.length > 2 && arguments[2] !== undefined ? arguments[2] : false; - - if (!group) { - return new _mathMLTree2.default.MathNode("mrow"); - } - - if (groupTypes[group.type]) { - // Call the groupTypes function - var result = groupTypes[group.type](group, options); - if (removeUnnecessaryRow) { - if (result.type === "mrow" && result.children.length === 1) { - return result.children[0]; - } - } - return result; - } else { - throw new _ParseError2.default("Got group of unknown type: '" + group.type + "'"); - } - }; - - /** - * Takes a full parse tree and settings and builds a MathML representation of - * it. In particular, we put the elements from building the parse tree into a - * tag so we can also include that TeX source as an annotation. - * - * Note that we actually return a domTree element with a `` inside it so - * we can do appropriate styling. - */ - var buildMathML = function buildMathML(tree, texExpression, options) { - var expression = buildExpression(tree, options); - - // Wrap up the expression in an mrow so it is presented in the semantics - // tag correctly. - var wrapper = new _mathMLTree2.default.MathNode("mrow", expression); - - // Build a TeX annotation of the source - var annotation = new _mathMLTree2.default.MathNode("annotation", [new _mathMLTree2.default.TextNode(texExpression)]); - - annotation.setAttribute("encoding", "application/x-tex"); - - var semantics = new _mathMLTree2.default.MathNode("semantics", [wrapper, annotation]); - - var math = new _mathMLTree2.default.MathNode("math", [semantics]); - - // You can't style nodes, so we wrap the node in a span. - return (0, _buildCommon.makeSpan)(["katex-mathml"], [math]); - }; - - module.exports = buildMathML; - - },{"./ParseError":29,"./Style":33,"./buildCommon":34,"./fontMetrics":41,"./mathMLTree":45,"./stretchy":47,"./symbols":48,"./utils":51}],37:[function(require,module,exports){ - - var _buildHTML = require("./buildHTML"); - - var _buildHTML2 = _interopRequireDefault(_buildHTML); - - var _buildMathML = require("./buildMathML"); - - var _buildMathML2 = _interopRequireDefault(_buildMathML); - - var _buildCommon = require("./buildCommon"); - - var _Options = require("./Options"); - - var _Options2 = _interopRequireDefault(_Options); - - var _Settings = require("./Settings"); - - var _Settings2 = _interopRequireDefault(_Settings); - - var _Style = require("./Style"); - - var _Style2 = _interopRequireDefault(_Style); - - function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { default: obj }; } - - var buildTree = function buildTree(tree, expression, settings) { - settings = settings || new _Settings2.default({}); - - var startStyle = _Style2.default.TEXT; - if (settings.displayMode) { - startStyle = _Style2.default.DISPLAY; - } - - // Setup the default options - var options = new _Options2.default({ - style: startStyle - }); - - // `buildHTML` sometimes messes with the parse tree (like turning bins -> - // ords), so we build the MathML version first. - var mathMLNode = (0, _buildMathML2.default)(tree, expression, options); - var htmlNode = (0, _buildHTML2.default)(tree, options); - - var katexNode = (0, _buildCommon.makeSpan)(["katex"], [mathMLNode, htmlNode]); - - if (settings.displayMode) { - return (0, _buildCommon.makeSpan)(["katex-display"], [katexNode]); - } else { - return katexNode; - } - }; - - module.exports = buildTree; - - },{"./Options":28,"./Settings":32,"./Style":33,"./buildCommon":34,"./buildHTML":35,"./buildMathML":36}],38:[function(require,module,exports){ - - var _ParseError = require("./ParseError"); - - var _ParseError2 = _interopRequireDefault(_ParseError); - - var _Style = require("./Style"); - - var _Style2 = _interopRequireDefault(_Style); - - var _buildCommon = require("./buildCommon"); - - var _buildCommon2 = _interopRequireDefault(_buildCommon); - - var _fontMetrics = require("./fontMetrics"); - - var _fontMetrics2 = _interopRequireDefault(_fontMetrics); - - var _symbols = require("./symbols"); - - var _symbols2 = _interopRequireDefault(_symbols); - - var _utils = require("./utils"); - - var _utils2 = _interopRequireDefault(_utils); - - function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { default: obj }; } - - /** - * Get the metrics for a given symbol and font, after transformation (i.e. - * after following replacement from symbols.js) - */ - /** - * This file deals with creating delimiters of various sizes. The TeXbook - * discusses these routines on page 441-442, in the "Another subroutine sets box - * x to a specified variable delimiter" paragraph. - * - * There are three main routines here. `makeSmallDelim` makes a delimiter in the - * normal font, but in either text, script, or scriptscript style. - * `makeLargeDelim` makes a delimiter in textstyle, but in one of the Size1, - * Size2, Size3, or Size4 fonts. `makeStackedDelim` makes a delimiter out of - * smaller pieces that are stacked on top of one another. - * - * The functions take a parameter `center`, which determines if the delimiter - * should be centered around the axis. - * - * Then, there are three exposed functions. `sizedDelim` makes a delimiter in - * one of the given sizes. This is used for things like `\bigl`. - * `customSizedDelim` makes a delimiter with a given total height+depth. It is - * called in places like `\sqrt`. `leftRightDelim` makes an appropriate - * delimiter which surrounds an expression of a given height an depth. It is - * used in `\left` and `\right`. - */ - - var getMetrics = function getMetrics(symbol, font) { - if (_symbols2.default.math[symbol] && _symbols2.default.math[symbol].replace) { - return _fontMetrics2.default.getCharacterMetrics(_symbols2.default.math[symbol].replace, font); - } else { - return _fontMetrics2.default.getCharacterMetrics(symbol, font); - } - }; - - /** - * Puts a delimiter span in a given style, and adds appropriate height, depth, - * and maxFontSizes. - */ - var styleWrap = function styleWrap(delim, toStyle, options, classes) { - var newOptions = options.havingBaseStyle(toStyle); - - var span = (0, _buildCommon.makeSpan)((classes || []).concat(newOptions.sizingClasses(options)), [delim], options); - - span.delimSizeMultiplier = newOptions.sizeMultiplier / options.sizeMultiplier; - span.height *= span.delimSizeMultiplier; - span.depth *= span.delimSizeMultiplier; - span.maxFontSize = newOptions.sizeMultiplier; - - return span; - }; - - var centerSpan = function centerSpan(span, options, style) { - var newOptions = options.havingBaseStyle(style); - var shift = (1 - options.sizeMultiplier / newOptions.sizeMultiplier) * options.fontMetrics().axisHeight; - - span.classes.push("delimcenter"); - span.style.top = shift + "em"; - span.height -= shift; - span.depth += shift; - }; - - /** - * Makes a small delimiter. This is a delimiter that comes in the Main-Regular - * font, but is restyled to either be in textstyle, scriptstyle, or - * scriptscriptstyle. - */ - var makeSmallDelim = function makeSmallDelim(delim, style, center, options, mode, classes) { - var text = _buildCommon2.default.makeSymbol(delim, "Main-Regular", mode, options); - var span = styleWrap(text, style, options, classes); - if (center) { - centerSpan(span, options, style); - } - return span; - }; - - /** - * Builds a symbol in the given font size (note size is an integer) - */ - var mathrmSize = function mathrmSize(value, size, mode, options) { - return _buildCommon2.default.makeSymbol(value, "Size" + size + "-Regular", mode, options); - }; - - /** - * Makes a large delimiter. This is a delimiter that comes in the Size1, Size2, - * Size3, or Size4 fonts. It is always rendered in textstyle. - */ - var makeLargeDelim = function makeLargeDelim(delim, size, center, options, mode, classes) { - var inner = mathrmSize(delim, size, mode, options); - var span = styleWrap((0, _buildCommon.makeSpan)(["delimsizing", "size" + size], [inner], options), _Style2.default.TEXT, options, classes); - if (center) { - centerSpan(span, options, _Style2.default.TEXT); - } - return span; - }; - - /** - * Make an inner span with the given offset and in the given font. This is used - * in `makeStackedDelim` to make the stacking pieces for the delimiter. - */ - var makeInner = function makeInner(symbol, font, mode) { - var sizeClass = void 0; - // Apply the correct CSS class to choose the right font. - if (font === "Size1-Regular") { - sizeClass = "delim-size1"; - } else if (font === "Size4-Regular") { - sizeClass = "delim-size4"; - } - - var inner = (0, _buildCommon.makeSpan)(["delimsizinginner", sizeClass], [(0, _buildCommon.makeSpan)([], [_buildCommon2.default.makeSymbol(symbol, font, mode)])]); - - // Since this will be passed into `makeVList` in the end, wrap the element - // in the appropriate tag that VList uses. - return { type: "elem", elem: inner }; - }; - - /** - * Make a stacked delimiter out of a given delimiter, with the total height at - * least `heightTotal`. This routine is mentioned on page 442 of the TeXbook. - */ - var makeStackedDelim = function makeStackedDelim(delim, heightTotal, center, options, mode, classes) { - // There are four parts, the top, an optional middle, a repeated part, and a - // bottom. - var top = void 0; - var middle = void 0; - var repeat = void 0; - var bottom = void 0; - top = repeat = bottom = delim; - middle = null; - // Also keep track of what font the delimiters are in - var font = "Size1-Regular"; - - // We set the parts and font based on the symbol. Note that we use - // '\u23d0' instead of '|' and '\u2016' instead of '\\|' for the - // repeats of the arrows - if (delim === "\\uparrow") { - repeat = bottom = "\u23D0"; - } else if (delim === "\\Uparrow") { - repeat = bottom = "\u2016"; - } else if (delim === "\\downarrow") { - top = repeat = "\u23D0"; - } else if (delim === "\\Downarrow") { - top = repeat = "\u2016"; - } else if (delim === "\\updownarrow") { - top = "\\uparrow"; - repeat = "\u23D0"; - bottom = "\\downarrow"; - } else if (delim === "\\Updownarrow") { - top = "\\Uparrow"; - repeat = "\u2016"; - bottom = "\\Downarrow"; - } else if (delim === "[" || delim === "\\lbrack") { - top = "\u23A1"; - repeat = "\u23A2"; - bottom = "\u23A3"; - font = "Size4-Regular"; - } else if (delim === "]" || delim === "\\rbrack") { - top = "\u23A4"; - repeat = "\u23A5"; - bottom = "\u23A6"; - font = "Size4-Regular"; - } else if (delim === "\\lfloor") { - repeat = top = "\u23A2"; - bottom = "\u23A3"; - font = "Size4-Regular"; - } else if (delim === "\\lceil") { - top = "\u23A1"; - repeat = bottom = "\u23A2"; - font = "Size4-Regular"; - } else if (delim === "\\rfloor") { - repeat = top = "\u23A5"; - bottom = "\u23A6"; - font = "Size4-Regular"; - } else if (delim === "\\rceil") { - top = "\u23A4"; - repeat = bottom = "\u23A5"; - font = "Size4-Regular"; - } else if (delim === "(") { - top = "\u239B"; - repeat = "\u239C"; - bottom = "\u239D"; - font = "Size4-Regular"; - } else if (delim === ")") { - top = "\u239E"; - repeat = "\u239F"; - bottom = "\u23A0"; - font = "Size4-Regular"; - } else if (delim === "\\{" || delim === "\\lbrace") { - top = "\u23A7"; - middle = "\u23A8"; - bottom = "\u23A9"; - repeat = "\u23AA"; - font = "Size4-Regular"; - } else if (delim === "\\}" || delim === "\\rbrace") { - top = "\u23AB"; - middle = "\u23AC"; - bottom = "\u23AD"; - repeat = "\u23AA"; - font = "Size4-Regular"; - } else if (delim === "\\lgroup") { - top = "\u23A7"; - bottom = "\u23A9"; - repeat = "\u23AA"; - font = "Size4-Regular"; - } else if (delim === "\\rgroup") { - top = "\u23AB"; - bottom = "\u23AD"; - repeat = "\u23AA"; - font = "Size4-Regular"; - } else if (delim === "\\lmoustache") { - top = "\u23A7"; - bottom = "\u23AD"; - repeat = "\u23AA"; - font = "Size4-Regular"; - } else if (delim === "\\rmoustache") { - top = "\u23AB"; - bottom = "\u23A9"; - repeat = "\u23AA"; - font = "Size4-Regular"; - } - - // Get the metrics of the four sections - var topMetrics = getMetrics(top, font); - var topHeightTotal = topMetrics.height + topMetrics.depth; - var repeatMetrics = getMetrics(repeat, font); - var repeatHeightTotal = repeatMetrics.height + repeatMetrics.depth; - var bottomMetrics = getMetrics(bottom, font); - var bottomHeightTotal = bottomMetrics.height + bottomMetrics.depth; - var middleHeightTotal = 0; - var middleFactor = 1; - if (middle !== null) { - var middleMetrics = getMetrics(middle, font); - middleHeightTotal = middleMetrics.height + middleMetrics.depth; - middleFactor = 2; // repeat symmetrically above and below middle - } - - // Calcuate the minimal height that the delimiter can have. - // It is at least the size of the top, bottom, and optional middle combined. - var minHeight = topHeightTotal + bottomHeightTotal + middleHeightTotal; - - // Compute the number of copies of the repeat symbol we will need - var repeatCount = Math.ceil((heightTotal - minHeight) / (middleFactor * repeatHeightTotal)); - - // Compute the total height of the delimiter including all the symbols - var realHeightTotal = minHeight + repeatCount * middleFactor * repeatHeightTotal; - - // The center of the delimiter is placed at the center of the axis. Note - // that in this context, "center" means that the delimiter should be - // centered around the axis in the current style, while normally it is - // centered around the axis in textstyle. - var axisHeight = options.fontMetrics().axisHeight; - if (center) { - axisHeight *= options.sizeMultiplier; - } - // Calculate the depth - var depth = realHeightTotal / 2 - axisHeight; - - // Now, we start building the pieces that will go into the vlist - - // Keep a list of the inner pieces - var inners = []; - - // Add the bottom symbol - inners.push(makeInner(bottom, font, mode)); - - if (middle === null) { - // Add that many symbols - for (var i = 0; i < repeatCount; i++) { - inners.push(makeInner(repeat, font, mode)); - } - } else { - // When there is a middle bit, we need the middle part and two repeated - // sections - for (var _i = 0; _i < repeatCount; _i++) { - inners.push(makeInner(repeat, font, mode)); - } - inners.push(makeInner(middle, font, mode)); - for (var _i2 = 0; _i2 < repeatCount; _i2++) { - inners.push(makeInner(repeat, font, mode)); - } - } - - // Add the top symbol - inners.push(makeInner(top, font, mode)); - - // Finally, build the vlist - var newOptions = options.havingBaseStyle(_Style2.default.TEXT); - var inner = _buildCommon2.default.makeVList(inners, "bottom", depth, newOptions); - - return styleWrap((0, _buildCommon.makeSpan)(["delimsizing", "mult"], [inner], newOptions), _Style2.default.TEXT, options, classes); - }; - - var sqrtInnerSVG = { - // The main path geometry is from glyph U221A in the font KaTeX Main - main: "", - - // size1 is from glyph U221A in the font KaTeX_Size1-Regular - 1: "", - - // size2 is from glyph U221A in the font KaTeX_Size2-Regular - 2: "", - - // size3 is from glyph U221A in the font KaTeX_Size3-Regular - 3: "", - - // size4 is from glyph U221A in the font KaTeX_Size4-Regular - 4: "", - - // tall is from glyph U23B7 in the font KaTeX_Size4-Regular - tall: "l-4 4-4 4c-.667.667-2 1.5-4 2.5s-4.167 1.833-6.5 2.5-5.5 1-9.5 1h\n-12l-28-84c-16.667-52-96.667 -294.333-240-727l-212 -643 -85 170c-4-3.333-8.333\n-7.667-13 -13l-13-13l77-155 77-156c66 199.333 139 419.667 219 661 l218 661z\nM702 0H400000v40H742z'/>" - }; - - var sqrtSpan = function sqrtSpan(height, delim, options) { - // Create a span containing an SVG image of a sqrt symbol. - var span = _buildCommon2.default.makeSpan([], [], options); - var sizeMultiplier = options.sizeMultiplier; // default - - if (delim.type === "small") { - // Get an SVG that is derived from glyph U+221A in font KaTeX-Main. - var newOptions = options.havingBaseStyle(delim.style); - sizeMultiplier = newOptions.sizeMultiplier / options.sizeMultiplier; - - span.height = 1 * sizeMultiplier; - span.style.height = span.height + "em"; - span.surdWidth = 0.833 * sizeMultiplier; // from the font. - //In the font, the glyph is 1000 units tall. The font scale is 1:1000. - - span.innerHTML = "\n " + sqrtInnerSVG['main'] + ""; - } else if (delim.type === "large") { - // These SVGs come from fonts: KaTeX_Size1, _Size2, etc. - // Get sqrt height from font data - span.height = sizeToMaxHeight[delim.size] / sizeMultiplier; - span.style.height = span.height + "em"; - span.surdWidth = 1.0 / sizeMultiplier; // from the font - - span.innerHTML = "\n " + sqrtInnerSVG[delim.size] + ""; - } else { - // Tall sqrt. In TeX, this would be stacked using multiple glyphs. - // We'll use a single SVG to accomplish the same thing. - span.height = height / sizeMultiplier; - span.style.height = span.height + "em"; - span.surdWidth = 1.056 / sizeMultiplier; - var viewBoxHeight = Math.floor(span.height * 1000); // scale = 1:1000 - var vertSegment = viewBoxHeight - 54; - - // This \sqrt is customized in both height and width. We set the - // height now. Then CSS will stretch the image to the correct width. - // This SVG path comes from glyph U+23B7, font KaTeX_Size4-Regular. - span.innerHTML = "\n \n "; - } - - span.sizeMultiplier = sizeMultiplier; - - return span; - }; - - // There are three kinds of delimiters, delimiters that stack when they become - // too large - var stackLargeDelimiters = ["(", ")", "[", "\\lbrack", "]", "\\rbrack", "\\{", "\\lbrace", "\\}", "\\rbrace", "\\lfloor", "\\rfloor", "\\lceil", "\\rceil", "\\surd"]; - - // delimiters that always stack - var stackAlwaysDelimiters = ["\\uparrow", "\\downarrow", "\\updownarrow", "\\Uparrow", "\\Downarrow", "\\Updownarrow", "|", "\\|", "\\vert", "\\Vert", "\\lvert", "\\rvert", "\\lVert", "\\rVert", "\\lgroup", "\\rgroup", "\\lmoustache", "\\rmoustache"]; - - // and delimiters that never stack - var stackNeverDelimiters = ["<", ">", "\\langle", "\\rangle", "/", "\\backslash", "\\lt", "\\gt"]; - - // Metrics of the different sizes. Found by looking at TeX's output of - // $\bigl| // \Bigl| \biggl| \Biggl| \showlists$ - // Used to create stacked delimiters of appropriate sizes in makeSizedDelim. - var sizeToMaxHeight = [0, 1.2, 1.8, 2.4, 3.0]; - - /** - * Used to create a delimiter of a specific size, where `size` is 1, 2, 3, or 4. - */ - var makeSizedDelim = function makeSizedDelim(delim, size, options, mode, classes) { - // < and > turn into \langle and \rangle in delimiters - if (delim === "<" || delim === "\\lt") { - delim = "\\langle"; - } else if (delim === ">" || delim === "\\gt") { - delim = "\\rangle"; - } - - // Sized delimiters are never centered. - if (_utils2.default.contains(stackLargeDelimiters, delim) || _utils2.default.contains(stackNeverDelimiters, delim)) { - return makeLargeDelim(delim, size, false, options, mode, classes); - } else if (_utils2.default.contains(stackAlwaysDelimiters, delim)) { - return makeStackedDelim(delim, sizeToMaxHeight[size], false, options, mode, classes); - } else { - throw new _ParseError2.default("Illegal delimiter: '" + delim + "'"); - } - }; - - /** - * There are three different sequences of delimiter sizes that the delimiters - * follow depending on the kind of delimiter. This is used when creating custom - * sized delimiters to decide whether to create a small, large, or stacked - * delimiter. - * - * In real TeX, these sequences aren't explicitly defined, but are instead - * defined inside the font metrics. Since there are only three sequences that - * are possible for the delimiters that TeX defines, it is easier to just encode - * them explicitly here. - */ - - // Delimiters that never stack try small delimiters and large delimiters only - var stackNeverDelimiterSequence = [{ type: "small", style: _Style2.default.SCRIPTSCRIPT }, { type: "small", style: _Style2.default.SCRIPT }, { type: "small", style: _Style2.default.TEXT }, { type: "large", size: 1 }, { type: "large", size: 2 }, { type: "large", size: 3 }, { type: "large", size: 4 }]; - - // Delimiters that always stack try the small delimiters first, then stack - var stackAlwaysDelimiterSequence = [{ type: "small", style: _Style2.default.SCRIPTSCRIPT }, { type: "small", style: _Style2.default.SCRIPT }, { type: "small", style: _Style2.default.TEXT }, { type: "stack" }]; - - // Delimiters that stack when large try the small and then large delimiters, and - // stack afterwards - var stackLargeDelimiterSequence = [{ type: "small", style: _Style2.default.SCRIPTSCRIPT }, { type: "small", style: _Style2.default.SCRIPT }, { type: "small", style: _Style2.default.TEXT }, { type: "large", size: 1 }, { type: "large", size: 2 }, { type: "large", size: 3 }, { type: "large", size: 4 }, { type: "stack" }]; - - /** - * Get the font used in a delimiter based on what kind of delimiter it is. - */ - var delimTypeToFont = function delimTypeToFont(type) { - if (type.type === "small") { - return "Main-Regular"; - } else if (type.type === "large") { - return "Size" + type.size + "-Regular"; - } else if (type.type === "stack") { - return "Size4-Regular"; - } - }; - - /** - * Traverse a sequence of types of delimiters to decide what kind of delimiter - * should be used to create a delimiter of the given height+depth. - */ - var traverseSequence = function traverseSequence(delim, height, sequence, options) { - // Here, we choose the index we should start at in the sequences. In smaller - // sizes (which correspond to larger numbers in style.size) we start earlier - // in the sequence. Thus, scriptscript starts at index 3-3=0, script starts - // at index 3-2=1, text starts at 3-1=2, and display starts at min(2,3-0)=2 - var start = Math.min(2, 3 - options.style.size); - for (var i = start; i < sequence.length; i++) { - if (sequence[i].type === "stack") { - // This is always the last delimiter, so we just break the loop now. - break; - } - - var metrics = getMetrics(delim, delimTypeToFont(sequence[i])); - var heightDepth = metrics.height + metrics.depth; - - // Small delimiters are scaled down versions of the same font, so we - // account for the style change size. - - if (sequence[i].type === "small") { - var newOptions = options.havingBaseStyle(sequence[i].style); - heightDepth *= newOptions.sizeMultiplier; - } - - // Check if the delimiter at this size works for the given height. - if (heightDepth > height) { - return sequence[i]; - } - } - - // If we reached the end of the sequence, return the last sequence element. - return sequence[sequence.length - 1]; - }; - - /** - * Make a delimiter of a given height+depth, with optional centering. Here, we - * traverse the sequences, and create a delimiter that the sequence tells us to. - */ - var makeCustomSizedDelim = function makeCustomSizedDelim(delim, height, center, options, mode, classes) { - if (delim === "<" || delim === "\\lt") { - delim = "\\langle"; - } else if (delim === ">" || delim === "\\gt") { - delim = "\\rangle"; - } - - // Decide what sequence to use - var sequence = void 0; - if (_utils2.default.contains(stackNeverDelimiters, delim)) { - sequence = stackNeverDelimiterSequence; - } else if (_utils2.default.contains(stackLargeDelimiters, delim)) { - sequence = stackLargeDelimiterSequence; - } else { - sequence = stackAlwaysDelimiterSequence; - } - - // Look through the sequence - var delimType = traverseSequence(delim, height, sequence, options); - - if (delim === "\\surd") { - // Get an SVG image for - return sqrtSpan(height, delimType, options); - } else { - // Get the delimiter from font glyphs. - // Depending on the sequence element we decided on, call the - // appropriate function. - if (delimType.type === "small") { - return makeSmallDelim(delim, delimType.style, center, options, mode, classes); - } else if (delimType.type === "large") { - return makeLargeDelim(delim, delimType.size, center, options, mode, classes); - } else if (delimType.type === "stack") { - return makeStackedDelim(delim, height, center, options, mode, classes); - } - } - }; - - /** - * Make a delimiter for use with `\left` and `\right`, given a height and depth - * of an expression that the delimiters surround. - */ - var makeLeftRightDelim = function makeLeftRightDelim(delim, height, depth, options, mode, classes) { - // We always center \left/\right delimiters, so the axis is always shifted - var axisHeight = options.fontMetrics().axisHeight * options.sizeMultiplier; - - // Taken from TeX source, tex.web, function make_left_right - var delimiterFactor = 901; - var delimiterExtend = 5.0 / options.fontMetrics().ptPerEm; - - var maxDistFromAxis = Math.max(height - axisHeight, depth + axisHeight); - - var totalHeight = Math.max( - // In real TeX, calculations are done using integral values which are - // 65536 per pt, or 655360 per em. So, the division here truncates in - // TeX but doesn't here, producing different results. If we wanted to - // exactly match TeX's calculation, we could do - // Math.floor(655360 * maxDistFromAxis / 500) * - // delimiterFactor / 655360 - // (To see the difference, compare - // x^{x^{\left(\rule{0.1em}{0.68em}\right)}} - // in TeX and KaTeX) - maxDistFromAxis / 500 * delimiterFactor, 2 * maxDistFromAxis - delimiterExtend); - - // Finally, we defer to `makeCustomSizedDelim` with our calculated total - // height - return makeCustomSizedDelim(delim, totalHeight, true, options, mode, classes); - }; - - module.exports = { - sizedDelim: makeSizedDelim, - customSizedDelim: makeCustomSizedDelim, - leftRightDelim: makeLeftRightDelim - }; - - },{"./ParseError":29,"./Style":33,"./buildCommon":34,"./fontMetrics":41,"./symbols":48,"./utils":51}],39:[function(require,module,exports){ - - var _classCallCheck2 = require("babel-runtime/helpers/classCallCheck"); - - var _classCallCheck3 = _interopRequireDefault(_classCallCheck2); - - var _createClass2 = require("babel-runtime/helpers/createClass"); - - var _createClass3 = _interopRequireDefault(_createClass2); - - var _unicodeRegexes = require("./unicodeRegexes"); - - var _unicodeRegexes2 = _interopRequireDefault(_unicodeRegexes); - - var _utils = require("./utils"); - - var _utils2 = _interopRequireDefault(_utils); - - function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { default: obj }; } - - /** - * Create an HTML className based on a list of classes. In addition to joining - * with spaces, we also remove null or empty classes. - */ - /** - * These objects store the data about the DOM nodes we create, as well as some - * extra data. They can then be transformed into real DOM nodes with the - * `toNode` function or HTML markup using `toMarkup`. They are useful for both - * storing extra properties on the nodes, as well as providing a way to easily - * work with the DOM. - * - * Similar functions for working with MathML nodes exist in mathMLTree.js. - */ - var createClass = function createClass(classes) { - classes = classes.slice(); - for (var i = classes.length - 1; i >= 0; i--) { - if (!classes[i]) { - classes.splice(i, 1); - } - } - - return classes.join(" "); - }; - - /** - * This node represents a span node, with a className, a list of children, and - * an inline style. It also contains information about its height, depth, and - * maxFontSize. - */ - - var span = function () { - function span(classes, children, options) { - (0, _classCallCheck3.default)(this, span); - - this.classes = classes || []; - this.children = children || []; - this.height = 0; - this.depth = 0; - this.maxFontSize = 0; - this.style = {}; - this.attributes = {}; - this.innerHTML; // used for inline SVG code. - if (options) { - if (options.style.isTight()) { - this.classes.push("mtight"); - } - if (options.getColor()) { - this.style.color = options.getColor(); - } - } - } - - /** - * Sets an arbitrary attribute on the span. Warning: use this wisely. Not all - * browsers support attributes the same, and having too many custom attributes - * is probably bad. - */ - - - (0, _createClass3.default)(span, [{ - key: "setAttribute", - value: function setAttribute(attribute, value) { - this.attributes[attribute] = value; - } - }, { - key: "tryCombine", - value: function tryCombine(sibling) { - return false; - } - - /** - * Convert the span into an HTML node - */ - - }, { - key: "toNode", - value: function toNode() { - var span = document.createElement("span"); - - // Apply the class - span.className = createClass(this.classes); - - // Apply inline styles - for (var style in this.style) { - if (Object.prototype.hasOwnProperty.call(this.style, style)) { - span.style[style] = this.style[style]; - } - } - - // Apply attributes - for (var attr in this.attributes) { - if (Object.prototype.hasOwnProperty.call(this.attributes, attr)) { - span.setAttribute(attr, this.attributes[attr]); - } - } - - if (this.innerHTML) { - span.innerHTML = this.innerHTML; - } - - // Append the children, also as HTML nodes - for (var i = 0; i < this.children.length; i++) { - span.appendChild(this.children[i].toNode()); - } - - return span; - } - - /** - * Convert the span into an HTML markup string - */ - - }, { - key: "toMarkup", - value: function toMarkup() { - var markup = " 0 || createClass(this.classes) !== createClass(sibling.classes) || this.skew !== sibling.skew || this.maxFontSize !== sibling.maxFontSize) { - return false; - } - for (var style in this.style) { - if (this.style.hasOwnProperty(style) && this.style[style] !== sibling.style[style]) { - return false; - } - } - for (var _style in sibling.style) { - if (sibling.style.hasOwnProperty(_style) && this.style[_style] !== sibling.style[_style]) { - return false; - } - } - this.value += sibling.value; - this.height = Math.max(this.height, sibling.height); - this.depth = Math.max(this.depth, sibling.depth); - this.italic = sibling.italic; - return true; - } - - /** - * Creates a text node or span from a symbol node. Note that a span is only - * created if it is needed. - */ - - }, { - key: "toNode", - value: function toNode() { - var node = document.createTextNode(this.value); - var span = null; - - if (this.italic > 0) { - span = document.createElement("span"); - span.style.marginRight = this.italic + "em"; - } - - if (this.classes.length > 0) { - span = span || document.createElement("span"); - span.className = createClass(this.classes); - } - - for (var style in this.style) { - if (this.style.hasOwnProperty(style)) { - span = span || document.createElement("span"); - span.style[style] = this.style[style]; - } - } - - if (span) { - span.appendChild(node); - return span; - } else { - return node; - } - } - - /** - * Creates markup for a symbol node. - */ - - }, { - key: "toMarkup", - value: function toMarkup() { - // TODO(alpert): More duplication than I'd like from - // span.prototype.toMarkup and symbolNode.prototype.toNode... - var needsSpan = false; - - var markup = " 0) { - styles += "margin-right:" + this.italic + "em;"; - } - for (var style in this.style) { - if (this.style.hasOwnProperty(style)) { - styles += _utils2.default.hyphenate(style) + ":" + this.style[style] + ";"; - } - } - - if (styles) { - needsSpan = true; - markup += " style=\"" + _utils2.default.escape(styles) + "\""; - } - - var escaped = _utils2.default.escape(this.value); - if (needsSpan) { - markup += ">"; - markup += escaped; - markup += "      "; - return markup; - } else { - return escaped; - } - } - }]); - return symbolNode; - }(); - - module.exports = { - span: span, - documentFragment: documentFragment, - symbolNode: symbolNode - }; - - },{"./unicodeRegexes":49,"./utils":51,"babel-runtime/helpers/classCallCheck":4,"babel-runtime/helpers/createClass":5}],40:[function(require,module,exports){ - - var _ParseNode = require("./ParseNode"); - - var _ParseNode2 = _interopRequireDefault(_ParseNode); - - var _ParseError = require("./ParseError"); - - var _ParseError2 = _interopRequireDefault(_ParseError); - - function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { default: obj }; } - - /** - * Parse the body of the environment, with rows delimited by \\ and - * columns delimited by &, and create a nested list in row-major order - * with one group per cell. If given an optional argument style - * ("text", "display", etc.), then each cell is cast into that style. - */ - /* eslint no-constant-condition:0 */ - function parseArray(parser, result, style) { - var row = []; - var body = [row]; - var rowGaps = []; - while (true) { - var cell = parser.parseExpression(false, null); - cell = new _ParseNode2.default("ordgroup", cell, parser.mode); - if (style) { - cell = new _ParseNode2.default("styling", { - style: style, - value: [cell] - }, parser.mode); - } - row.push(cell); - var next = parser.nextToken.text; - if (next === "&") { - parser.consume(); - } else if (next === "\\end") { - break; - } else if (next === "\\\\" || next === "\\cr") { - var cr = parser.parseFunction(); - rowGaps.push(cr.value.size); - row = []; - body.push(row); - } else { - throw new _ParseError2.default("Expected & or \\\\ or \\end", parser.nextToken); - } - } - result.body = body; - result.rowGaps = rowGaps; - return new _ParseNode2.default(result.type, result, parser.mode); - } - - /* - * An environment definition is very similar to a function definition: - * it is declared with a name or a list of names, a set of properties - * and a handler containing the actual implementation. - * - * The properties include: - * - numArgs: The number of arguments after the \begin{name} function. - * - argTypes: (optional) Just like for a function - * - allowedInText: (optional) Whether or not the environment is allowed inside - * text mode (default false) (not enforced yet) - * - numOptionalArgs: (optional) Just like for a function - * A bare number instead of that object indicates the numArgs value. - * - * The handler function will receive two arguments - * - context: information and references provided by the parser - * - args: an array of arguments passed to \begin{name} - * The context contains the following properties: - * - envName: the name of the environment, one of the listed names. - * - parser: the parser object - * - lexer: the lexer object - * - positions: the positions associated with these arguments from args. - * The handler must return a ParseResult. - */ - function defineEnvironment(names, props, handler) { - if (typeof names === "string") { - names = [names]; - } - if (typeof props === "number") { - props = { numArgs: props }; - } - // Set default values of environments - var data = { - numArgs: props.numArgs || 0, - argTypes: props.argTypes, - greediness: 1, - allowedInText: !!props.allowedInText, - numOptionalArgs: props.numOptionalArgs || 0, - handler: handler - }; - for (var i = 0; i < names.length; ++i) { - module.exports[names[i]] = data; - } - } - - // Decides on a style for cells in an array according to whether the given - // environment name starts with the letter 'd'. - function dCellStyle(envName) { - if (envName.substr(0, 1) === "d") { - return "display"; - } else { - return "text"; - } - } - - // Arrays are part of LaTeX, defined in lttab.dtx so its documentation - // is part of the source2e.pdf file of LaTeX2e source documentation. - // {darray} is an {array} environment where cells are set in \displaystyle, - // as defined in nccmath.sty. - defineEnvironment(["array", "darray"], { - numArgs: 1 - }, function (context, args) { - var colalign = args[0]; - colalign = colalign.value.map ? colalign.value : [colalign]; - var cols = colalign.map(function (node) { - var ca = node.value; - if ("lcr".indexOf(ca) !== -1) { - return { - type: "align", - align: ca - }; - } else if (ca === "|") { - return { - type: "separator", - separator: "|" - }; - } - throw new _ParseError2.default("Unknown column alignment: " + node.value, node); - }); - var res = { - type: "array", - cols: cols, - hskipBeforeAndAfter: true }; - res = parseArray(context.parser, res, dCellStyle(context.envName)); - return res; - }); - - // The matrix environments of amsmath builds on the array environment - // of LaTeX, which is discussed above. - defineEnvironment(["matrix", "pmatrix", "bmatrix", "Bmatrix", "vmatrix", "Vmatrix"], {}, function (context) { - var delimiters = { - "matrix": null, - "pmatrix": ["(", ")"], - "bmatrix": ["[", "]"], - "Bmatrix": ["\\{", "\\}"], - "vmatrix": ["|", "|"], - "Vmatrix": ["\\Vert", "\\Vert"] - }[context.envName]; - var res = { - type: "array", - hskipBeforeAndAfter: false }; - res = parseArray(context.parser, res, dCellStyle(context.envName)); - if (delimiters) { - res = new _ParseNode2.default("leftright", { - body: [res], - left: delimiters[0], - right: delimiters[1] - }, context.mode); - } - return res; - }); - - // A cases environment (in amsmath.sty) is almost equivalent to - // \def\arraystretch{1.2}% - // \left\{\begin{array}{@{}l@{\quad}l@{}} … \end{array}\right. - // {dcases} is a {cases} environment where cells are set in \displaystyle, - // as defined in mathtools.sty. - defineEnvironment(["cases", "dcases"], {}, function (context) { - var res = { - type: "array", - arraystretch: 1.2, - cols: [{ - type: "align", - align: "l", - pregap: 0, - // TODO(kevinb) get the current style. - // For now we use the metrics for TEXT style which is what we were - // doing before. Before attempting to get the current style we - // should look at TeX's behavior especially for \over and matrices. - postgap: 1.0 }, { - type: "align", - align: "l", - pregap: 0, - postgap: 0 - }] - }; - res = parseArray(context.parser, res, dCellStyle(context.envName)); - res = new _ParseNode2.default("leftright", { - body: [res], - left: "\\{", - right: "." - }, context.mode); - return res; - }); - - // An aligned environment is like the align* environment - // except it operates within math mode. - // Note that we assume \nomallineskiplimit to be zero, - // so that \strut@ is the same as \strut. - defineEnvironment("aligned", {}, function (context) { - var res = { - type: "array", - cols: [], - addJot: true - }; - res = parseArray(context.parser, res, "display"); - // Count number of columns = maximum number of cells in each row. - // At the same time, prepend empty group {} at beginning of every second - // cell in each row (starting with second cell) so that operators become - // binary. This behavior is implemented in amsmath's \start@aligned. - var emptyGroup = new _ParseNode2.default("ordgroup", [], context.mode); - var numCols = 0; - res.value.body.forEach(function (row) { - for (var i = 1; i < row.length; i += 2) { - // Modify ordgroup node within styling node - var ordgroup = row[i].value.value[0]; - ordgroup.value.unshift(emptyGroup); - } - if (numCols < row.length) { - numCols = row.length; - } - }); - for (var i = 0; i < numCols; ++i) { - var align = "r"; - var pregap = 0; - if (i % 2 === 1) { - align = "l"; - } else if (i > 0) { - pregap = 2; // one \qquad between columns - } - res.value.cols[i] = { - type: "align", - align: align, - pregap: pregap, - postgap: 0 - }; - } - return res; - }); - - // A gathered environment is like an array environment with one centered - // column, but where rows are considered lines so get \jot line spacing - // and contents are set in \displaystyle. - defineEnvironment("gathered", {}, function (context) { - var res = { - type: "array", - cols: [{ - type: "align", - align: "c" - }], - addJot: true - }; - res = parseArray(context.parser, res, "display"); - return res; - }); - - },{"./ParseError":29,"./ParseNode":30}],41:[function(require,module,exports){ - - var _unicodeRegexes = require("./unicodeRegexes"); - - var _fontMetricsData = require("./fontMetricsData"); - - var _fontMetricsData2 = _interopRequireDefault(_fontMetricsData); - - function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { default: obj }; } - - /** - * This file contains metrics regarding fonts and individual symbols. The sigma - * and xi variables, as well as the metricMap map contain data extracted from - * TeX, TeX font metrics, and the TTF files. These data are then exposed via the - * `metrics` variable and the getCharacterMetrics function. - */ - - // In TeX, there are actually three sets of dimensions, one for each of - // textstyle (size index 5 and higher: >=9pt), scriptstyle (size index 3 and 4: - // 7-8pt), and scriptscriptstyle (size index 1 and 2: 5-6pt). These are - // provided in the the arrays below, in that order. - // - // The font metrics are stored in fonts cmsy10, cmsy7, and cmsy5 respsectively. - // This was determined by running the following script: - // - // latex -interaction=nonstopmode \ - // '\documentclass{article}\usepackage{amsmath}\begin{document}' \ - // '$a$ \expandafter\show\the\textfont2' \ - // '\expandafter\show\the\scriptfont2' \ - // '\expandafter\show\the\scriptscriptfont2' \ - // '\stop' - // - // The metrics themselves were retreived using the following commands: - // - // tftopl cmsy10 - // tftopl cmsy7 - // tftopl cmsy5 - // - // The output of each of these commands is quite lengthy. The only part we - // care about is the FONTDIMEN section. Each value is measured in EMs. - var sigmasAndXis = { - slant: [0.250, 0.250, 0.250], // sigma1 - space: [0.000, 0.000, 0.000], // sigma2 - stretch: [0.000, 0.000, 0.000], // sigma3 - shrink: [0.000, 0.000, 0.000], // sigma4 - xHeight: [0.431, 0.431, 0.431], // sigma5 - quad: [1.000, 1.171, 1.472], // sigma6 - extraSpace: [0.000, 0.000, 0.000], // sigma7 - num1: [0.677, 0.732, 0.925], // sigma8 - num2: [0.394, 0.384, 0.387], // sigma9 - num3: [0.444, 0.471, 0.504], // sigma10 - denom1: [0.686, 0.752, 1.025], // sigma11 - denom2: [0.345, 0.344, 0.532], // sigma12 - sup1: [0.413, 0.503, 0.504], // sigma13 - sup2: [0.363, 0.431, 0.404], // sigma14 - sup3: [0.289, 0.286, 0.294], // sigma15 - sub1: [0.150, 0.143, 0.200], // sigma16 - sub2: [0.247, 0.286, 0.400], // sigma17 - supDrop: [0.386, 0.353, 0.494], // sigma18 - subDrop: [0.050, 0.071, 0.100], // sigma19 - delim1: [2.390, 1.700, 1.980], // sigma20 - delim2: [1.010, 1.157, 1.420], // sigma21 - axisHeight: [0.250, 0.250, 0.250], // sigma22 - - // These font metrics are extracted from TeX by using tftopl on cmex10.tfm; - // they correspond to the font parameters of the extension fonts (family 3). - // See the TeXbook, page 441. In AMSTeX, the extension fonts scale; to - // match cmex7, we'd use cmex7.tfm values for script and scriptscript - // values. - defaultRuleThickness: [0.04, 0.049, 0.049], // xi8; cmex7: 0.049 - bigOpSpacing1: [0.111, 0.111, 0.111], // xi9 - bigOpSpacing2: [0.166, 0.166, 0.166], // xi10 - bigOpSpacing3: [0.2, 0.2, 0.2], // xi11 - bigOpSpacing4: [0.6, 0.611, 0.611], // xi12; cmex7: 0.611 - bigOpSpacing5: [0.1, 0.143, 0.143], // xi13; cmex7: 0.143 - - // The \sqrt rule width is taken from the height of the surd character. - // Since we use the same font at all sizes, this thickness doesn't scale. - sqrtRuleThickness: [0.04, 0.04, 0.04], - - // This value determines how large a pt is, for metrics which are defined - // in terms of pts. - // This value is also used in katex.less; if you change it make sure the - // values match. - ptPerEm: [10.0, 10.0, 10.0], - - // The space between adjacent `|` columns in an array definition. From - // `\showthe\doublerulesep` in LaTeX. Equals 2.0 / ptPerEm. - doubleRuleSep: [0.2, 0.2, 0.2] - }; - - // This map contains a mapping from font name and character code to character - // metrics, including height, depth, italic correction, and skew (kern from the - // character to the corresponding \skewchar) - // This map is generated via `make metrics`. It should not be changed manually. - - - // These are very rough approximations. We default to Times New Roman which - // should have Latin-1 and Cyrillic characters, but may not depending on the - // operating system. The metrics do not account for extra height from the - // accents. In the case of Cyrillic characters which have both ascenders and - // descenders we prefer approximations with ascenders, primarily to prevent - // the fraction bar or root line from intersecting the glyph. - // TODO(kevinb) allow union of multiple glyph metrics for better accuracy. - var extraCharacterMap = { - // Latin-1 - 'À': 'A', - 'Á': 'A', - 'Â': 'A', - 'Ã': 'A', - 'Ä': 'A', - 'Å': 'A', - 'Æ': 'A', - 'Ç': 'C', - 'È': 'E', - 'É': 'E', - 'Ê': 'E', - 'Ë': 'E', - 'Ì': 'I', - 'Í': 'I', - 'Î': 'I', - 'Ï': 'I', - 'Ð': 'D', - 'Ñ': 'N', - 'Ò': 'O', - 'Ó': 'O', - 'Ô': 'O', - 'Õ': 'O', - 'Ö': 'O', - 'Ø': 'O', - 'Ù': 'U', - 'Ú': 'U', - 'Û': 'U', - 'Ü': 'U', - 'Ý': 'Y', - 'Þ': 'o', - 'ß': 'B', - 'à': 'a', - 'á': 'a', - 'â': 'a', - 'ã': 'a', - 'ä': 'a', - 'å': 'a', - 'æ': 'a', - 'ç': 'c', - 'è': 'e', - 'é': 'e', - 'ê': 'e', - 'ë': 'e', - 'ì': 'i', - 'í': 'i', - 'î': 'i', - 'ï': 'i', - 'ð': 'd', - 'ñ': 'n', - 'ò': 'o', - 'ó': 'o', - 'ô': 'o', - 'õ': 'o', - 'ö': 'o', - 'ø': 'o', - 'ù': 'u', - 'ú': 'u', - 'û': 'u', - 'ü': 'u', - 'ý': 'y', - 'þ': 'o', - 'ÿ': 'y', - - // Cyrillic - 'А': 'A', - 'Б': 'B', - 'В': 'B', - 'Г': 'F', - 'Д': 'A', - 'Е': 'E', - 'Ж': 'K', - 'З': '3', - 'И': 'N', - 'Й': 'N', - 'К': 'K', - 'Л': 'N', - 'М': 'M', - 'Н': 'H', - 'О': 'O', - 'П': 'N', - 'Р': 'P', - 'С': 'C', - 'Т': 'T', - 'У': 'y', - 'Ф': 'O', - 'Х': 'X', - 'Ц': 'U', - 'Ч': 'h', - 'Ш': 'W', - 'Щ': 'W', - 'Ъ': 'B', - 'Ы': 'X', - 'Ь': 'B', - 'Э': '3', - 'Ю': 'X', - 'Я': 'R', - 'а': 'a', - 'б': 'b', - 'в': 'a', - 'г': 'r', - 'д': 'y', - 'е': 'e', - 'ж': 'm', - 'з': 'e', - 'и': 'n', - 'й': 'n', - 'к': 'n', - 'л': 'n', - 'м': 'm', - 'н': 'n', - 'о': 'o', - 'п': 'n', - 'р': 'p', - 'с': 'c', - 'т': 'o', - 'у': 'y', - 'ф': 'b', - 'х': 'x', - 'ц': 'n', - 'ч': 'n', - 'ш': 'w', - 'щ': 'w', - 'ъ': 'a', - 'ы': 'm', - 'ь': 'a', - 'э': 'e', - 'ю': 'm', - 'я': 'r' - }; - - /** - * This function is a convenience function for looking up information in the - * metricMap table. It takes a character as a string, and a style. - * - * Note: the `width` property may be undefined if fontMetricsData.js wasn't - * built using `Make extended_metrics`. - */ - var getCharacterMetrics = function getCharacterMetrics(character, style) { - var ch = character.charCodeAt(0); - if (character[0] in extraCharacterMap) { - ch = extraCharacterMap[character[0]].charCodeAt(0); - } else if (_unicodeRegexes.cjkRegex.test(character[0])) { - ch = 'M'.charCodeAt(0); - } - var metrics = _fontMetricsData2.default[style][ch]; - if (metrics) { - return { - depth: metrics[0], - height: metrics[1], - italic: metrics[2], - skew: metrics[3], - width: metrics[4] - }; - } - }; - - var fontMetricsBySizeIndex = {}; - - /** - * Get the font metrics for a given size. - */ - var getFontMetrics = function getFontMetrics(size) { - var sizeIndex = void 0; - if (size >= 5) { - sizeIndex = 0; - } else if (size >= 3) { - sizeIndex = 1; - } else { - sizeIndex = 2; - } - if (!fontMetricsBySizeIndex[sizeIndex]) { - var metrics = fontMetricsBySizeIndex[sizeIndex] = {}; - for (var key in sigmasAndXis) { - if (sigmasAndXis.hasOwnProperty(key)) { - metrics[key] = sigmasAndXis[key][sizeIndex]; - } - } - metrics.cssEmPerMu = metrics.quad / 18; - } - return fontMetricsBySizeIndex[sizeIndex]; - }; - - module.exports = { - getFontMetrics: getFontMetrics, - getCharacterMetrics: getCharacterMetrics - }; - - },{"./fontMetricsData":42,"./unicodeRegexes":49}],42:[function(require,module,exports){ - - module.exports = { - "AMS-Regular": { - "65": [0, 0.68889, 0, 0], - "66": [0, 0.68889, 0, 0], - "67": [0, 0.68889, 0, 0], - "68": [0, 0.68889, 0, 0], - "69": [0, 0.68889, 0, 0], - "70": [0, 0.68889, 0, 0], - "71": [0, 0.68889, 0, 0], - "72": [0, 0.68889, 0, 0], - "73": [0, 0.68889, 0, 0], - "74": [0.16667, 0.68889, 0, 0], - "75": [0, 0.68889, 0, 0], - "76": [0, 0.68889, 0, 0], - "77": [0, 0.68889, 0, 0], - "78": [0, 0.68889, 0, 0], - "79": [0.16667, 0.68889, 0, 0], - "80": [0, 0.68889, 0, 0], - "81": [0.16667, 0.68889, 0, 0], - "82": [0, 0.68889, 0, 0], - "83": [0, 0.68889, 0, 0], - "84": [0, 0.68889, 0, 0], - "85": [0, 0.68889, 0, 0], - "86": [0, 0.68889, 0, 0], - "87": [0, 0.68889, 0, 0], - "88": [0, 0.68889, 0, 0], - "89": [0, 0.68889, 0, 0], - "90": [0, 0.68889, 0, 0], - "107": [0, 0.68889, 0, 0], - "165": [0, 0.675, 0.025, 0], - "174": [0.15559, 0.69224, 0, 0], - "240": [0, 0.68889, 0, 0], - "295": [0, 0.68889, 0, 0], - "710": [0, 0.825, 0, 0], - "732": [0, 0.9, 0, 0], - "770": [0, 0.825, 0, 0], - "771": [0, 0.9, 0, 0], - "989": [0.08167, 0.58167, 0, 0], - "1008": [0, 0.43056, 0.04028, 0], - "8245": [0, 0.54986, 0, 0], - "8463": [0, 0.68889, 0, 0], - "8487": [0, 0.68889, 0, 0], - "8498": [0, 0.68889, 0, 0], - "8502": [0, 0.68889, 0, 0], - "8503": [0, 0.68889, 0, 0], - "8504": [0, 0.68889, 0, 0], - "8513": [0, 0.68889, 0, 0], - "8592": [-0.03598, 0.46402, 0, 0], - "8594": [-0.03598, 0.46402, 0, 0], - "8602": [-0.13313, 0.36687, 0, 0], - "8603": [-0.13313, 0.36687, 0, 0], - "8606": [0.01354, 0.52239, 0, 0], - "8608": [0.01354, 0.52239, 0, 0], - "8610": [0.01354, 0.52239, 0, 0], - "8611": [0.01354, 0.52239, 0, 0], - "8619": [0, 0.54986, 0, 0], - "8620": [0, 0.54986, 0, 0], - "8621": [-0.13313, 0.37788, 0, 0], - "8622": [-0.13313, 0.36687, 0, 0], - "8624": [0, 0.69224, 0, 0], - "8625": [0, 0.69224, 0, 0], - "8630": [0, 0.43056, 0, 0], - "8631": [0, 0.43056, 0, 0], - "8634": [0.08198, 0.58198, 0, 0], - "8635": [0.08198, 0.58198, 0, 0], - "8638": [0.19444, 0.69224, 0, 0], - "8639": [0.19444, 0.69224, 0, 0], - "8642": [0.19444, 0.69224, 0, 0], - "8643": [0.19444, 0.69224, 0, 0], - "8644": [0.1808, 0.675, 0, 0], - "8646": [0.1808, 0.675, 0, 0], - "8647": [0.1808, 0.675, 0, 0], - "8648": [0.19444, 0.69224, 0, 0], - "8649": [0.1808, 0.675, 0, 0], - "8650": [0.19444, 0.69224, 0, 0], - "8651": [0.01354, 0.52239, 0, 0], - "8652": [0.01354, 0.52239, 0, 0], - "8653": [-0.13313, 0.36687, 0, 0], - "8654": [-0.13313, 0.36687, 0, 0], - "8655": [-0.13313, 0.36687, 0, 0], - "8666": [0.13667, 0.63667, 0, 0], - "8667": [0.13667, 0.63667, 0, 0], - "8669": [-0.13313, 0.37788, 0, 0], - "8672": [-0.064, 0.437, 0, 0], - "8674": [-0.064, 0.437, 0, 0], - "8705": [0, 0.825, 0, 0], - "8708": [0, 0.68889, 0, 0], - "8709": [0.08167, 0.58167, 0, 0], - "8717": [0, 0.43056, 0, 0], - "8722": [-0.03598, 0.46402, 0, 0], - "8724": [0.08198, 0.69224, 0, 0], - "8726": [0.08167, 0.58167, 0, 0], - "8733": [0, 0.69224, 0, 0], - "8736": [0, 0.69224, 0, 0], - "8737": [0, 0.69224, 0, 0], - "8738": [0.03517, 0.52239, 0, 0], - "8739": [0.08167, 0.58167, 0, 0], - "8740": [0.25142, 0.74111, 0, 0], - "8741": [0.08167, 0.58167, 0, 0], - "8742": [0.25142, 0.74111, 0, 0], - "8756": [0, 0.69224, 0, 0], - "8757": [0, 0.69224, 0, 0], - "8764": [-0.13313, 0.36687, 0, 0], - "8765": [-0.13313, 0.37788, 0, 0], - "8769": [-0.13313, 0.36687, 0, 0], - "8770": [-0.03625, 0.46375, 0, 0], - "8774": [0.30274, 0.79383, 0, 0], - "8776": [-0.01688, 0.48312, 0, 0], - "8778": [0.08167, 0.58167, 0, 0], - "8782": [0.06062, 0.54986, 0, 0], - "8783": [0.06062, 0.54986, 0, 0], - "8785": [0.08198, 0.58198, 0, 0], - "8786": [0.08198, 0.58198, 0, 0], - "8787": [0.08198, 0.58198, 0, 0], - "8790": [0, 0.69224, 0, 0], - "8791": [0.22958, 0.72958, 0, 0], - "8796": [0.08198, 0.91667, 0, 0], - "8806": [0.25583, 0.75583, 0, 0], - "8807": [0.25583, 0.75583, 0, 0], - "8808": [0.25142, 0.75726, 0, 0], - "8809": [0.25142, 0.75726, 0, 0], - "8812": [0.25583, 0.75583, 0, 0], - "8814": [0.20576, 0.70576, 0, 0], - "8815": [0.20576, 0.70576, 0, 0], - "8816": [0.30274, 0.79383, 0, 0], - "8817": [0.30274, 0.79383, 0, 0], - "8818": [0.22958, 0.72958, 0, 0], - "8819": [0.22958, 0.72958, 0, 0], - "8822": [0.1808, 0.675, 0, 0], - "8823": [0.1808, 0.675, 0, 0], - "8828": [0.13667, 0.63667, 0, 0], - "8829": [0.13667, 0.63667, 0, 0], - "8830": [0.22958, 0.72958, 0, 0], - "8831": [0.22958, 0.72958, 0, 0], - "8832": [0.20576, 0.70576, 0, 0], - "8833": [0.20576, 0.70576, 0, 0], - "8840": [0.30274, 0.79383, 0, 0], - "8841": [0.30274, 0.79383, 0, 0], - "8842": [0.13597, 0.63597, 0, 0], - "8843": [0.13597, 0.63597, 0, 0], - "8847": [0.03517, 0.54986, 0, 0], - "8848": [0.03517, 0.54986, 0, 0], - "8858": [0.08198, 0.58198, 0, 0], - "8859": [0.08198, 0.58198, 0, 0], - "8861": [0.08198, 0.58198, 0, 0], - "8862": [0, 0.675, 0, 0], - "8863": [0, 0.675, 0, 0], - "8864": [0, 0.675, 0, 0], - "8865": [0, 0.675, 0, 0], - "8872": [0, 0.69224, 0, 0], - "8873": [0, 0.69224, 0, 0], - "8874": [0, 0.69224, 0, 0], - "8876": [0, 0.68889, 0, 0], - "8877": [0, 0.68889, 0, 0], - "8878": [0, 0.68889, 0, 0], - "8879": [0, 0.68889, 0, 0], - "8882": [0.03517, 0.54986, 0, 0], - "8883": [0.03517, 0.54986, 0, 0], - "8884": [0.13667, 0.63667, 0, 0], - "8885": [0.13667, 0.63667, 0, 0], - "8888": [0, 0.54986, 0, 0], - "8890": [0.19444, 0.43056, 0, 0], - "8891": [0.19444, 0.69224, 0, 0], - "8892": [0.19444, 0.69224, 0, 0], - "8901": [0, 0.54986, 0, 0], - "8903": [0.08167, 0.58167, 0, 0], - "8905": [0.08167, 0.58167, 0, 0], - "8906": [0.08167, 0.58167, 0, 0], - "8907": [0, 0.69224, 0, 0], - "8908": [0, 0.69224, 0, 0], - "8909": [-0.03598, 0.46402, 0, 0], - "8910": [0, 0.54986, 0, 0], - "8911": [0, 0.54986, 0, 0], - "8912": [0.03517, 0.54986, 0, 0], - "8913": [0.03517, 0.54986, 0, 0], - "8914": [0, 0.54986, 0, 0], - "8915": [0, 0.54986, 0, 0], - "8916": [0, 0.69224, 0, 0], - "8918": [0.0391, 0.5391, 0, 0], - "8919": [0.0391, 0.5391, 0, 0], - "8920": [0.03517, 0.54986, 0, 0], - "8921": [0.03517, 0.54986, 0, 0], - "8922": [0.38569, 0.88569, 0, 0], - "8923": [0.38569, 0.88569, 0, 0], - "8926": [0.13667, 0.63667, 0, 0], - "8927": [0.13667, 0.63667, 0, 0], - "8928": [0.30274, 0.79383, 0, 0], - "8929": [0.30274, 0.79383, 0, 0], - "8934": [0.23222, 0.74111, 0, 0], - "8935": [0.23222, 0.74111, 0, 0], - "8936": [0.23222, 0.74111, 0, 0], - "8937": [0.23222, 0.74111, 0, 0], - "8938": [0.20576, 0.70576, 0, 0], - "8939": [0.20576, 0.70576, 0, 0], - "8940": [0.30274, 0.79383, 0, 0], - "8941": [0.30274, 0.79383, 0, 0], - "8994": [0.19444, 0.69224, 0, 0], - "8995": [0.19444, 0.69224, 0, 0], - "9416": [0.15559, 0.69224, 0, 0], - "9484": [0, 0.69224, 0, 0], - "9488": [0, 0.69224, 0, 0], - "9492": [0, 0.37788, 0, 0], - "9496": [0, 0.37788, 0, 0], - "9585": [0.19444, 0.68889, 0, 0], - "9586": [0.19444, 0.74111, 0, 0], - "9632": [0, 0.675, 0, 0], - "9633": [0, 0.675, 0, 0], - "9650": [0, 0.54986, 0, 0], - "9651": [0, 0.54986, 0, 0], - "9654": [0.03517, 0.54986, 0, 0], - "9660": [0, 0.54986, 0, 0], - "9661": [0, 0.54986, 0, 0], - "9664": [0.03517, 0.54986, 0, 0], - "9674": [0.11111, 0.69224, 0, 0], - "9733": [0.19444, 0.69224, 0, 0], - "10003": [0, 0.69224, 0, 0], - "10016": [0, 0.69224, 0, 0], - "10731": [0.11111, 0.69224, 0, 0], - "10846": [0.19444, 0.75583, 0, 0], - "10877": [0.13667, 0.63667, 0, 0], - "10878": [0.13667, 0.63667, 0, 0], - "10885": [0.25583, 0.75583, 0, 0], - "10886": [0.25583, 0.75583, 0, 0], - "10887": [0.13597, 0.63597, 0, 0], - "10888": [0.13597, 0.63597, 0, 0], - "10889": [0.26167, 0.75726, 0, 0], - "10890": [0.26167, 0.75726, 0, 0], - "10891": [0.48256, 0.98256, 0, 0], - "10892": [0.48256, 0.98256, 0, 0], - "10901": [0.13667, 0.63667, 0, 0], - 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- /* This file contains a list of functions that we parse, identified by - * the calls to defineFunction. - * - * The first argument to defineFunction is a single name or a list of names. - * All functions named in such a list will share a single implementation. - * - * Each declared function can have associated properties, which - * include the following: - * - * - numArgs: The number of arguments the function takes. - * If this is the only property, it can be passed as a number - * instead of an element of a properties object. - * - argTypes: (optional) An array corresponding to each argument of the - * function, giving the type of argument that should be parsed. Its - * length should be equal to `numArgs + numOptionalArgs`. Valid - * types: - * - "size": A size-like thing, such as "1em" or "5ex" - * - "color": An html color, like "#abc" or "blue" - * - "original": The same type as the environment that the - * function being parsed is in (e.g. used for the - * bodies of functions like \textcolor where the - * first argument is special and the second - * argument is parsed normally) - * Other possible types (probably shouldn't be used) - * - "text": Text-like (e.g. \text) - * - "math": Normal math - * If undefined, this will be treated as an appropriate length - * array of "original" strings - * - greediness: (optional) The greediness of the function to use ungrouped - * arguments. - * - * E.g. if you have an expression - * \sqrt \frac 1 2 - * since \frac has greediness=2 vs \sqrt's greediness=1, \frac - * will use the two arguments '1' and '2' as its two arguments, - * then that whole function will be used as the argument to - * \sqrt. On the other hand, the expressions - * \frac \frac 1 2 3 - * and - * \frac \sqrt 1 2 - * will fail because \frac and \frac have equal greediness - * and \sqrt has a lower greediness than \frac respectively. To - * make these parse, we would have to change them to: - * \frac {\frac 1 2} 3 - * and - * \frac {\sqrt 1} 2 - * - * The default value is `1` - * - allowedInText: (optional) Whether or not the function is allowed inside - * text mode (default false) - * - numOptionalArgs: (optional) The number of optional arguments the function - * should parse. If the optional arguments aren't found, - * `null` will be passed to the handler in their place. - * (default 0) - * - infix: (optional) Must be true if the function is an infix operator. - * - * The last argument is that implementation, the handler for the function(s). - * It is called to handle these functions and their arguments. - * It receives two arguments: - * - context contains information and references provided by the parser - * - args is an array of arguments obtained from TeX input - * The context contains the following properties: - * - funcName: the text (i.e. name) of the function, including \ - * - parser: the parser object - * - lexer: the lexer object - * - positions: the positions in the overall string of the function - * and the arguments. - * The latter three should only be used to produce error messages. - * - * The function should return an object with the following keys: - * - type: The type of element that this is. This is then used in - * buildHTML/buildMathML to determine which function - * should be called to build this node into a DOM node - * Any other data can be added to the object, which will be passed - * in to the function in buildHTML/buildMathML as `group.value`. - */ - - function defineFunction(names, props, handler) { - if (typeof names === "string") { - names = [names]; - } - if (typeof props === "number") { - props = { numArgs: props }; - } - // Set default values of functions - var data = { - numArgs: props.numArgs, - argTypes: props.argTypes, - greediness: props.greediness === undefined ? 1 : props.greediness, - allowedInText: !!props.allowedInText, - allowedInMath: props.allowedInMath, - numOptionalArgs: props.numOptionalArgs || 0, - infix: !!props.infix, - handler: handler - }; - for (var i = 0; i < names.length; ++i) { - module.exports[names[i]] = data; - } - } - - // Since the corresponding buildHTML/buildMathML function expects a - // list of elements, we normalize for different kinds of arguments - var ordargument = function ordargument(arg) { - if (arg.type === "ordgroup") { - return arg.value; - } else { - return [arg]; - } - }; - - // A normal square root - defineFunction("\\sqrt", { - numArgs: 1, - numOptionalArgs: 1 - }, function (context, args) { - var index = args[0]; - var body = args[1]; - return { - type: "sqrt", - body: body, - index: index - }; - }); - - // Non-mathy text, possibly in a font - var textFunctionStyles = { - "\\text": undefined, "\\textrm": "mathrm", "\\textsf": "mathsf", - "\\texttt": "mathtt", "\\textnormal": "mathrm", "\\textbf": "mathbf", - "\\textit": "textit" - }; - - defineFunction(["\\text", "\\textrm", "\\textsf", "\\texttt", "\\textnormal", "\\textbf", "\\textit"], { - numArgs: 1, - argTypes: ["text"], - greediness: 2, - allowedInText: true - }, function (context, args) { - var body = args[0]; - return { - type: "text", - body: ordargument(body), - style: textFunctionStyles[context.funcName] - }; - }); - - // A two-argument custom color - defineFunction("\\textcolor", { - numArgs: 2, - allowedInText: true, - greediness: 3, - argTypes: ["color", "original"] - }, function (context, args) { - var color = args[0]; - var body = args[1]; - return { - type: "color", - color: color.value, - value: ordargument(body) - }; - }); - - // \color is handled in Parser.js's parseImplicitGroup - defineFunction("\\color", { - numArgs: 1, - allowedInText: true, - greediness: 3, - argTypes: ["color"] - }, null); - - // An overline - defineFunction("\\overline", { - numArgs: 1 - }, function (context, args) { - var body = args[0]; - return { - type: "overline", - body: body - }; - }); - - // An underline - defineFunction("\\underline", { - numArgs: 1 - }, function (context, args) { - var body = args[0]; - return { - type: "underline", - body: body - }; - }); - - // A box of the width and height - defineFunction("\\rule", { - numArgs: 2, - numOptionalArgs: 1, - argTypes: ["size", "size", "size"] - }, function (context, args) { - var shift = args[0]; - var width = args[1]; - var height = args[2]; - return { - type: "rule", - shift: shift && shift.value, - width: width.value, - height: height.value - }; - }); - - // TODO: In TeX, \mkern only accepts mu-units, and \kern does not accept - // mu-units. In current KaTeX we relax this; both commands accept any unit. - defineFunction(["\\kern", "\\mkern"], { - numArgs: 1, - argTypes: ["size"] - }, function (context, args) { - return { - type: "kern", - dimension: args[0].value - }; - }); - - // A KaTeX logo - defineFunction("\\KaTeX", { - numArgs: 0 - }, function (context) { - return { - type: "katex" - }; - }); - - defineFunction("\\phantom", { - numArgs: 1 - }, function (context, args) { - var body = args[0]; - return { - type: "phantom", - value: ordargument(body) - }; - }); - - // Math class commands except \mathop - defineFunction(["\\mathord", "\\mathbin", "\\mathrel", "\\mathopen", "\\mathclose", "\\mathpunct", "\\mathinner"], { - numArgs: 1 - }, function (context, args) { - var body = args[0]; - return { - type: "mclass", - mclass: "m" + context.funcName.substr(5), - value: ordargument(body) - }; - }); - - // Build a relation by placing one symbol on top of another - defineFunction("\\stackrel", { - numArgs: 2 - }, function (context, args) { - var top = args[0]; - var bottom = args[1]; - - var bottomop = new _ParseNode2.default("op", { - type: "op", - limits: true, - alwaysHandleSupSub: true, - symbol: false, - value: ordargument(bottom) - }, bottom.mode); - - var supsub = new _ParseNode2.default("supsub", { - base: bottomop, - sup: top, - sub: null - }, top.mode); - - return { - type: "mclass", - mclass: "mrel", - value: [supsub] - }; - }); - - // \mod-type functions - defineFunction("\\bmod", { - numArgs: 0 - }, function (context, args) { - return { - type: "mod", - modType: "bmod", - value: null - }; - }); - - defineFunction(["\\pod", "\\pmod", "\\mod"], { - numArgs: 1 - }, function (context, args) { - var body = args[0]; - return { - type: "mod", - modType: context.funcName.substr(1), - value: ordargument(body) - }; - }); - - // Extra data needed for the delimiter handler down below - var delimiterSizes = { - "\\bigl": { mclass: "mopen", size: 1 }, - "\\Bigl": { mclass: "mopen", size: 2 }, - "\\biggl": { mclass: "mopen", size: 3 }, - "\\Biggl": { mclass: "mopen", size: 4 }, - "\\bigr": { mclass: "mclose", size: 1 }, - "\\Bigr": { mclass: "mclose", size: 2 }, - "\\biggr": { mclass: "mclose", size: 3 }, - "\\Biggr": { mclass: "mclose", size: 4 }, - "\\bigm": { mclass: "mrel", size: 1 }, - "\\Bigm": { mclass: "mrel", size: 2 }, - "\\biggm": { mclass: "mrel", size: 3 }, - "\\Biggm": { mclass: "mrel", size: 4 }, - "\\big": { mclass: "mord", size: 1 }, - "\\Big": { mclass: "mord", size: 2 }, - "\\bigg": { mclass: "mord", size: 3 }, - "\\Bigg": { mclass: "mord", size: 4 } - }; - - var delimiters = ["(", ")", "[", "\\lbrack", "]", "\\rbrack", "\\{", "\\lbrace", "\\}", "\\rbrace", "\\lfloor", "\\rfloor", "\\lceil", "\\rceil", "<", ">", "\\langle", "\\rangle", "\\lt", "\\gt", "\\lvert", "\\rvert", "\\lVert", "\\rVert", "\\lgroup", "\\rgroup", "\\lmoustache", "\\rmoustache", "/", "\\backslash", "|", "\\vert", "\\|", "\\Vert", "\\uparrow", "\\Uparrow", "\\downarrow", "\\Downarrow", "\\updownarrow", "\\Updownarrow", "."]; - - var fontAliases = { - "\\Bbb": "\\mathbb", - "\\bold": "\\mathbf", - "\\frak": "\\mathfrak" - }; - - // Single-argument color functions - defineFunction(["\\blue", "\\orange", "\\pink", "\\red", "\\green", "\\gray", "\\purple", "\\blueA", "\\blueB", "\\blueC", "\\blueD", "\\blueE", "\\tealA", "\\tealB", "\\tealC", "\\tealD", "\\tealE", "\\greenA", "\\greenB", "\\greenC", "\\greenD", "\\greenE", "\\goldA", "\\goldB", "\\goldC", "\\goldD", "\\goldE", "\\redA", "\\redB", "\\redC", "\\redD", "\\redE", "\\maroonA", "\\maroonB", "\\maroonC", "\\maroonD", "\\maroonE", "\\purpleA", "\\purpleB", "\\purpleC", "\\purpleD", "\\purpleE", "\\mintA", "\\mintB", "\\mintC", "\\grayA", "\\grayB", "\\grayC", "\\grayD", "\\grayE", "\\grayF", "\\grayG", "\\grayH", "\\grayI", "\\kaBlue", "\\kaGreen"], { - numArgs: 1, - allowedInText: true, - greediness: 3 - }, function (context, args) { - var body = args[0]; - return { - type: "color", - color: "katex-" + context.funcName.slice(1), - value: ordargument(body) - }; - }); - - // There are 2 flags for operators; whether they produce limits in - // displaystyle, and whether they are symbols and should grow in - // displaystyle. These four groups cover the four possible choices. - - // No limits, not symbols - defineFunction(["\\arcsin", "\\arccos", "\\arctan", "\\arctg", "\\arcctg", "\\arg", "\\ch", "\\cos", "\\cosec", "\\cosh", "\\cot", "\\cotg", "\\coth", "\\csc", "\\ctg", "\\cth", "\\deg", "\\dim", "\\exp", "\\hom", "\\ker", "\\lg", "\\ln", "\\log", "\\sec", "\\sin", "\\sinh", "\\sh", "\\tan", "\\tanh", "\\tg", "\\th"], { - numArgs: 0 - }, function (context) { - return { - type: "op", - limits: false, - symbol: false, - body: context.funcName - }; - }); - - // Limits, not symbols - defineFunction(["\\det", "\\gcd", "\\inf", "\\lim", "\\liminf", "\\limsup", "\\max", "\\min", "\\Pr", "\\sup"], { - numArgs: 0 - }, function (context) { - return { - type: "op", - limits: true, - symbol: false, - body: context.funcName - }; - }); - - // No limits, symbols - defineFunction(["\\int", "\\iint", "\\iiint", "\\oint"], { - numArgs: 0 - }, function (context) { - return { - type: "op", - limits: false, - symbol: true, - body: context.funcName - }; - }); - - // Limits, symbols - defineFunction(["\\coprod", "\\bigvee", "\\bigwedge", "\\biguplus", "\\bigcap", "\\bigcup", "\\intop", "\\prod", "\\sum", "\\bigotimes", "\\bigoplus", "\\bigodot", "\\bigsqcup", "\\smallint"], { - numArgs: 0 - }, function (context) { - return { - type: "op", - limits: true, - symbol: true, - body: context.funcName - }; - }); - - // \mathop class command - defineFunction("\\mathop", { - numArgs: 1 - }, function (context, args) { - var body = args[0]; - return { - type: "op", - limits: false, - symbol: false, - value: ordargument(body) - }; - }); - - // Fractions - defineFunction(["\\dfrac", "\\frac", "\\tfrac", "\\dbinom", "\\binom", "\\tbinom", "\\\\atopfrac"], { - numArgs: 2, - greediness: 2 - }, function (context, args) { - var numer = args[0]; - var denom = args[1]; - var hasBarLine = void 0; - var leftDelim = null; - var rightDelim = null; - var size = "auto"; - - switch (context.funcName) { - case "\\dfrac": - case "\\frac": - case "\\tfrac": - hasBarLine = true; - break; - case "\\\\atopfrac": - hasBarLine = false; - break; - case "\\dbinom": - case "\\binom": - case "\\tbinom": - hasBarLine = false; - leftDelim = "("; - rightDelim = ")"; - break; - default: - throw new Error("Unrecognized genfrac command"); - } - - switch (context.funcName) { - case "\\dfrac": - case "\\dbinom": - size = "display"; - break; - case "\\tfrac": - case "\\tbinom": - size = "text"; - break; - } - - return { - type: "genfrac", - numer: numer, - denom: denom, - hasBarLine: hasBarLine, - leftDelim: leftDelim, - rightDelim: rightDelim, - size: size - }; - }); - - // Left and right overlap functions - defineFunction(["\\llap", "\\rlap"], { - numArgs: 1, - allowedInText: true - }, function (context, args) { - var body = args[0]; - return { - type: context.funcName.slice(1), - body: body - }; - }); - - // Delimiter functions - var checkDelimiter = function checkDelimiter(delim, context) { - if (_utils2.default.contains(delimiters, delim.value)) { - return delim; - } else { - throw new _ParseError2.default("Invalid delimiter: '" + delim.value + "' after '" + context.funcName + "'", delim); - } - }; - - defineFunction(["\\bigl", "\\Bigl", "\\biggl", "\\Biggl", "\\bigr", "\\Bigr", "\\biggr", "\\Biggr", "\\bigm", "\\Bigm", "\\biggm", "\\Biggm", "\\big", "\\Big", "\\bigg", "\\Bigg"], { - numArgs: 1 - }, function (context, args) { - var delim = checkDelimiter(args[0], context); - - return { - type: "delimsizing", - size: delimiterSizes[context.funcName].size, - mclass: delimiterSizes[context.funcName].mclass, - value: delim.value - }; - }); - - defineFunction(["\\left", "\\right"], { - numArgs: 1 - }, function (context, args) { - var delim = checkDelimiter(args[0], context); - - // \left and \right are caught somewhere in Parser.js, which is - // why this data doesn't match what is in buildHTML. - return { - type: "leftright", - value: delim.value - }; - }); - - defineFunction("\\middle", { - numArgs: 1 - }, function (context, args) { - var delim = checkDelimiter(args[0], context); - if (!context.parser.leftrightDepth) { - throw new _ParseError2.default("\\middle without preceding \\left", delim); - } - - return { - type: "middle", - value: delim.value - }; - }); - - // Sizing functions (handled in Parser.js explicitly, hence no handler) - defineFunction(["\\tiny", "\\scriptsize", "\\footnotesize", "\\small", "\\normalsize", "\\large", "\\Large", "\\LARGE", "\\huge", "\\Huge"], 0, null); - - // Style changing functions (handled in Parser.js explicitly, hence no - // handler) - defineFunction(["\\displaystyle", "\\textstyle", "\\scriptstyle", "\\scriptscriptstyle"], 0, null); - - // Old font changing functions - defineFunction(["\\rm", "\\sf", "\\tt", "\\bf", "\\it"], 0, null); - - defineFunction([ - // styles - "\\mathrm", "\\mathit", "\\mathbf", - - // families - "\\mathbb", "\\mathcal", "\\mathfrak", "\\mathscr", "\\mathsf", "\\mathtt", - - // aliases - "\\Bbb", "\\bold", "\\frak"], { - numArgs: 1, - greediness: 2 - }, function (context, args) { - var body = args[0]; - var func = context.funcName; - if (func in fontAliases) { - func = fontAliases[func]; - } - return { - type: "font", - font: func.slice(1), - body: body - }; - }); - - // Accents - defineFunction(["\\acute", "\\grave", "\\ddot", "\\tilde", "\\bar", "\\breve", "\\check", "\\hat", "\\vec", "\\dot", "\\widehat", "\\widetilde", "\\overrightarrow", "\\overleftarrow", "\\Overrightarrow", "\\overleftrightarrow", "\\overgroup", "\\overlinesegment", "\\overleftharpoon", "\\overrightharpoon"], { - numArgs: 1 - }, function (context, args) { - var base = args[0]; - - var isStretchy = !_utils2.default.contains(["\\acute", "\\grave", "\\ddot", "\\tilde", "\\bar", "\\breve", "\\check", "\\hat", "\\vec", "\\dot"], context.funcName); - - var isShifty = !isStretchy || _utils2.default.contains(["\\widehat", "\\widetilde"], context.funcName); - - return { - type: "accent", - label: context.funcName, - isStretchy: isStretchy, - isShifty: isShifty, - value: ordargument(base), - base: base - }; - }); - - // Text-mode accents - defineFunction(["\\'", "\\`", "\\^", "\\~", "\\=", "\\u", "\\.", '\\"', "\\r", "\\H", "\\v"], { - numArgs: 1, - allowedInText: true, - allowedInMath: false - }, function (context, args) { - var base = args[0]; - - return { - type: "accent", - label: context.funcName, - isStretchy: false, - isShifty: true, - value: ordargument(base), - base: base - }; - }); - - // Horizontal stretchy braces - defineFunction(["\\overbrace", "\\underbrace"], { - numArgs: 1 - }, function (context, args) { - var base = args[0]; - return { - type: "horizBrace", - label: context.funcName, - isOver: /^\\over/.test(context.funcName), - base: base - }; - }); - - // Stretchy accents under the body - defineFunction(["\\underleftarrow", "\\underrightarrow", "\\underleftrightarrow", "\\undergroup", "\\underlinesegment", "\\undertilde"], { - numArgs: 1 - }, function (context, args) { - var body = args[0]; - return { - type: "accentUnder", - label: context.funcName, - value: ordargument(body), - body: body - }; - }); - - // Stretchy arrows with an optional argument - defineFunction(["\\xleftarrow", "\\xrightarrow", "\\xLeftarrow", "\\xRightarrow", "\\xleftrightarrow", "\\xLeftrightarrow", "\\xhookleftarrow", "\\xhookrightarrow", "\\xmapsto", "\\xrightharpoondown", "\\xrightharpoonup", "\\xleftharpoondown", "\\xleftharpoonup", "\\xrightleftharpoons", "\\xleftrightharpoons", "\\xLongequal", "\\xtwoheadrightarrow", "\\xtwoheadleftarrow", "\\xLongequal", "\\xtofrom"], { - numArgs: 1, - numOptionalArgs: 1 - }, function (context, args) { - var below = args[0]; - var body = args[1]; - return { - type: "xArrow", // x for extensible - label: context.funcName, - body: body, - below: below - }; - }); - - // enclose - defineFunction(["\\cancel", "\\bcancel", "\\xcancel", "\\sout", "\\fbox"], { - numArgs: 1 - }, function (context, args) { - var body = args[0]; - return { - type: "enclose", - label: context.funcName, - body: body - }; - }); - - // Infix generalized fractions - defineFunction(["\\over", "\\choose", "\\atop"], { - numArgs: 0, - infix: true - }, function (context) { - var replaceWith = void 0; - switch (context.funcName) { - case "\\over": - replaceWith = "\\frac"; - break; - case "\\choose": - replaceWith = "\\binom"; - break; - case "\\atop": - replaceWith = "\\\\atopfrac"; - break; - default: - throw new Error("Unrecognized infix genfrac command"); - } - return { - type: "infix", - replaceWith: replaceWith, - token: context.token - }; - }); - - // Row breaks for aligned data - defineFunction(["\\\\", "\\cr"], { - numArgs: 0, - numOptionalArgs: 1, - argTypes: ["size"] - }, function (context, args) { - var size = args[0]; - return { - type: "cr", - size: size - }; - }); - - // Environment delimiters - defineFunction(["\\begin", "\\end"], { - numArgs: 1, - argTypes: ["text"] - }, function (context, args) { - var nameGroup = args[0]; - if (nameGroup.type !== "ordgroup") { - throw new _ParseError2.default("Invalid environment name", nameGroup); - } - var name = ""; - for (var i = 0; i < nameGroup.value.length; ++i) { - name += nameGroup.value[i].value; - } - return { - type: "environment", - name: name, - nameGroup: nameGroup - }; - }); - - },{"./ParseError":29,"./ParseNode":30,"./utils":51}],44:[function(require,module,exports){ - - /** - * Predefined macros for KaTeX. - * This can be used to define some commands in terms of others. - */ - - // This function might one day accept additional argument and do more things. - function defineMacro(name, body) { - module.exports[name] = body; - } - - ////////////////////////////////////////////////////////////////////// - // basics - defineMacro("\\bgroup", "{"); - defineMacro("\\egroup", "}"); - defineMacro("\\begingroup", "{"); - defineMacro("\\endgroup", "}"); - - // We don't distinguish between math and nonmath kerns. - // (In TeX, the mu unit works only with \mkern.) - defineMacro("\\mkern", "\\kern"); - - ////////////////////////////////////////////////////////////////////// - // amsmath.sty - - // \def\overset#1#2{\binrel@{#2}\binrel@@{\mathop{\kern\z@#2}\limits^{#1}}} - defineMacro("\\overset", "\\mathop{#2}\\limits^{#1}"); - defineMacro("\\underset", "\\mathop{#2}\\limits_{#1}"); - - // \newcommand{\boxed}[1]{\fbox{\m@th$\displaystyle#1$}} - defineMacro("\\boxed", "\\fbox{\\displaystyle{#1}}"); - - //TODO: When implementing \dots, should ideally add the \DOTSB indicator - // into the macro, to indicate these are binary operators. - // \def\iff{\DOTSB\;\Longleftrightarrow\;} - // \def\implies{\DOTSB\;\Longrightarrow\;} - // \def\impliedby{\DOTSB\;\Longleftarrow\;} - defineMacro("\\iff", "\\;\\Longleftrightarrow\\;"); - defineMacro("\\implies", "\\;\\Longrightarrow\\;"); - defineMacro("\\impliedby", "\\;\\Longleftarrow\\;"); - - ////////////////////////////////////////////////////////////////////// - // mathtools.sty - - //\providecommand\ordinarycolon{:} - defineMacro("\\ordinarycolon", ":"); - //\def\vcentcolon{\mathrel{\mathop\ordinarycolon}} - //TODO(edemaine): Not yet centered. Fix via \raisebox or #726 - defineMacro("\\vcentcolon", "\\mathrel{\\mathop\\ordinarycolon}"); - // \providecommand*\dblcolon{\vcentcolon\mathrel{\mkern-.9mu}\vcentcolon} - defineMacro("\\dblcolon", "\\vcentcolon\\mathrel{\\mkern-.9mu}\\vcentcolon"); - // \providecommand*\coloneqq{\vcentcolon\mathrel{\mkern-1.2mu}=} - defineMacro("\\coloneqq", "\\vcentcolon\\mathrel{\\mkern-1.2mu}="); - // \providecommand*\Coloneqq{\dblcolon\mathrel{\mkern-1.2mu}=} - defineMacro("\\Coloneqq", "\\dblcolon\\mathrel{\\mkern-1.2mu}="); - // \providecommand*\coloneq{\vcentcolon\mathrel{\mkern-1.2mu}\mathrel{-}} - defineMacro("\\coloneq", "\\vcentcolon\\mathrel{\\mkern-1.2mu}\\mathrel{-}"); - // \providecommand*\Coloneq{\dblcolon\mathrel{\mkern-1.2mu}\mathrel{-}} - defineMacro("\\Coloneq", "\\dblcolon\\mathrel{\\mkern-1.2mu}\\mathrel{-}"); - // \providecommand*\eqqcolon{=\mathrel{\mkern-1.2mu}\vcentcolon} - defineMacro("\\eqqcolon", "=\\mathrel{\\mkern-1.2mu}\\vcentcolon"); - // \providecommand*\Eqqcolon{=\mathrel{\mkern-1.2mu}\dblcolon} - defineMacro("\\Eqqcolon", "=\\mathrel{\\mkern-1.2mu}\\dblcolon"); - // \providecommand*\eqcolon{\mathrel{-}\mathrel{\mkern-1.2mu}\vcentcolon} - defineMacro("\\eqcolon", "\\mathrel{-}\\mathrel{\\mkern-1.2mu}\\vcentcolon"); - // \providecommand*\Eqcolon{\mathrel{-}\mathrel{\mkern-1.2mu}\dblcolon} - defineMacro("\\Eqcolon", "\\mathrel{-}\\mathrel{\\mkern-1.2mu}\\dblcolon"); - // \providecommand*\colonapprox{\vcentcolon\mathrel{\mkern-1.2mu}\approx} - defineMacro("\\colonapprox", "\\vcentcolon\\mathrel{\\mkern-1.2mu}\\approx"); - // \providecommand*\Colonapprox{\dblcolon\mathrel{\mkern-1.2mu}\approx} - defineMacro("\\Colonapprox", "\\dblcolon\\mathrel{\\mkern-1.2mu}\\approx"); - // \providecommand*\colonsim{\vcentcolon\mathrel{\mkern-1.2mu}\sim} - defineMacro("\\colonsim", "\\vcentcolon\\mathrel{\\mkern-1.2mu}\\sim"); - // \providecommand*\Colonsim{\dblcolon\mathrel{\mkern-1.2mu}\sim} - defineMacro("\\Colonsim", "\\dblcolon\\mathrel{\\mkern-1.2mu}\\sim"); - - ////////////////////////////////////////////////////////////////////// - // colonequals.sty - - // Alternate names for mathtools's macros: - defineMacro("\\ratio", "\\vcentcolon"); - defineMacro("\\coloncolon", "\\dblcolon"); - defineMacro("\\colonequals", "\\coloneqq"); - defineMacro("\\coloncolonequals", "\\Coloneqq"); - defineMacro("\\equalscolon", "\\eqqcolon"); - defineMacro("\\equalscoloncolon", "\\Eqqcolon"); - defineMacro("\\colonminus", "\\coloneq"); - defineMacro("\\coloncolonminus", "\\Coloneq"); - defineMacro("\\minuscolon", "\\eqcolon"); - defineMacro("\\minuscoloncolon", "\\Eqcolon"); - // \colonapprox name is same in mathtools and colonequals. - defineMacro("\\coloncolonapprox", "\\Colonapprox"); - // \colonsim name is same in mathtools and colonequals. - defineMacro("\\coloncolonsim", "\\Colonsim"); - - // Additional macros, implemented by analogy with mathtools definitions: - defineMacro("\\simcolon", "\\sim\\mathrel{\\mkern-1.2mu}\\vcentcolon"); - defineMacro("\\simcoloncolon", "\\sim\\mathrel{\\mkern-1.2mu}\\dblcolon"); - defineMacro("\\approxcolon", "\\approx\\mathrel{\\mkern-1.2mu}\\vcentcolon"); - defineMacro("\\approxcoloncolon", "\\approx\\mathrel{\\mkern-1.2mu}\\dblcolon"); - - },{}],45:[function(require,module,exports){ - - var _classCallCheck2 = require("babel-runtime/helpers/classCallCheck"); - - var _classCallCheck3 = _interopRequireDefault(_classCallCheck2); - - var _createClass2 = require("babel-runtime/helpers/createClass"); - - var _createClass3 = _interopRequireDefault(_createClass2); - - var _utils = require("./utils"); - - var _utils2 = _interopRequireDefault(_utils); - - function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { default: obj }; } - - /** - * This node represents a general purpose MathML node of any type. The - * constructor requires the type of node to create (for example, `"mo"` or - * `"mspace"`, corresponding to `` and `` tags). - */ - var MathNode = function () { - function MathNode(type, children) { - (0, _classCallCheck3.default)(this, MathNode); - - this.type = type; - this.attributes = {}; - this.children = children || []; - } - - /** - * Sets an attribute on a MathML node. MathML depends on attributes to convey a - * semantic content, so this is used heavily. - */ - - - (0, _createClass3.default)(MathNode, [{ - key: "setAttribute", - value: function setAttribute(name, value) { - this.attributes[name] = value; - } - - /** - * Converts the math node into a MathML-namespaced DOM element. - */ - - }, { - key: "toNode", - value: function toNode() { - var node = document.createElementNS("http://www.w3.org/1998/Math/MathML", this.type); - - for (var attr in this.attributes) { - if (Object.prototype.hasOwnProperty.call(this.attributes, attr)) { - node.setAttribute(attr, this.attributes[attr]); - } - } - - for (var i = 0; i < this.children.length; i++) { - node.appendChild(this.children[i].toNode()); - } - - return node; - } - - /** - * Converts the math node into an HTML markup string. - */ - - }, { - key: "toMarkup", - value: function toMarkup() { - var markup = "<" + this.type; - - // Add the attributes - for (var attr in this.attributes) { - if (Object.prototype.hasOwnProperty.call(this.attributes, attr)) { - markup += " " + attr + "=\""; - markup += _utils2.default.escape(this.attributes[attr]); - markup += "\""; - } - } - - markup += ">"; - - for (var i = 0; i < this.children.length; i++) { - markup += this.children[i].toMarkup(); - } - - markup += ""; - - return markup; - } - }]); - return MathNode; - }(); - - /** - * This node represents a piece of text. - */ - /** - * These objects store data about MathML nodes. This is the MathML equivalent - * of the types in domTree.js. Since MathML handles its own rendering, and - * since we're mainly using MathML to improve accessibility, we don't manage - * any of the styling state that the plain DOM nodes do. - * - * The `toNode` and `toMarkup` functions work simlarly to how they do in - * domTree.js, creating namespaced DOM nodes and HTML text markup respectively. - */ - - var TextNode = function () { - function TextNode(text) { - (0, _classCallCheck3.default)(this, TextNode); - - this.text = text; - } - - /** - * Converts the text node into a DOM text node. - */ - - - (0, _createClass3.default)(TextNode, [{ - key: "toNode", - value: function toNode() { - return document.createTextNode(this.text); - } - - /** - * Converts the text node into HTML markup (which is just the text itself). - */ - - }, { - key: "toMarkup", - value: function toMarkup() { - return _utils2.default.escape(this.text); - } - }]); - return TextNode; - }(); - - module.exports = { - MathNode: MathNode, - TextNode: TextNode - }; - - },{"./utils":51,"babel-runtime/helpers/classCallCheck":4,"babel-runtime/helpers/createClass":5}],46:[function(require,module,exports){ - - var _Parser = require('./Parser'); - - var _Parser2 = _interopRequireDefault(_Parser); - - function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { default: obj }; } - - /** - * Parses an expression using a Parser, then returns the parsed result. - */ - var parseTree = function parseTree(toParse, settings) { - if (!(typeof toParse === 'string' || toParse instanceof String)) { - throw new TypeError('KaTeX can only parse string typed expression'); - } - var parser = new _Parser2.default(toParse, settings); - - return parser.parse(); - }; /** - * Provides a single function for parsing an expression using a Parser - * TODO(emily): Remove this - */ - - module.exports = parseTree; - - },{"./Parser":31}],47:[function(require,module,exports){ - - /** - * This file provides support to buildMathML.js and buildHTML.js - * for stretchy wide elements rendered from SVG files - * and other CSS trickery. - */ - - var buildCommon = require("./buildCommon"); - var mathMLTree = require("./mathMLTree"); - var utils = require("./utils"); - - var stretchyCodePoint = { - widehat: "^", - widetilde: "~", - undertilde: "~", - overleftarrow: "\u2190", - underleftarrow: "\u2190", - xleftarrow: "\u2190", - overrightarrow: "\u2192", - underrightarrow: "\u2192", - xrightarrow: "\u2192", - underbrace: "\u23B5", - overbrace: "\u23DE", - overleftrightarrow: "\u2194", - underleftrightarrow: "\u2194", - xleftrightarrow: "\u2194", - Overrightarrow: "\u21D2", - xRightarrow: "\u21D2", - overleftharpoon: "\u21BC", - xleftharpoonup: "\u21BC", - overrightharpoon: "\u21C0", - xrightharpoonup: "\u21C0", - xLeftarrow: "\u21D0", - xLeftrightarrow: "\u21D4", - xhookleftarrow: "\u21A9", - xhookrightarrow: "\u21AA", - xmapsto: "\u21A6", - xrightharpoondown: "\u21C1", - xleftharpoondown: "\u21BD", - xrightleftharpoons: "\u21CC", - xleftrightharpoons: "\u21CB", - xtwoheadleftarrow: "\u219E", - xtwoheadrightarrow: "\u21A0", - xLongequal: "=", - xtofrom: "\u21C4" - }; - - var mathMLnode = function mathMLnode(label) { - var node = new mathMLTree.MathNode("mo", [new mathMLTree.TextNode(stretchyCodePoint[label.substr(1)])]); - node.setAttribute("stretchy", "true"); - return node; - }; - - // In the katexImagesData object just below, the dimensions all - // correspond to path geometry inside the relevant SVG. - // For example, \rightarrow uses the same arrowhead as glyph U+2192 - // from the KaTeX Main font. The scaling factor is 1000. - // That is, inside the font, that arrowhead is 522 units tall, which - // corresponds to 0.522 em inside the document. - // And for extensible arrows, we split that distance around the math axis. - - var katexImagesData = { - // height, depth, imageName, minWidth - overleftarrow: [0.522, 0, "leftarrow", 0.5], - underleftarrow: [0.522, 0, "leftarrow", 0.5], - xleftarrow: [0.261, 0.261, "leftarrow", 0.783], - overrightarrow: [0.522, 0, "rightarrow", 0.5], - underrightarrow: [0.522, 0, "rightarrow", 0.5], - xrightarrow: [0.261, 0.261, "rightarrow", 0.783], - overbrace: [0.548, 0, "overbrace", 1.6], - underbrace: [0.548, 0, "underbrace", 1.6], - overleftrightarrow: [0.522, 0, "leftrightarrow", 0.5], - underleftrightarrow: [0.522, 0, "leftrightarrow", 0.5], - xleftrightarrow: [0.261, 0.261, "leftrightarrow", 0.783], - Overrightarrow: [0.56, 0, "doublerightarrow", 0.5], - xLeftarrow: [0.28, 0.28, "doubleleftarrow", 0.783], - xRightarrow: [0.28, 0.28, "doublerightarrow", 0.783], - xLeftrightarrow: [0.28, 0.28, "doubleleftrightarrow", 0.955], - overleftharpoon: [0.522, 0, "leftharpoon", 0.5], - overrightharpoon: [0.522, 0, "rightharpoon", 0.5], - xleftharpoonup: [0.261, 0.261, "leftharpoon", 0.783], - xrightharpoonup: [0.261, 0.261, "rightharpoon", 0.783], - xhookleftarrow: [0.261, 0.261, "hookleftarrow", 0.87], - xhookrightarrow: [0.261, 0.261, "hookrightarrow", 0.87], - overlinesegment: [0.414, 0, "linesegment", 0.5], - underlinesegment: [0.414, 0, "linesegment", 0.5], - xmapsto: [0.261, 0.261, "mapsto", 0.783], - xrightharpoondown: [0.261, 0.261, "rightharpoondown", 0.783], - xleftharpoondown: [0.261, 0.261, "leftharpoondown", 0.783], - xrightleftharpoons: [0.358, 0.358, "rightleftharpoons", 0.716], - xleftrightharpoons: [0.358, 0.358, "leftrightharpoons", 0.716], - overgroup: [0.342, 0, "overgroup", 0.87], - undergroup: [0.342, 0, "undergroup", 0.87], - xtwoheadleftarrow: [0.167, 0.167, "twoheadleftarrow", 0.86], - xtwoheadrightarrow: [0.167, 0.167, "twoheadrightarrow", 0.86], - xLongequal: [0.167, 0.167, "longequal", 0.5], - xtofrom: [0.264, 0.264, "tofrom", 0.86] - }; - - // Many of the KaTeX SVG images have been adapted from glyphs in KaTeX fonts. - // Copyright (c) 2009-2010, Design Science, Inc. () - // Copyright (c) 2014-2017 Khan Academy () - // Licensed under the SIL Open Font License, Version 1.1. - // See \nhttp://scripts.sil.org/OFL - - // Nested SVGs - // Many of the KaTeX SVG images contain a nested SVG. This is done to - // achieve a stretchy image while avoiding distortion of arrowheads or - // brace corners. - - // The inner SVG typically contains a very long (400 em) arrow. - - // The outer SVG acts like a window that exposes only part of the inner SVG. - // The outer SVG will grow or shrink to match the dimensions set by CSS. - - // The inner SVG always has a longer, thinner aspect ratio than the outer - // SVG. After the inner SVG fills 100% of the height of the outer SVG, - // there is a long arrow shaft left over. That left-over shaft is not shown. - // Instead, it is sliced off because the inner SVG is set to - // "preserveAspectRatio='... slice'". - - // Thus, the reader sees an arrow that matches the subject matter width - // without distortion. - - // Some functions, such as \cancel, need to vary their aspect ratio. These - // functions do not get the nested SVG treatment. - - // Second Brush Stroke - // Low resolution monitors struggle to display images in fine detail. - // So browsers apply anti-aliasing. A long straight arrow shaft therefore - // will sometimes appear as if it has a blurred edge. - - // To mitigate this, these SVG files contain a second "brush-stroke" on the - // arrow shafts. That is, a second long thin rectangular SVG path has been - // written directly on top of each arrow shaft. This reinforcement causes - // some of the screen pixels to display as black instead of the anti-aliased - // gray pixel that a single path would generate. So we get arrow shafts - // whose edges appear to be sharper. - - var svgPath = { - doubleleftarrow: "", - - doublerightarrow: "", - - leftarrow: "", - - rightarrow: "" - }; - - var innerSVG = { - // Since bcancel's SVG is inline and it omits the viewBox attribute, - // it's stroke-width will not vary with span area. - bcancel: "", - - cancel: "", - - // The doubleleftarrow geometry is from glyph U+21D0 in the font KaTeX Main - doubleleftarrow: ">" + svgPath["doubleleftarrow"] + "", - - // doubleleftrightarrow is from glyph U+21D4 in font KaTeX Main - doubleleftrightarrow: ">" + svgPath["doubleleftarrow"] + "\n" + svgPath["doublerightarrow"] + "", - - // doublerightarrow is from glyph U+21D2 in font KaTeX Main - doublerightarrow: ">" + svgPath["doublerightarrow"] + "", - - // hookleftarrow is from glyph U+21A9 in font KaTeX Main - hookleftarrow: ">" + svgPath["leftarrow"] + "\n", - - // hookrightarrow is from glyph U+21AA in font KaTeX Main - hookrightarrow: ">" + svgPath["rightarrow"] + "", - - // leftarrow is from glyph U+2190 in font KaTeX Main - leftarrow: ">" + svgPath["leftarrow"] + "", - - // leftharpoon is from glyph U+21BD in font KaTeX Main - leftharpoon: ">", - - // leftharpoondown is from glyph U+21BD in font KaTeX Main - leftharpoondown: ">", - - // leftrightarrow is from glyph U+2194 in font KaTeX Main - leftrightarrow: ">" + svgPath["leftarrow"] + "\n" + svgPath["rightarrow"] + "", - - // leftrightharpoons is from glyphs U+21BC/21B1 in font KaTeX Main - leftrightharpoons: ">\n", - - linesegment: ">\n", - - longequal: " viewBox='0 0 100 334' preserveAspectRatio='none'>\n", - - // mapsto is from glyph U+21A6 in font KaTeX Main - mapsto: ">" + svgPath["rightarrow"] + "", - - // overbrace is from glyphs U+23A9/23A8/23A7 in font KaTeX_Size4-Regular - overbrace: ">\n", - - // overgroup is from the MnSymbol package (public domain) - overgroup: ">", - - // rightarrow is from glyph U+2192 in font KaTeX Main - rightarrow: ">" + svgPath["rightarrow"] + "", - - // rightharpoon is from glyph U+21C0 in font KaTeX Main - rightharpoon: ">", - - // rightharpoondown is from glyph U+21C1 in font KaTeX Main - rightharpoondown: ">", - - // rightleftharpoons is from glyph U+21CC in font KaTeX Main - rightleftharpoons: ">", - - // tilde1 is a modified version of a glyph from the MnSymbol package - tilde1: " viewBox='0 0 600 260' preserveAspectRatio='none'>\n", - - // Ditto tilde2, tilde3, and tilde 4 - tilde2: " viewBox='0 0 1033 286' preserveAspectRatio='none'>\n", - - tilde3: " viewBox='0 0 2339 306' preserveAspectRatio='none'>\n", - - tilde4: " viewBox='0 0 2340 312' preserveAspectRatio='none'>\n", - - // tofrom is from glyph U+21C4 in font KaTeX AMS Regular - tofrom: ">", - - // twoheadleftarrow is from glyph U+219E in font KaTeX AMS Regular - twoheadleftarrow: ">\n", - - // twoheadrightarrow is from glyph U+21A0 in font KaTeX AMS Regular - twoheadrightarrow: ">\n", - - // underbrace is from glyphs U+23A9/23A8/23A7 in font KaTeX_Size4-Regular - underbrace: ">\n", - - // undergroup is from the MnSymbol package (public domain) - undergroup: ">", - - // widehat1 is a modified version of a glyph from the MnSymbol package - widehat1: " viewBox='0 0 1062 239' preserveAspectRatio='none'>\n", - - // Ditto widehat2, widehat3, and widehat4 - widehat2: " viewBox='0 0 2364 300' preserveAspectRatio='none'>\n", - - widehat3: " viewBox='0 0 2364 360' preserveAspectRatio='none'>\n", - - widehat4: " viewBox='0 0 2364 420' preserveAspectRatio='none'>\n", - - xcancel: "\n" - }; - - var svgSpan = function svgSpan(group, options) { - // Create a span with inline SVG for the element. - var label = group.value.label.substr(1); - var height = 0; - var depth = 0; - var imageName = ""; - var minWidth = 0; - - if (utils.contains(["widehat", "widetilde", "undertilde"], label)) { - // There are four SVG images available for each function. - // Choose a taller image when there are more characters. - var numChars = group.value.value.length; - if (numChars > 5) { - height = 0.312; - imageName = (label === "widehat" ? "widehat" : "tilde") + "4"; - } else { - var imgIndex = [1, 1, 2, 2, 3, 3][numChars]; - if (label === "widehat") { - height = [0, 0.24, 0.30, 0.30, 0.36, 0.36][numChars]; - imageName = "widehat" + imgIndex; - } else { - height = [0, 0.26, 0.30, 0.30, 0.34, 0.34][numChars]; - imageName = "tilde" + imgIndex; - } - } - } else { - var imgData = katexImagesData[label]; - height = imgData[0]; - depth = imgData[1]; - imageName = imgData[2]; - minWidth = imgData[3]; - } - - var span = buildCommon.makeSpan([], [], options); - span.height = height; - span.depth = depth; - var totalHeight = height + depth; - span.style.height = totalHeight + "em"; - if (minWidth > 0) { - span.style.minWidth = minWidth + "em"; - } - - span.innerHTML = ""; - - return span; - }; - - var encloseSpan = function encloseSpan(inner, label, pad, options) { - // Return an image span for \cancel, \bcancel, \xcancel, or \fbox - var img = void 0; - var totalHeight = inner.height + inner.depth + 2 * pad; - - if (label === "fbox") { - img = buildCommon.makeSpan(["stretchy", label], [], options); - if (options.color) { - img.style.borderColor = options.getColor(); - } - } else { - img = buildCommon.makeSpan([], [], options); - img.innerHTML = "" + innerSVG[label] + ""; - } - - img.height = totalHeight; - img.style.height = totalHeight + "em"; - - return img; - }; - - module.exports = { - encloseSpan: encloseSpan, - mathMLnode: mathMLnode, - svgSpan: svgSpan - }; - - },{"./buildCommon":34,"./mathMLTree":45,"./utils":51}],48:[function(require,module,exports){ - - /** - * This file holds a list of all no-argument functions and single-character - * symbols (like 'a' or ';'). - * - * For each of the symbols, there are three properties they can have: - * - font (required): the font to be used for this symbol. Either "main" (the - normal font), or "ams" (the ams fonts). - * - group (required): the ParseNode group type the symbol should have (i.e. - "textord", "mathord", etc). - See https://github.com/Khan/KaTeX/wiki/Examining-TeX#group-types - * - replace: the character that this symbol or function should be - * replaced with (i.e. "\phi" has a replace value of "\u03d5", the phi - * character in the main font). - * - * The outermost map in the table indicates what mode the symbols should be - * accepted in (e.g. "math" or "text"). - */ - - module.exports = { - math: {}, - text: {} - }; - - function defineSymbol(mode, font, group, replace, name, acceptUnicodeChar) { - module.exports[mode][name] = { - font: font, - group: group, - replace: replace - }; - - if (acceptUnicodeChar) { - module.exports[mode][replace] = module.exports[mode][name]; - } - } - - // Some abbreviations for commonly used strings. - // This helps minify the code, and also spotting typos using jshint. - - // modes: - var math = "math"; - var text = "text"; - - // fonts: - var main = "main"; - var ams = "ams"; - - // groups: - var accent = "accent"; - var bin = "bin"; - var close = "close"; - var inner = "inner"; - var mathord = "mathord"; - var op = "op"; - var open = "open"; - var punct = "punct"; - var rel = "rel"; - var spacing = "spacing"; - var textord = "textord"; - - // Now comes the symbol table - - // Relation Symbols - defineSymbol(math, main, rel, "\u2261", "\\equiv"); - defineSymbol(math, main, rel, "\u227A", "\\prec"); - defineSymbol(math, main, rel, "\u227B", "\\succ"); - defineSymbol(math, main, rel, "\u223C", "\\sim"); - defineSymbol(math, main, rel, "\u22A5", "\\perp"); - defineSymbol(math, main, rel, "\u2AAF", "\\preceq"); - defineSymbol(math, main, rel, "\u2AB0", "\\succeq"); - defineSymbol(math, main, rel, "\u2243", "\\simeq"); - defineSymbol(math, main, rel, "\u2223", "\\mid"); - defineSymbol(math, main, rel, "\u226A", "\\ll"); - defineSymbol(math, main, rel, "\u226B", "\\gg"); - defineSymbol(math, main, rel, "\u224D", "\\asymp"); - defineSymbol(math, main, rel, "\u2225", "\\parallel"); - defineSymbol(math, main, rel, "\u22C8", "\\bowtie"); - defineSymbol(math, main, rel, "\u2323", "\\smile"); - defineSymbol(math, main, rel, "\u2291", "\\sqsubseteq"); - defineSymbol(math, main, rel, "\u2292", "\\sqsupseteq"); - defineSymbol(math, main, rel, "\u2250", "\\doteq"); - defineSymbol(math, main, rel, "\u2322", "\\frown"); - defineSymbol(math, main, rel, "\u220B", "\\ni"); - defineSymbol(math, main, rel, "\u221D", "\\propto"); - defineSymbol(math, main, rel, "\u22A2", "\\vdash"); - defineSymbol(math, main, rel, "\u22A3", "\\dashv"); - defineSymbol(math, main, rel, "\u220B", "\\owns"); - - // Punctuation - defineSymbol(math, main, punct, ".", "\\ldotp"); - defineSymbol(math, main, punct, "\u22C5", "\\cdotp"); - - // Misc Symbols - defineSymbol(math, main, textord, "#", "\\#"); - defineSymbol(text, main, textord, "#", "\\#"); - defineSymbol(math, main, textord, "&", "\\&"); - defineSymbol(text, main, textord, "&", "\\&"); - defineSymbol(math, main, textord, "\u2135", "\\aleph"); - defineSymbol(math, main, textord, "\u2200", "\\forall"); - defineSymbol(math, main, textord, "\u210F", "\\hbar"); - defineSymbol(math, main, textord, "\u2203", "\\exists"); - defineSymbol(math, main, textord, "\u2207", "\\nabla"); - defineSymbol(math, main, textord, "\u266D", "\\flat"); - defineSymbol(math, main, textord, "\u2113", "\\ell"); - defineSymbol(math, main, textord, "\u266E", "\\natural"); - defineSymbol(math, main, textord, "\u2663", "\\clubsuit"); - defineSymbol(math, main, textord, "\u2118", "\\wp"); - defineSymbol(math, main, textord, "\u266F", "\\sharp"); - defineSymbol(math, main, textord, "\u2662", "\\diamondsuit"); - defineSymbol(math, main, textord, "\u211C", "\\Re"); - defineSymbol(math, main, textord, "\u2661", "\\heartsuit"); - defineSymbol(math, main, textord, "\u2111", "\\Im"); - defineSymbol(math, main, textord, "\u2660", "\\spadesuit"); - - // Math and Text - defineSymbol(math, main, textord, "\u2020", "\\dag"); - defineSymbol(text, main, textord, "\u2020", "\\dag"); - defineSymbol(text, main, textord, "\u2020", "\\textdagger"); - defineSymbol(math, main, textord, "\u2021", "\\ddag"); - defineSymbol(text, main, textord, "\u2021", "\\ddag"); - defineSymbol(text, main, textord, "\u2020", "\\textdaggerdbl"); - - // Large Delimiters - defineSymbol(math, main, close, "\u23B1", "\\rmoustache"); - defineSymbol(math, main, open, "\u23B0", "\\lmoustache"); - defineSymbol(math, main, close, "\u27EF", "\\rgroup"); - defineSymbol(math, main, open, "\u27EE", "\\lgroup"); - - // Binary Operators - defineSymbol(math, main, bin, "\u2213", "\\mp"); - defineSymbol(math, main, bin, "\u2296", "\\ominus"); - defineSymbol(math, main, bin, "\u228E", "\\uplus"); - defineSymbol(math, main, bin, "\u2293", "\\sqcap"); - defineSymbol(math, main, bin, "\u2217", "\\ast"); - defineSymbol(math, main, bin, "\u2294", "\\sqcup"); - defineSymbol(math, main, bin, "\u25EF", "\\bigcirc"); - defineSymbol(math, main, bin, "\u2219", "\\bullet"); - defineSymbol(math, main, bin, "\u2021", "\\ddagger"); - defineSymbol(math, main, bin, "\u2240", "\\wr"); - defineSymbol(math, main, bin, "\u2A3F", "\\amalg"); - - // Arrow Symbols - defineSymbol(math, main, rel, "\u27F5", "\\longleftarrow"); - defineSymbol(math, main, rel, "\u21D0", "\\Leftarrow"); - defineSymbol(math, main, rel, "\u27F8", "\\Longleftarrow"); - defineSymbol(math, main, rel, "\u27F6", "\\longrightarrow"); - defineSymbol(math, main, rel, "\u21D2", "\\Rightarrow"); - defineSymbol(math, main, rel, "\u27F9", "\\Longrightarrow"); - defineSymbol(math, main, rel, "\u2194", "\\leftrightarrow"); - defineSymbol(math, main, rel, "\u27F7", "\\longleftrightarrow"); - defineSymbol(math, main, rel, "\u21D4", "\\Leftrightarrow"); - defineSymbol(math, main, rel, "\u27FA", "\\Longleftrightarrow"); - defineSymbol(math, main, rel, "\u21A6", "\\mapsto"); - defineSymbol(math, main, rel, "\u27FC", "\\longmapsto"); - defineSymbol(math, main, rel, "\u2197", "\\nearrow"); - defineSymbol(math, main, rel, "\u21A9", "\\hookleftarrow"); - defineSymbol(math, main, rel, "\u21AA", "\\hookrightarrow"); - defineSymbol(math, main, rel, "\u2198", "\\searrow"); - defineSymbol(math, main, rel, "\u21BC", "\\leftharpoonup"); - defineSymbol(math, main, rel, "\u21C0", "\\rightharpoonup"); - defineSymbol(math, main, rel, "\u2199", "\\swarrow"); - defineSymbol(math, main, rel, "\u21BD", "\\leftharpoondown"); - defineSymbol(math, main, rel, "\u21C1", "\\rightharpoondown"); - defineSymbol(math, main, rel, "\u2196", "\\nwarrow"); - defineSymbol(math, main, rel, "\u21CC", "\\rightleftharpoons"); - - // AMS Negated Binary Relations - defineSymbol(math, ams, rel, "\u226E", "\\nless"); - defineSymbol(math, ams, rel, "\uE010", "\\nleqslant"); - defineSymbol(math, ams, rel, "\uE011", "\\nleqq"); - defineSymbol(math, ams, rel, "\u2A87", "\\lneq"); - defineSymbol(math, ams, rel, "\u2268", "\\lneqq"); - defineSymbol(math, ams, rel, "\uE00C", "\\lvertneqq"); - defineSymbol(math, ams, rel, "\u22E6", "\\lnsim"); - defineSymbol(math, ams, rel, "\u2A89", "\\lnapprox"); - defineSymbol(math, ams, rel, "\u2280", "\\nprec"); - defineSymbol(math, ams, rel, "\u22E0", "\\npreceq"); - defineSymbol(math, ams, rel, "\u22E8", "\\precnsim"); - defineSymbol(math, ams, rel, "\u2AB9", "\\precnapprox"); - defineSymbol(math, ams, rel, "\u2241", "\\nsim"); - defineSymbol(math, ams, rel, "\uE006", "\\nshortmid"); - defineSymbol(math, ams, rel, "\u2224", "\\nmid"); - defineSymbol(math, ams, rel, "\u22AC", "\\nvdash"); - defineSymbol(math, ams, rel, "\u22AD", "\\nvDash"); - defineSymbol(math, ams, rel, "\u22EA", "\\ntriangleleft"); - defineSymbol(math, ams, rel, "\u22EC", "\\ntrianglelefteq"); - defineSymbol(math, ams, rel, "\u228A", "\\subsetneq"); - defineSymbol(math, ams, rel, "\uE01A", "\\varsubsetneq"); - defineSymbol(math, ams, rel, "\u2ACB", "\\subsetneqq"); - defineSymbol(math, ams, rel, "\uE017", "\\varsubsetneqq"); - defineSymbol(math, ams, rel, "\u226F", "\\ngtr"); - defineSymbol(math, ams, rel, "\uE00F", "\\ngeqslant"); - defineSymbol(math, ams, rel, "\uE00E", "\\ngeqq"); - defineSymbol(math, ams, rel, "\u2A88", "\\gneq"); - defineSymbol(math, ams, rel, "\u2269", "\\gneqq"); - defineSymbol(math, ams, rel, "\uE00D", "\\gvertneqq"); - defineSymbol(math, ams, rel, "\u22E7", "\\gnsim"); - defineSymbol(math, ams, rel, "\u2A8A", "\\gnapprox"); - defineSymbol(math, ams, rel, "\u2281", "\\nsucc"); - defineSymbol(math, ams, rel, "\u22E1", "\\nsucceq"); - defineSymbol(math, ams, rel, "\u22E9", "\\succnsim"); - defineSymbol(math, ams, rel, "\u2ABA", "\\succnapprox"); - defineSymbol(math, ams, rel, "\u2246", "\\ncong"); - defineSymbol(math, ams, rel, "\uE007", "\\nshortparallel"); - defineSymbol(math, ams, rel, "\u2226", "\\nparallel"); - defineSymbol(math, ams, rel, "\u22AF", "\\nVDash"); - defineSymbol(math, ams, rel, "\u22EB", "\\ntriangleright"); - defineSymbol(math, ams, rel, "\u22ED", "\\ntrianglerighteq"); - defineSymbol(math, ams, rel, "\uE018", "\\nsupseteqq"); - defineSymbol(math, ams, rel, "\u228B", "\\supsetneq"); - defineSymbol(math, ams, rel, "\uE01B", "\\varsupsetneq"); - defineSymbol(math, ams, rel, "\u2ACC", "\\supsetneqq"); - defineSymbol(math, ams, rel, "\uE019", "\\varsupsetneqq"); - defineSymbol(math, ams, rel, "\u22AE", "\\nVdash"); - defineSymbol(math, ams, rel, "\u2AB5", "\\precneqq"); - defineSymbol(math, ams, rel, "\u2AB6", "\\succneqq"); - defineSymbol(math, ams, rel, "\uE016", "\\nsubseteqq"); - defineSymbol(math, ams, bin, "\u22B4", "\\unlhd"); - defineSymbol(math, ams, bin, "\u22B5", "\\unrhd"); - - // AMS Negated Arrows - defineSymbol(math, ams, rel, "\u219A", "\\nleftarrow"); - defineSymbol(math, ams, rel, "\u219B", "\\nrightarrow"); - defineSymbol(math, ams, rel, "\u21CD", "\\nLeftarrow"); - defineSymbol(math, ams, rel, "\u21CF", "\\nRightarrow"); - defineSymbol(math, ams, rel, "\u21AE", "\\nleftrightarrow"); - defineSymbol(math, ams, rel, "\u21CE", "\\nLeftrightarrow"); - - // AMS Misc - defineSymbol(math, ams, rel, "\u25B3", "\\vartriangle"); - defineSymbol(math, ams, textord, "\u210F", "\\hslash"); - defineSymbol(math, ams, textord, "\u25BD", "\\triangledown"); - defineSymbol(math, ams, textord, "\u25CA", "\\lozenge"); - defineSymbol(math, ams, textord, "\u24C8", "\\circledS"); - defineSymbol(math, ams, textord, "\xAE", "\\circledR"); - defineSymbol(text, ams, textord, "\xAE", "\\circledR"); - defineSymbol(math, ams, textord, "\u2221", "\\measuredangle"); - defineSymbol(math, ams, textord, "\u2204", "\\nexists"); - defineSymbol(math, ams, textord, "\u2127", "\\mho"); - defineSymbol(math, ams, textord, "\u2132", "\\Finv"); - defineSymbol(math, ams, textord, "\u2141", "\\Game"); - defineSymbol(math, ams, textord, "k", "\\Bbbk"); - defineSymbol(math, ams, textord, "\u2035", "\\backprime"); - defineSymbol(math, ams, textord, "\u25B2", "\\blacktriangle"); - defineSymbol(math, ams, textord, "\u25BC", "\\blacktriangledown"); - defineSymbol(math, ams, textord, "\u25A0", "\\blacksquare"); - defineSymbol(math, ams, textord, "\u29EB", "\\blacklozenge"); - defineSymbol(math, ams, textord, "\u2605", "\\bigstar"); - defineSymbol(math, ams, textord, "\u2222", "\\sphericalangle"); - defineSymbol(math, ams, textord, "\u2201", "\\complement"); - defineSymbol(math, ams, textord, "\xF0", "\\eth"); - defineSymbol(math, ams, textord, "\u2571", "\\diagup"); - defineSymbol(math, ams, textord, "\u2572", "\\diagdown"); - defineSymbol(math, ams, textord, "\u25A1", "\\square"); - defineSymbol(math, ams, textord, "\u25A1", "\\Box"); - defineSymbol(math, ams, textord, "\u25CA", "\\Diamond"); - defineSymbol(math, ams, textord, "\xA5", "\\yen"); - defineSymbol(math, ams, textord, "\u2713", "\\checkmark"); - defineSymbol(text, ams, textord, "\u2713", "\\checkmark"); - - // AMS Hebrew - defineSymbol(math, ams, textord, "\u2136", "\\beth"); - defineSymbol(math, ams, textord, "\u2138", "\\daleth"); - defineSymbol(math, ams, textord, "\u2137", "\\gimel"); - - // AMS Greek - defineSymbol(math, ams, textord, "\u03DD", "\\digamma"); - defineSymbol(math, ams, textord, "\u03F0", "\\varkappa"); - - // AMS Delimiters - defineSymbol(math, ams, open, "\u250C", "\\ulcorner"); - defineSymbol(math, ams, close, "\u2510", "\\urcorner"); - defineSymbol(math, ams, open, "\u2514", "\\llcorner"); - defineSymbol(math, ams, close, "\u2518", "\\lrcorner"); - - // AMS Binary Relations - defineSymbol(math, ams, rel, "\u2266", "\\leqq"); - defineSymbol(math, ams, rel, "\u2A7D", "\\leqslant"); - defineSymbol(math, ams, rel, "\u2A95", "\\eqslantless"); - defineSymbol(math, ams, rel, "\u2272", "\\lesssim"); - defineSymbol(math, ams, rel, "\u2A85", "\\lessapprox"); - defineSymbol(math, ams, rel, "\u224A", "\\approxeq"); - defineSymbol(math, ams, bin, "\u22D6", "\\lessdot"); - defineSymbol(math, ams, rel, "\u22D8", "\\lll"); - defineSymbol(math, ams, rel, "\u2276", "\\lessgtr"); - defineSymbol(math, ams, rel, "\u22DA", "\\lesseqgtr"); - defineSymbol(math, ams, rel, "\u2A8B", "\\lesseqqgtr"); - defineSymbol(math, ams, rel, "\u2251", "\\doteqdot"); - defineSymbol(math, ams, rel, "\u2253", "\\risingdotseq"); - defineSymbol(math, ams, rel, "\u2252", "\\fallingdotseq"); - defineSymbol(math, ams, rel, "\u223D", "\\backsim"); - defineSymbol(math, ams, rel, "\u22CD", "\\backsimeq"); - defineSymbol(math, ams, rel, "\u2AC5", "\\subseteqq"); - defineSymbol(math, ams, rel, "\u22D0", "\\Subset"); - defineSymbol(math, ams, rel, "\u228F", "\\sqsubset"); - defineSymbol(math, ams, rel, "\u227C", "\\preccurlyeq"); - defineSymbol(math, ams, rel, "\u22DE", "\\curlyeqprec"); - defineSymbol(math, ams, rel, "\u227E", "\\precsim"); - defineSymbol(math, ams, rel, "\u2AB7", "\\precapprox"); - defineSymbol(math, ams, rel, "\u22B2", "\\vartriangleleft"); - defineSymbol(math, ams, rel, "\u22B4", "\\trianglelefteq"); - defineSymbol(math, ams, rel, "\u22A8", "\\vDash"); - defineSymbol(math, ams, rel, "\u22AA", "\\Vvdash"); - defineSymbol(math, ams, rel, "\u2323", "\\smallsmile"); - defineSymbol(math, ams, rel, "\u2322", "\\smallfrown"); - defineSymbol(math, ams, rel, "\u224F", "\\bumpeq"); - defineSymbol(math, ams, rel, "\u224E", "\\Bumpeq"); - defineSymbol(math, ams, rel, "\u2267", "\\geqq"); - defineSymbol(math, ams, rel, "\u2A7E", "\\geqslant"); - defineSymbol(math, ams, rel, "\u2A96", "\\eqslantgtr"); - defineSymbol(math, ams, rel, "\u2273", "\\gtrsim"); - defineSymbol(math, ams, rel, "\u2A86", "\\gtrapprox"); - defineSymbol(math, ams, bin, "\u22D7", "\\gtrdot"); - defineSymbol(math, ams, rel, "\u22D9", "\\ggg"); - defineSymbol(math, ams, rel, "\u2277", "\\gtrless"); - defineSymbol(math, ams, rel, "\u22DB", "\\gtreqless"); - defineSymbol(math, ams, rel, "\u2A8C", "\\gtreqqless"); - defineSymbol(math, ams, rel, "\u2256", "\\eqcirc"); - defineSymbol(math, ams, rel, "\u2257", "\\circeq"); - defineSymbol(math, ams, rel, "\u225C", "\\triangleq"); - defineSymbol(math, ams, rel, "\u223C", "\\thicksim"); - defineSymbol(math, ams, rel, "\u2248", "\\thickapprox"); - defineSymbol(math, ams, rel, "\u2AC6", "\\supseteqq"); - defineSymbol(math, ams, rel, "\u22D1", "\\Supset"); - defineSymbol(math, ams, rel, "\u2290", "\\sqsupset"); - defineSymbol(math, ams, rel, "\u227D", "\\succcurlyeq"); - defineSymbol(math, ams, rel, "\u22DF", "\\curlyeqsucc"); - defineSymbol(math, ams, rel, "\u227F", "\\succsim"); - defineSymbol(math, ams, rel, "\u2AB8", "\\succapprox"); - defineSymbol(math, ams, rel, "\u22B3", "\\vartriangleright"); - defineSymbol(math, ams, rel, "\u22B5", "\\trianglerighteq"); - defineSymbol(math, ams, rel, "\u22A9", "\\Vdash"); - defineSymbol(math, ams, rel, "\u2223", "\\shortmid"); - defineSymbol(math, ams, rel, "\u2225", "\\shortparallel"); - defineSymbol(math, ams, rel, "\u226C", "\\between"); - defineSymbol(math, ams, rel, "\u22D4", "\\pitchfork"); - defineSymbol(math, ams, rel, "\u221D", "\\varpropto"); - defineSymbol(math, ams, rel, "\u25C0", "\\blacktriangleleft"); - defineSymbol(math, ams, rel, "\u2234", "\\therefore"); - defineSymbol(math, ams, rel, "\u220D", "\\backepsilon"); - defineSymbol(math, ams, rel, "\u25B6", "\\blacktriangleright"); - defineSymbol(math, ams, rel, "\u2235", "\\because"); - defineSymbol(math, ams, rel, "\u22D8", "\\llless"); - defineSymbol(math, ams, rel, "\u22D9", "\\gggtr"); - defineSymbol(math, ams, bin, "\u22B2", "\\lhd"); - defineSymbol(math, ams, bin, "\u22B3", "\\rhd"); - defineSymbol(math, ams, rel, "\u2242", "\\eqsim"); - defineSymbol(math, main, rel, "\u22C8", "\\Join"); - defineSymbol(math, ams, rel, "\u2251", "\\Doteq"); - - // AMS Binary Operators - defineSymbol(math, ams, bin, "\u2214", "\\dotplus"); - defineSymbol(math, ams, bin, "\u2216", "\\smallsetminus"); - defineSymbol(math, ams, bin, "\u22D2", "\\Cap"); - defineSymbol(math, ams, bin, "\u22D3", "\\Cup"); - defineSymbol(math, ams, bin, "\u2A5E", "\\doublebarwedge"); - defineSymbol(math, ams, bin, "\u229F", "\\boxminus"); - defineSymbol(math, ams, bin, "\u229E", "\\boxplus"); - defineSymbol(math, ams, bin, "\u22C7", "\\divideontimes"); - defineSymbol(math, ams, bin, "\u22C9", "\\ltimes"); - defineSymbol(math, ams, bin, "\u22CA", "\\rtimes"); - defineSymbol(math, ams, bin, "\u22CB", "\\leftthreetimes"); - defineSymbol(math, ams, bin, "\u22CC", "\\rightthreetimes"); - defineSymbol(math, ams, bin, "\u22CF", "\\curlywedge"); - defineSymbol(math, ams, bin, "\u22CE", "\\curlyvee"); - defineSymbol(math, ams, bin, "\u229D", "\\circleddash"); - defineSymbol(math, ams, bin, "\u229B", "\\circledast"); - defineSymbol(math, ams, bin, "\u22C5", "\\centerdot"); - defineSymbol(math, ams, bin, "\u22BA", "\\intercal"); - defineSymbol(math, ams, bin, "\u22D2", "\\doublecap"); - defineSymbol(math, ams, bin, "\u22D3", "\\doublecup"); - defineSymbol(math, ams, bin, "\u22A0", "\\boxtimes"); - - // AMS Arrows - defineSymbol(math, ams, rel, "\u21E2", "\\dashrightarrow"); - defineSymbol(math, ams, rel, "\u21E0", "\\dashleftarrow"); - defineSymbol(math, ams, rel, "\u21C7", "\\leftleftarrows"); - defineSymbol(math, ams, rel, "\u21C6", "\\leftrightarrows"); - defineSymbol(math, ams, rel, "\u21DA", "\\Lleftarrow"); - defineSymbol(math, ams, rel, "\u219E", "\\twoheadleftarrow"); - defineSymbol(math, ams, rel, "\u21A2", "\\leftarrowtail"); - defineSymbol(math, ams, rel, "\u21AB", "\\looparrowleft"); - defineSymbol(math, ams, rel, "\u21CB", "\\leftrightharpoons"); - defineSymbol(math, ams, rel, "\u21B6", "\\curvearrowleft"); - defineSymbol(math, ams, rel, "\u21BA", "\\circlearrowleft"); - defineSymbol(math, ams, rel, "\u21B0", "\\Lsh"); - defineSymbol(math, ams, rel, "\u21C8", "\\upuparrows"); - defineSymbol(math, ams, rel, "\u21BF", "\\upharpoonleft"); - defineSymbol(math, ams, rel, "\u21C3", "\\downharpoonleft"); - defineSymbol(math, ams, rel, "\u22B8", "\\multimap"); - defineSymbol(math, ams, rel, "\u21AD", "\\leftrightsquigarrow"); - defineSymbol(math, ams, rel, "\u21C9", "\\rightrightarrows"); - defineSymbol(math, ams, rel, "\u21C4", "\\rightleftarrows"); - defineSymbol(math, ams, rel, "\u21A0", "\\twoheadrightarrow"); - defineSymbol(math, ams, rel, "\u21A3", "\\rightarrowtail"); - defineSymbol(math, ams, rel, "\u21AC", "\\looparrowright"); - defineSymbol(math, ams, rel, "\u21B7", "\\curvearrowright"); - defineSymbol(math, ams, rel, "\u21BB", "\\circlearrowright"); - defineSymbol(math, ams, rel, "\u21B1", "\\Rsh"); - defineSymbol(math, ams, rel, "\u21CA", "\\downdownarrows"); - defineSymbol(math, ams, rel, "\u21BE", "\\upharpoonright"); - defineSymbol(math, ams, rel, "\u21C2", "\\downharpoonright"); - defineSymbol(math, ams, rel, "\u21DD", "\\rightsquigarrow"); - defineSymbol(math, ams, rel, "\u21DD", "\\leadsto"); - defineSymbol(math, ams, rel, "\u21DB", "\\Rrightarrow"); - defineSymbol(math, ams, rel, "\u21BE", "\\restriction"); - - defineSymbol(math, main, textord, "\u2018", "`"); - defineSymbol(math, main, textord, "$", "\\$"); - defineSymbol(text, main, textord, "$", "\\$"); - defineSymbol(text, main, textord, "$", "\\textdollar"); - defineSymbol(math, main, textord, "%", "\\%"); - defineSymbol(text, main, textord, "%", "\\%"); - defineSymbol(math, main, textord, "_", "\\_"); - defineSymbol(text, main, textord, "_", "\\_"); - defineSymbol(text, main, textord, "_", "\\textunderscore"); - defineSymbol(math, main, textord, "\u2220", "\\angle"); - defineSymbol(math, main, textord, "\u221E", "\\infty"); - defineSymbol(math, main, textord, "\u2032", "\\prime"); - defineSymbol(math, main, textord, "\u25B3", "\\triangle"); - defineSymbol(math, main, textord, "\u0393", "\\Gamma", true); - defineSymbol(math, main, textord, "\u0394", "\\Delta", true); - defineSymbol(math, main, textord, "\u0398", "\\Theta", true); - defineSymbol(math, main, textord, "\u039B", "\\Lambda", true); - defineSymbol(math, main, textord, "\u039E", "\\Xi", true); - defineSymbol(math, main, textord, "\u03A0", "\\Pi", true); - defineSymbol(math, main, textord, "\u03A3", "\\Sigma", true); - defineSymbol(math, main, textord, "\u03A5", "\\Upsilon", true); - defineSymbol(math, main, textord, "\u03A6", "\\Phi", true); - defineSymbol(math, main, textord, "\u03A8", "\\Psi", true); - defineSymbol(math, main, textord, "\u03A9", "\\Omega", true); - defineSymbol(math, main, textord, "\xAC", "\\neg"); - defineSymbol(math, main, textord, "\xAC", "\\lnot"); - defineSymbol(math, main, textord, "\u22A4", "\\top"); - defineSymbol(math, main, textord, "\u22A5", "\\bot"); - defineSymbol(math, main, textord, "\u2205", "\\emptyset"); - defineSymbol(math, ams, textord, "\u2205", "\\varnothing"); - defineSymbol(math, main, mathord, "\u03B1", "\\alpha", true); - defineSymbol(math, main, mathord, "\u03B2", "\\beta", true); - defineSymbol(math, main, mathord, "\u03B3", "\\gamma", true); - defineSymbol(math, main, mathord, "\u03B4", "\\delta", true); - defineSymbol(math, main, mathord, "\u03F5", "\\epsilon", true); - defineSymbol(math, main, mathord, "\u03B6", "\\zeta", true); - defineSymbol(math, main, mathord, "\u03B7", "\\eta", true); - defineSymbol(math, main, mathord, "\u03B8", "\\theta", true); - defineSymbol(math, main, mathord, "\u03B9", "\\iota", true); - defineSymbol(math, main, mathord, "\u03BA", "\\kappa", true); - defineSymbol(math, main, mathord, "\u03BB", "\\lambda", true); - defineSymbol(math, main, mathord, "\u03BC", "\\mu", true); - defineSymbol(math, main, mathord, "\u03BD", "\\nu", true); - defineSymbol(math, main, mathord, "\u03BE", "\\xi", true); - defineSymbol(math, main, mathord, "\u03BF", "\\omicron", true); - defineSymbol(math, main, mathord, "\u03C0", "\\pi", true); - defineSymbol(math, main, mathord, "\u03C1", "\\rho", true); - defineSymbol(math, main, mathord, "\u03C3", "\\sigma", true); - defineSymbol(math, main, mathord, "\u03C4", "\\tau", true); - defineSymbol(math, main, mathord, "\u03C5", "\\upsilon", true); - defineSymbol(math, main, mathord, "\u03D5", "\\phi", true); - defineSymbol(math, main, mathord, "\u03C7", "\\chi", true); - defineSymbol(math, main, mathord, "\u03C8", "\\psi", true); - defineSymbol(math, main, mathord, "\u03C9", "\\omega", true); - defineSymbol(math, main, mathord, "\u03B5", "\\varepsilon", true); - defineSymbol(math, main, mathord, "\u03D1", "\\vartheta", true); - defineSymbol(math, main, mathord, "\u03D6", "\\varpi", true); - defineSymbol(math, main, mathord, "\u03F1", "\\varrho", true); - defineSymbol(math, main, mathord, "\u03C2", "\\varsigma", true); - defineSymbol(math, main, mathord, "\u03C6", "\\varphi", true); - defineSymbol(math, main, bin, "\u2217", "*"); - defineSymbol(math, main, bin, "+", "+"); - defineSymbol(math, main, bin, "\u2212", "-"); - defineSymbol(math, main, bin, "\u22C5", "\\cdot"); - defineSymbol(math, main, bin, "\u2218", "\\circ"); - defineSymbol(math, main, bin, "\xF7", "\\div"); - defineSymbol(math, main, bin, "\xB1", "\\pm"); - defineSymbol(math, main, bin, "\xD7", "\\times"); - defineSymbol(math, main, bin, "\u2229", "\\cap"); - defineSymbol(math, main, bin, "\u222A", "\\cup"); - defineSymbol(math, main, bin, "\u2216", "\\setminus"); - defineSymbol(math, main, bin, "\u2227", "\\land"); - defineSymbol(math, main, bin, "\u2228", "\\lor"); - defineSymbol(math, main, bin, "\u2227", "\\wedge"); - defineSymbol(math, main, bin, "\u2228", "\\vee"); - defineSymbol(math, main, textord, "\u221A", "\\surd"); - defineSymbol(math, main, open, "(", "("); - defineSymbol(math, main, open, "[", "["); - defineSymbol(math, main, open, "\u27E8", "\\langle"); - defineSymbol(math, main, open, "\u2223", "\\lvert"); - defineSymbol(math, main, open, "\u2225", "\\lVert"); - defineSymbol(math, main, close, ")", ")"); - defineSymbol(math, main, close, "]", "]"); - defineSymbol(math, main, close, "?", "?"); - defineSymbol(math, main, close, "!", "!"); - defineSymbol(math, main, close, "\u27E9", "\\rangle"); - defineSymbol(math, main, close, "\u2223", "\\rvert"); - defineSymbol(math, main, close, "\u2225", "\\rVert"); - defineSymbol(math, main, rel, "=", "="); - defineSymbol(math, main, rel, "<", "<"); - defineSymbol(math, main, rel, ">", ">"); - defineSymbol(math, main, rel, ":", ":"); - defineSymbol(math, main, rel, "\u2248", "\\approx"); - defineSymbol(math, main, rel, "\u2245", "\\cong"); - defineSymbol(math, main, rel, "\u2265", "\\ge"); - defineSymbol(math, main, rel, "\u2265", "\\geq"); - defineSymbol(math, main, rel, "\u2190", "\\gets"); - defineSymbol(math, main, rel, ">", "\\gt"); - defineSymbol(math, main, rel, "\u2208", "\\in"); - defineSymbol(math, main, rel, "\u2209", "\\notin"); - defineSymbol(math, main, rel, "\u0338", "\\not"); - defineSymbol(math, main, rel, "\u2282", "\\subset"); - defineSymbol(math, main, rel, "\u2283", "\\supset"); - defineSymbol(math, main, rel, "\u2286", "\\subseteq"); - defineSymbol(math, main, rel, "\u2287", "\\supseteq"); - defineSymbol(math, ams, rel, "\u2288", "\\nsubseteq"); - defineSymbol(math, ams, rel, "\u2289", "\\nsupseteq"); - defineSymbol(math, main, rel, "\u22A8", "\\models"); - defineSymbol(math, main, rel, "\u2190", "\\leftarrow"); - defineSymbol(math, main, rel, "\u2264", "\\le"); - defineSymbol(math, main, rel, "\u2264", "\\leq"); - defineSymbol(math, main, rel, "<", "\\lt"); - defineSymbol(math, main, rel, "\u2260", "\\ne"); - defineSymbol(math, main, rel, "\u2260", "\\neq"); - defineSymbol(math, main, rel, "\u2192", "\\rightarrow"); - defineSymbol(math, main, rel, "\u2192", "\\to"); - defineSymbol(math, ams, rel, "\u2271", "\\ngeq"); - defineSymbol(math, ams, rel, "\u2270", "\\nleq"); - defineSymbol(math, main, spacing, null, "\\!"); - defineSymbol(math, main, spacing, "\xA0", "\\ "); - defineSymbol(math, main, spacing, "\xA0", "~"); - defineSymbol(math, main, spacing, null, "\\,"); - defineSymbol(math, main, spacing, null, "\\:"); - defineSymbol(math, main, spacing, null, "\\;"); - defineSymbol(math, main, spacing, null, "\\enspace"); - defineSymbol(math, main, spacing, null, "\\qquad"); - defineSymbol(math, main, spacing, null, "\\quad"); - defineSymbol(math, main, spacing, "\xA0", "\\space"); - defineSymbol(math, main, punct, ",", ","); - defineSymbol(math, main, punct, ";", ";"); - defineSymbol(math, main, punct, ":", "\\colon"); - defineSymbol(math, ams, bin, "\u22BC", "\\barwedge"); - defineSymbol(math, ams, bin, "\u22BB", "\\veebar"); - defineSymbol(math, main, bin, "\u2299", "\\odot"); - defineSymbol(math, main, bin, "\u2295", "\\oplus"); - defineSymbol(math, main, bin, "\u2297", "\\otimes"); - defineSymbol(math, main, textord, "\u2202", "\\partial"); - defineSymbol(math, main, bin, "\u2298", "\\oslash"); - defineSymbol(math, ams, bin, "\u229A", "\\circledcirc"); - defineSymbol(math, ams, bin, "\u22A1", "\\boxdot"); - defineSymbol(math, main, bin, "\u25B3", "\\bigtriangleup"); - defineSymbol(math, main, bin, "\u25BD", "\\bigtriangledown"); - defineSymbol(math, main, bin, "\u2020", "\\dagger"); - defineSymbol(math, main, bin, "\u22C4", "\\diamond"); - defineSymbol(math, main, bin, "\u22C6", "\\star"); - defineSymbol(math, main, bin, "\u25C3", "\\triangleleft"); - defineSymbol(math, main, bin, "\u25B9", "\\triangleright"); - defineSymbol(math, main, open, "{", "\\{"); - defineSymbol(text, main, textord, "{", "\\{"); - defineSymbol(text, main, textord, "{", "\\textbraceleft"); - defineSymbol(math, main, close, "}", "\\}"); - defineSymbol(text, main, textord, "}", "\\}"); - defineSymbol(text, main, textord, "}", "\\textbraceright"); - defineSymbol(math, main, open, "{", "\\lbrace"); - defineSymbol(math, main, close, "}", "\\rbrace"); - defineSymbol(math, main, open, "[", "\\lbrack"); - defineSymbol(math, main, close, "]", "\\rbrack"); - defineSymbol(text, main, textord, "<", "\\textless"); // in T1 fontenc - defineSymbol(text, main, textord, ">", "\\textgreater"); // in T1 fontenc - defineSymbol(math, main, open, "\u230A", "\\lfloor"); - defineSymbol(math, main, close, "\u230B", "\\rfloor"); - defineSymbol(math, main, open, "\u2308", "\\lceil"); - defineSymbol(math, main, close, "\u2309", "\\rceil"); - defineSymbol(math, main, textord, "\\", "\\backslash"); - defineSymbol(math, main, textord, "\u2223", "|"); - defineSymbol(math, main, textord, "\u2223", "\\vert"); - defineSymbol(text, main, textord, "|", "\\textbar"); // in T1 fontenc - defineSymbol(math, main, textord, "\u2225", "\\|"); - defineSymbol(math, main, textord, "\u2225", "\\Vert"); - defineSymbol(text, main, textord, "\u2225", "\\textbardbl"); - defineSymbol(math, main, rel, "\u2191", "\\uparrow"); - defineSymbol(math, main, rel, "\u21D1", "\\Uparrow"); - defineSymbol(math, main, rel, "\u2193", "\\downarrow"); - defineSymbol(math, main, rel, "\u21D3", "\\Downarrow"); - defineSymbol(math, main, rel, "\u2195", "\\updownarrow"); - defineSymbol(math, main, rel, "\u21D5", "\\Updownarrow"); - defineSymbol(math, main, op, "\u2210", "\\coprod"); - defineSymbol(math, main, op, "\u22C1", "\\bigvee"); - defineSymbol(math, main, op, "\u22C0", "\\bigwedge"); - defineSymbol(math, main, op, "\u2A04", "\\biguplus"); - defineSymbol(math, main, op, "\u22C2", "\\bigcap"); - defineSymbol(math, main, op, "\u22C3", "\\bigcup"); - defineSymbol(math, main, op, "\u222B", "\\int"); - defineSymbol(math, main, op, "\u222B", "\\intop"); - defineSymbol(math, main, op, "\u222C", "\\iint"); - defineSymbol(math, main, op, "\u222D", "\\iiint"); - defineSymbol(math, main, op, "\u220F", "\\prod"); - defineSymbol(math, main, op, "\u2211", "\\sum"); - defineSymbol(math, main, op, "\u2A02", "\\bigotimes"); - defineSymbol(math, main, op, "\u2A01", "\\bigoplus"); - defineSymbol(math, main, op, "\u2A00", "\\bigodot"); - defineSymbol(math, main, op, "\u222E", "\\oint"); - defineSymbol(math, main, op, "\u2A06", "\\bigsqcup"); - defineSymbol(math, main, op, "\u222B", "\\smallint"); - defineSymbol(text, main, inner, "\u2026", "\\textellipsis"); - defineSymbol(math, main, inner, "\u2026", "\\mathellipsis"); - defineSymbol(text, main, inner, "\u2026", "\\ldots", true); - defineSymbol(math, main, inner, "\u2026", "\\ldots", true); - defineSymbol(math, main, inner, "\u22EF", "\\cdots", true); - defineSymbol(math, main, inner, "\u22F1", "\\ddots", true); - defineSymbol(math, main, textord, "\u22EE", "\\vdots", true); - defineSymbol(math, main, accent, "\xB4", "\\acute"); - defineSymbol(math, main, accent, "`", "\\grave"); - defineSymbol(math, main, accent, "\xA8", "\\ddot"); - defineSymbol(math, main, accent, "~", "\\tilde"); - defineSymbol(math, main, accent, "\xAF", "\\bar"); - defineSymbol(math, main, accent, "\u02D8", "\\breve"); - defineSymbol(math, main, accent, "\u02C7", "\\check"); - defineSymbol(math, main, accent, "^", "\\hat"); - defineSymbol(math, main, accent, "\u20D7", "\\vec"); - defineSymbol(math, main, accent, "\u02D9", "\\dot"); - defineSymbol(math, main, mathord, "\u0131", "\\imath"); - defineSymbol(math, main, mathord, "\u0237", "\\jmath"); - defineSymbol(text, main, accent, "\u02CA", "\\'"); // acute - defineSymbol(text, main, accent, "\u02CB", "\\`"); // grave - defineSymbol(text, main, accent, "\u02C6", "\\^"); // circumflex - defineSymbol(text, main, accent, "\u02DC", "\\~"); // tilde - defineSymbol(text, main, accent, "\u02C9", "\\="); // macron - defineSymbol(text, main, accent, "\u02D8", "\\u"); // breve - defineSymbol(text, main, accent, "\u02D9", "\\."); // dot above - defineSymbol(text, main, accent, "\u02DA", "\\r"); // ring above - defineSymbol(text, main, accent, "\u02C7", "\\v"); // caron - defineSymbol(text, main, accent, "\xA8", '\\"'); // diaresis - defineSymbol(text, main, accent, "\u030B", "\\H"); // double acute - - defineSymbol(text, main, textord, "\u2013", "--"); - defineSymbol(text, main, textord, "\u2013", "\\textendash"); - defineSymbol(text, main, textord, "\u2014", "---"); - defineSymbol(text, main, textord, "\u2014", "\\textemdash"); - defineSymbol(text, main, textord, "\u2018", "`"); - defineSymbol(text, main, textord, "\u2018", "\\textquoteleft"); - defineSymbol(text, main, textord, "\u2019", "'"); - defineSymbol(text, main, textord, "\u2019", "\\textquoteright"); - defineSymbol(text, main, textord, "\u201C", "``"); - defineSymbol(text, main, textord, "\u201C", "\\textquotedblleft"); - defineSymbol(text, main, textord, "\u201D", "''"); - defineSymbol(text, main, textord, "\u201D", "\\textquotedblright"); - defineSymbol(math, main, textord, "\xB0", "\\degree"); - defineSymbol(text, main, textord, "\xB0", "\\degree"); - // TODO: In LaTeX, \pounds can generate a different character in text and math - // mode, but among our fonts, only Main-Italic defines this character "163". - defineSymbol(math, main, mathord, "\xA3", "\\pounds"); - defineSymbol(math, main, mathord, "\xA3", "\\mathsterling"); - defineSymbol(text, main, mathord, "\xA3", "\\pounds"); - defineSymbol(text, main, mathord, "\xA3", "\\textsterling"); - defineSymbol(math, ams, textord, "\u2720", "\\maltese"); - defineSymbol(text, ams, textord, "\u2720", "\\maltese"); - - defineSymbol(text, main, spacing, "\xA0", "\\ "); - defineSymbol(text, main, spacing, "\xA0", " "); - defineSymbol(text, main, spacing, "\xA0", "~"); - - // There are lots of symbols which are the same, so we add them in afterwards. - - // All of these are textords in math mode - var mathTextSymbols = "0123456789/@.\""; - for (var i = 0; i < mathTextSymbols.length; i++) { - var ch = mathTextSymbols.charAt(i); - defineSymbol(math, main, textord, ch, ch); - } - - // All of these are textords in text mode - var textSymbols = "0123456789!@*()-=+[]<>|\";:?/.,"; - for (var _i = 0; _i < textSymbols.length; _i++) { - var _ch = textSymbols.charAt(_i); - defineSymbol(text, main, textord, _ch, _ch); - } - - // All of these are textords in text mode, and mathords in math mode - var letters = "abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ"; - for (var _i2 = 0; _i2 < letters.length; _i2++) { - var _ch2 = letters.charAt(_i2); - defineSymbol(math, main, mathord, _ch2, _ch2); - defineSymbol(text, main, textord, _ch2, _ch2); - } - - // Latin-1 letters - for (var _i3 = 0x00C0; _i3 <= 0x00D6; _i3++) { - var _ch3 = String.fromCharCode(_i3); - defineSymbol(math, main, mathord, _ch3, _ch3); - defineSymbol(text, main, textord, _ch3, _ch3); - } - - for (var _i4 = 0x00D8; _i4 <= 0x00F6; _i4++) { - var _ch4 = String.fromCharCode(_i4); - defineSymbol(math, main, mathord, _ch4, _ch4); - defineSymbol(text, main, textord, _ch4, _ch4); - } - - for (var _i5 = 0x00F8; _i5 <= 0x00FF; _i5++) { - var _ch5 = String.fromCharCode(_i5); - defineSymbol(math, main, mathord, _ch5, _ch5); - defineSymbol(text, main, textord, _ch5, _ch5); - } - - // Cyrillic - for (var _i6 = 0x0410; _i6 <= 0x044F; _i6++) { - var _ch6 = String.fromCharCode(_i6); - defineSymbol(text, main, textord, _ch6, _ch6); - } - - // Unicode versions of existing characters - defineSymbol(text, main, textord, "\u2013", "–"); - defineSymbol(text, main, textord, "\u2014", "—"); - defineSymbol(text, main, textord, "\u2018", "‘"); - defineSymbol(text, main, textord, "\u2019", "’"); - defineSymbol(text, main, textord, "\u201C", "“"); - defineSymbol(text, main, textord, "\u201D", "”"); - - },{}],49:[function(require,module,exports){ - - var hangulRegex = /[\uAC00-\uD7AF]/; - - // This regex combines - // - CJK symbols and punctuation: [\u3000-\u303F] - // - Hiragana: [\u3040-\u309F] - // - Katakana: [\u30A0-\u30FF] - // - CJK ideograms: [\u4E00-\u9FAF] - // - Hangul syllables: [\uAC00-\uD7AF] - // - Fullwidth punctuation: [\uFF00-\uFF60] - // Notably missing are halfwidth Katakana and Romanji glyphs. - var cjkRegex = /[\u3000-\u30FF\u4E00-\u9FAF\uAC00-\uD7AF\uFF00-\uFF60]/; - - module.exports = { - cjkRegex: cjkRegex, - hangulRegex: hangulRegex - }; - - },{}],50:[function(require,module,exports){ - - var _ParseError = require("./ParseError"); - - var _ParseError2 = _interopRequireDefault(_ParseError); - - function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { default: obj }; } - - // This table gives the number of TeX pts in one of each *absolute* TeX unit. - // Thus, multiplying a length by this number converts the length from units - // into pts. Dividing the result by ptPerEm gives the number of ems - // *assuming* a font size of ptPerEm (normal size, normal style). - var ptPerUnit = { - // https://en.wikibooks.org/wiki/LaTeX/Lengths and - // https://tex.stackexchange.com/a/8263 - "pt": 1, // TeX point - "mm": 7227 / 2540, // millimeter - "cm": 7227 / 254, // centimeter - "in": 72.27, // inch - "bp": 803 / 800, // big (PostScript) points - "pc": 12, // pica - "dd": 1238 / 1157, // didot - "cc": 14856 / 1157, // cicero (12 didot) - "nd": 685 / 642, // new didot - "nc": 1370 / 107, // new cicero (12 new didot) - "sp": 1 / 65536, // scaled point (TeX's internal smallest unit) - // https://tex.stackexchange.com/a/41371 - "px": 803 / 800 }; - - // Dictionary of relative units, for fast validity testing. - /* eslint no-console:0 */ - - /** - * This file does conversion between units. In particular, it provides - * calculateSize to convert other units into ems. - */ - - var relativeUnit = { - "ex": true, - "em": true, - "mu": true - }; - - /** - * Determine whether the specified unit (either a string defining the unit - * or a "size" parse node containing a unit field) is valid. - */ - var validUnit = function validUnit(unit) { - if (unit.unit) { - unit = unit.unit; - } - return unit in ptPerUnit || unit in relativeUnit || unit === "ex"; - }; - - /* - * Convert a "size" parse node (with numeric "number" and string "unit" fields, - * as parsed by functions.js argType "size") into a CSS em value for the - * current style/scale. `options` gives the current options. - */ - var calculateSize = function calculateSize(sizeValue, options) { - var scale = void 0; - if (sizeValue.unit in ptPerUnit) { - // Absolute units - scale = ptPerUnit[sizeValue.unit] // Convert unit to pt - / options.fontMetrics().ptPerEm // Convert pt to CSS em - / options.sizeMultiplier; // Unscale to make absolute units - } else if (sizeValue.unit === "mu") { - // `mu` units scale with scriptstyle/scriptscriptstyle. - scale = options.fontMetrics().cssEmPerMu; - } else { - // Other relative units always refer to the *textstyle* font - // in the current size. - var unitOptions = void 0; - if (options.style.isTight()) { - // isTight() means current style is script/scriptscript. - unitOptions = options.havingStyle(options.style.text()); - } else { - unitOptions = options; - } - // TODO: In TeX these units are relative to the quad of the current - // *text* font, e.g. cmr10. KaTeX instead uses values from the - // comparably-sized *Computer Modern symbol* font. At 10pt, these - // match. At 7pt and 5pt, they differ: cmr7=1.138894, cmsy7=1.170641; - // cmr5=1.361133, cmsy5=1.472241. Consider $\scriptsize a\kern1emb$. - // TeX \showlists shows a kern of 1.13889 * fontsize; - // KaTeX shows a kern of 1.171 * fontsize. - if (sizeValue.unit === "ex") { - scale = unitOptions.fontMetrics().xHeight; - } else if (sizeValue.unit === "em") { - scale = unitOptions.fontMetrics().quad; - } else { - throw new _ParseError2.default("Invalid unit: '" + sizeValue.unit + "'"); - } - if (unitOptions !== options) { - scale *= unitOptions.sizeMultiplier / options.sizeMultiplier; - } - } - return sizeValue.number * scale; - }; - - module.exports = { - validUnit: validUnit, - calculateSize: calculateSize - }; - - },{"./ParseError":29}],51:[function(require,module,exports){ - - /** - * This file contains a list of utility functions which are useful in other - * files. - */ - - /** - * Provide an `indexOf` function which works in IE8, but defers to native if - * possible. - */ - var nativeIndexOf = Array.prototype.indexOf; - var indexOf = function indexOf(list, elem) { - if (list == null) { - return -1; - } - if (nativeIndexOf && list.indexOf === nativeIndexOf) { - return list.indexOf(elem); - } - var l = list.length; - for (var i = 0; i < l; i++) { - if (list[i] === elem) { - return i; - } - } - return -1; - }; - - /** - * Return whether an element is contained in a list - */ - var contains = function contains(list, elem) { - return indexOf(list, elem) !== -1; - }; - - /** - * Provide a default value if a setting is undefined - */ - var deflt = function deflt(setting, defaultIfUndefined) { - return setting === undefined ? defaultIfUndefined : setting; - }; - - // hyphenate and escape adapted from Facebook's React under Apache 2 license - - var uppercase = /([A-Z])/g; - var hyphenate = function hyphenate(str) { - return str.replace(uppercase, "-$1").toLowerCase(); - }; - - var ESCAPE_LOOKUP = { - "&": "&", - ">": ">", - "<": "<", - "\"": """, - "'": "'" - }; - - var ESCAPE_REGEX = /[&><"']/g; - - function escaper(match) { - return ESCAPE_LOOKUP[match]; - } - - /** - * Escapes text to prevent scripting attacks. - * - * @param {*} text Text value to escape. - * @return {string} An escaped string. - */ - function escape(text) { - return ("" + text).replace(ESCAPE_REGEX, escaper); - } - - /** - * A function to set the text content of a DOM element in all supported - * browsers. Note that we don't define this if there is no document. - */ - var setTextContent = void 0; - if (typeof document !== "undefined") { - var testNode = document.createElement("span"); - if ("textContent" in testNode) { - setTextContent = function setTextContent(node, text) { - node.textContent = text; - }; - } else { - setTextContent = function setTextContent(node, text) { - node.innerText = text; - }; - } - } - - /** - * A function to clear a node. - */ - function clearNode(node) { - setTextContent(node, ""); - } - - module.exports = { - contains: contains, - deflt: deflt, - escape: escape, - hyphenate: hyphenate, - indexOf: indexOf, - setTextContent: setTextContent, - clearNode: clearNode - }; - - },{}]},{},[1])(1) - }); - }); - - var katex$2 = unwrapExports(katex$1); - - // Copyright 2018 The Distill Template Authors - // - // Licensed under the Apache License, Version 2.0 (the "License"); - // you may not use this file except in compliance with the License. - // You may obtain a copy of the License at - // - // http://www.apache.org/licenses/LICENSE-2.0 - // - // Unless required by applicable law or agreed to in writing, software - // distributed under the License is distributed on an "AS IS" BASIS, - // WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - // See the License for the specific language governing permissions and - // limitations under the License. - - // This is a straight concatenation of code from KaTeX's contrib folder, - // but we aren't using some of their helpers that don't work well outside a browser environment. - - /*global katex */ - - const findEndOfMath = function(delimiter, text, startIndex) { - // Adapted from - // https://github.com/Khan/perseus/blob/master/src/perseus-markdown.jsx - let index = startIndex; - let braceLevel = 0; - - const delimLength = delimiter.length; - - while (index < text.length) { - const character = text[index]; - - if ( - braceLevel <= 0 && - text.slice(index, index + delimLength) === delimiter - ) { - return index; - } else if (character === "\\") { - index++; - } else if (character === "{") { - braceLevel++; - } else if (character === "}") { - braceLevel--; - } - - index++; - } - - return -1; - }; - - const splitAtDelimiters = function(startData, leftDelim, rightDelim, display) { - const finalData = []; - - for (let i = 0; i < startData.length; i++) { - if (startData[i].type === "text") { - const text = startData[i].data; - - let lookingForLeft = true; - let currIndex = 0; - let nextIndex; - - nextIndex = text.indexOf(leftDelim); - if (nextIndex !== -1) { - currIndex = nextIndex; - finalData.push({ - type: "text", - data: text.slice(0, currIndex) - }); - lookingForLeft = false; - } - - while (true) { - // eslint-disable-line no-constant-condition - if (lookingForLeft) { - nextIndex = text.indexOf(leftDelim, currIndex); - if (nextIndex === -1) { - break; - } - - finalData.push({ - type: "text", - data: text.slice(currIndex, nextIndex) - }); - - currIndex = nextIndex; - } else { - nextIndex = findEndOfMath( - rightDelim, - text, - currIndex + leftDelim.length - ); - if (nextIndex === -1) { - break; - } - - finalData.push({ - type: "math", - data: text.slice(currIndex + leftDelim.length, nextIndex), - rawData: text.slice(currIndex, nextIndex + rightDelim.length), - display: display - }); - - currIndex = nextIndex + rightDelim.length; - } - - lookingForLeft = !lookingForLeft; - } - - finalData.push({ - type: "text", - data: text.slice(currIndex) - }); - } else { - finalData.push(startData[i]); - } - } - - return finalData; - }; - - const splitWithDelimiters = function(text, delimiters) { - let data = [{ type: "text", data: text }]; - for (let i = 0; i < delimiters.length; i++) { - const delimiter = delimiters[i]; - data = splitAtDelimiters( - data, - delimiter.left, - delimiter.right, - delimiter.display || false - ); - } - return data; - }; - - /* Note: optionsCopy is mutated by this method. If it is ever exposed in the - * API, we should copy it before mutating. - */ - const renderMathInText = function(text, optionsCopy) { - const data = splitWithDelimiters(text, optionsCopy.delimiters); - const fragment = document.createDocumentFragment(); - - for (let i = 0; i < data.length; i++) { - if (data[i].type === "text") { - fragment.appendChild(document.createTextNode(data[i].data)); - } else { - const tag = document.createElement("d-math"); - const math = data[i].data; - // Override any display mode defined in the settings with that - // defined by the text itself - optionsCopy.displayMode = data[i].display; - try { - tag.textContent = math; - if (optionsCopy.displayMode) { - tag.setAttribute("block", ""); - } - } catch (e) { - if (!(e instanceof katex.ParseError)) { - throw e; - } - optionsCopy.errorCallback( - "KaTeX auto-render: Failed to parse `" + data[i].data + "` with ", - e - ); - fragment.appendChild(document.createTextNode(data[i].rawData)); - continue; - } - fragment.appendChild(tag); - } - } - - return fragment; - }; - - const renderElem = function(elem, optionsCopy) { - for (let i = 0; i < elem.childNodes.length; i++) { - const childNode = elem.childNodes[i]; - if (childNode.nodeType === 3) { - // Text node - const text = childNode.textContent; - if (optionsCopy.mightHaveMath(text)) { - const frag = renderMathInText(text, optionsCopy); - i += frag.childNodes.length - 1; - elem.replaceChild(frag, childNode); - } - } else if (childNode.nodeType === 1) { - // Element node - const shouldRender = - optionsCopy.ignoredTags.indexOf(childNode.nodeName.toLowerCase()) === - -1; - - if (shouldRender) { - renderElem(childNode, optionsCopy); - } - } - // Otherwise, it's something else, and ignore it. - } - }; - - const defaultAutoRenderOptions = { - delimiters: [ - { left: "$$", right: "$$", display: true }, - { left: "\\[", right: "\\]", display: true }, - { left: "\\(", right: "\\)", display: false } - // LaTeX uses this, but it ruins the display of normal `$` in text: - // {left: '$', right: '$', display: false}, - ], - - ignoredTags: [ - "script", - "noscript", - "style", - "textarea", - "pre", - "code", - "svg" - ], - - errorCallback: function(msg, err) { - console.error(msg, err); - } - }; - - const renderMathInElement = function(elem, options) { - if (!elem) { - throw new Error("No element provided to render"); - } - - const optionsCopy = Object.assign({}, defaultAutoRenderOptions, options); - const delimiterStrings = optionsCopy.delimiters.flatMap(d => [ - d.left, - d.right - ]); - const mightHaveMath = text => - delimiterStrings.some(d => text.indexOf(d) !== -1); - optionsCopy.mightHaveMath = mightHaveMath; - renderElem(elem, optionsCopy); - }; - - // Copyright 2018 The Distill Template Authors - - function Mathematics(dom, data) { - let needsCSS = false; - const body = dom.querySelector('body'); - - if (!body) { - console.warn("No body tag found!"); - return; - } - - if (data.katex && data.katex.delimiters) { - global.document = dom; - renderMathInElement(body, data.katex); - } - - // render d-math tags - const mathTags = body.querySelectorAll('d-math'); - if (mathTags.length > 0) { - needsCSS = true; - console.warn(`Prerendering ${mathTags.length} math tags...`); 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+/*! * escape-html * Copyright(c) 2012-2013 TJ Holowaychuk * Copyright(c) 2015 Andreas Lubbe * Copyright(c) 2015 Tiancheng "Timothy" Gu * MIT Licensed */ - - /** - * Module variables. - * @private - */ - - var matchHtmlRegExp = /["'&<>]/; - - /** - * Module exports. - * @public - */ - - var escapeHtml_1 = escapeHtml; - - /** - * Escape special characters in the given string of html. - * - * @param {string} string The string to escape for inserting into HTML - * @return {string} - * @public - */ - - function escapeHtml(string) { - var str = '' + string; - var match = matchHtmlRegExp.exec(str); - - if (!match) { - return str; - } - - var escape; - var html = ''; - var index = 0; - var lastIndex = 0; - - for (index = match.index; index < str.length; index++) { - switch (str.charCodeAt(index)) { - case 34: // " - escape = '"'; - break; - case 38: // & - escape = '&'; - break; - case 39: // ' - escape = '''; - break; - case 60: // < - escape = '<'; - break; - case 62: // > - escape = '>'; - break; - default: - continue; - } - - if (lastIndex !== index) { - html += str.substring(lastIndex, index); - } - - lastIndex = index + 1; - html += escape; - } - - return lastIndex !== index - ? html + str.substring(lastIndex, index) - : html; - } - - // Copyright 2018 The Distill Template Authors - - function Meta(dom, data) { - let head = dom.querySelector('head'); - let appendHead = html => appendHtml(head, html); - - function meta(name, content, force) { - if (content || force) - appendHead(` \n`); - } - - appendHead(` - - - - `); - - if (data.title) { - appendHead(` - ${escapeHtml_1(data.title)} - `); - } - - if (data.url) { - appendHead(` - - `); - } - - - if (data.publishedDate){ - appendHead(` - - - - - `); - } - - if (data.updatedDate) { - appendHead(` - - `); - } - - (data.authors || []).forEach((a) => { - appendHtml(head, ` - `); - }); - - appendHead(` - - - - - - - - - `); - - appendHead(` - - - - - - - - - `); - - // if this is a proprer article, generate Google Scholar meta data - if (data.doiSuffix){ - appendHead(` - \n`); - - meta('citation_title', data.title); - meta('citation_fulltext_html_url', data.url); - meta('citation_volume', data.volume); - meta('citation_issue', data.issue); - meta('citation_firstpage', data.doiSuffix ? `e${data.doiSuffix}` : undefined); - meta('citation_doi', data.doi); - - let journal = data.journal || {}; - meta('citation_journal_title', journal.full_title || journal.title); - meta('citation_journal_abbrev', journal.abbrev_title); - meta('citation_issn', journal.issn); - meta('citation_publisher', journal.publisher); - meta('citation_fulltext_world_readable', '', true); - - if (data.publishedDate){ - meta('citation_online_date', `${data.publishedYear}/${data.publishedMonthPadded}/${data.publishedDayPadded}`); - meta('citation_publication_date', `${data.publishedYear}/${data.publishedMonthPadded}/${data.publishedDayPadded}`); - } - - (data.authors || []).forEach((a) => { - meta('citation_author', `${a.lastName}, ${a.firstName}`); - meta('citation_author_institution', a.affiliation); - }); - } else { - console.warn('No DOI suffix in data; not adding citation meta tags!'); - } - - if (data.citations) { - data.citations.forEach(key => { - if (data.bibliography && data.bibliography.has(key)) { - const entry = data.bibliography.get(key); - meta('citation_reference', citation_meta_content(entry) ); - } else { - console.warn('No bibliography data found for ' + key); - } - }); - } else { - console.warn('No citations found; not adding any references meta tags!'); - } - } - - function appendHtml(el, html) { - el.innerHTML += html; - } - - function citation_meta_content(ref){ - var content = `citation_title=${ref.title};`; - - if (ref.author && ref.author !== '') { - ref.author.split(' and ').forEach(name => { - name = name.trim(); - let last, firsts; - if (name.indexOf(',') != -1){ - last = name.split(',')[0].trim(); - firsts = name.split(',')[1].trim(); - } else { - last = name.split(' ').slice(-1)[0].trim(); - firsts = name.split(' ').slice(0,-1).join(' '); - } - content += `citation_author=${firsts} ${last};`; - }); - } - - if ('year' in ref) { - content += `citation_publication_date=${ref.year};`; - } - - // Special test for arxiv - let arxiv_id_search = /https?:\/\/arxiv\.org\/pdf\/([0-9]*\.[0-9]*)\.pdf/.exec(ref.url); - arxiv_id_search = arxiv_id_search || /https?:\/\/arxiv\.org\/abs\/([0-9]*\.[0-9]*)/.exec(ref.url); - arxiv_id_search = arxiv_id_search || /arXiv preprint arXiv:([0-9]*\.[0-9]*)/.exec(ref.journal); - if (arxiv_id_search && arxiv_id_search[1]){ - content += `citation_arxiv_id=${arxiv_id_search[1]};`; - return content; // arXiv is not considered a journal, so we don't need journal/volume/issue - } - if ('journal' in ref){ - content += `citation_journal_title=${escapeHtml_1(ref.journal)};`; - } - if ('volume' in ref) { - content += `citation_volume=${escapeHtml_1(ref.volume)};`; - } - if ('issue' in ref || 'number' in ref){ - content += `citation_number=${escapeHtml_1(ref.issue || ref.number)};`; - } - return content; - } - - var base = "/*\n * Copyright 2018 The Distill Template Authors\n *\n * Licensed under the Apache License, Version 2.0 (the \"License\");\n * you may not use this file except in compliance with the License.\n * You may obtain a copy of the License at\n *\n * http://www.apache.org/licenses/LICENSE-2.0\n *\n * Unless required by applicable law or agreed to in writing, software\n * distributed under the License is distributed on an \"AS IS\" BASIS,\n * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\n * See the License for the specific language governing permissions and\n * limitations under the License.\n */\n\nhtml {\n font-size: 14px;\n\tline-height: 1.6em;\n /* font-family: \"Libre Franklin\", \"Helvetica Neue\", sans-serif; */\n font-family: -apple-system, BlinkMacSystemFont, \"Segoe UI\", Roboto, Oxygen, Ubuntu, Cantarell, \"Fira Sans\", \"Droid Sans\", \"Helvetica Neue\", Arial, sans-serif;\n /*, \"Apple Color Emoji\", \"Segoe UI Emoji\", \"Segoe UI Symbol\";*/\n text-size-adjust: 100%;\n -ms-text-size-adjust: 100%;\n -webkit-text-size-adjust: 100%;\n}\n\n@media(min-width: 768px) {\n html {\n font-size: 16px;\n }\n}\n\nbody {\n margin: 0;\n}\n\na {\n color: #004276;\n}\n\nfigure {\n margin: 0;\n}\n\ntable {\n\tborder-collapse: collapse;\n\tborder-spacing: 0;\n}\n\ntable th {\n\ttext-align: left;\n}\n\ntable thead {\n border-bottom: 1px solid rgba(0, 0, 0, 0.05);\n}\n\ntable thead th {\n padding-bottom: 0.5em;\n}\n\ntable tbody :first-child td {\n padding-top: 0.5em;\n}\n\npre {\n overflow: auto;\n max-width: 100%;\n}\n\np {\n margin-top: 0;\n margin-bottom: 1em;\n}\n\nsup, sub {\n vertical-align: baseline;\n position: relative;\n top: -0.4em;\n line-height: 1em;\n}\n\nsub {\n top: 0.4em;\n}\n\n.kicker,\n.marker {\n font-size: 15px;\n font-weight: 600;\n color: rgba(0, 0, 0, 0.5);\n}\n\n\n/* Headline */\n\n@media(min-width: 1024px) {\n d-title h1 span {\n display: block;\n }\n}\n\n/* Figure */\n\nfigure {\n position: relative;\n margin-bottom: 2.5em;\n margin-top: 1.5em;\n}\n\nfigcaption+figure {\n\n}\n\nfigure img {\n width: 100%;\n}\n\nfigure svg text,\nfigure svg tspan {\n}\n\nfigcaption,\n.figcaption {\n color: rgba(0, 0, 0, 0.6);\n font-size: 12px;\n line-height: 1.5em;\n}\n\n@media(min-width: 1024px) {\nfigcaption,\n.figcaption {\n font-size: 13px;\n }\n}\n\nfigure.external img {\n background: white;\n border: 1px solid rgba(0, 0, 0, 0.1);\n box-shadow: 0 1px 8px rgba(0, 0, 0, 0.1);\n padding: 18px;\n box-sizing: border-box;\n}\n\nfigcaption a {\n color: rgba(0, 0, 0, 0.6);\n}\n\nfigcaption b,\nfigcaption strong, {\n font-weight: 600;\n color: rgba(0, 0, 0, 1.0);\n}\n"; - - var layout = "/*\n * Copyright 2018 The Distill Template Authors\n *\n * Licensed under the Apache License, Version 2.0 (the \"License\");\n * you may not use this file except in compliance with the License.\n * You may obtain a copy of the License at\n *\n * http://www.apache.org/licenses/LICENSE-2.0\n *\n * Unless required by applicable law or agreed to in writing, software\n * distributed under the License is distributed on an \"AS IS\" BASIS,\n * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\n * See the License for the specific language governing permissions and\n * limitations under the License.\n */\n\n@supports not (display: grid) {\n .base-grid,\n distill-header,\n d-title,\n d-abstract,\n d-article,\n d-appendix,\n distill-appendix,\n d-byline,\n d-footnote-list,\n d-citation-list,\n distill-footer {\n display: block;\n padding: 8px;\n }\n}\n\n.base-grid,\ndistill-header,\nd-title,\nd-abstract,\nd-article,\nd-appendix,\ndistill-appendix,\nd-byline,\nd-footnote-list,\nd-citation-list,\ndistill-footer {\n display: grid;\n justify-items: stretch;\n grid-template-columns: [screen-start] 8px [page-start kicker-start text-start gutter-start middle-start] 1fr 1fr 1fr 1fr 1fr 1fr 1fr 1fr [text-end page-end gutter-end kicker-end middle-end] 8px [screen-end];\n grid-column-gap: 8px;\n}\n\n.grid {\n display: grid;\n grid-column-gap: 8px;\n}\n\n@media(min-width: 768px) {\n .base-grid,\n distill-header,\n d-title,\n d-abstract,\n d-article,\n d-appendix,\n distill-appendix,\n d-byline,\n d-footnote-list,\n d-citation-list,\n distill-footer {\n grid-template-columns: [screen-start] 1fr [page-start kicker-start middle-start text-start] 45px 45px 45px 45px 45px 45px 45px 45px [ kicker-end text-end gutter-start] 45px [middle-end] 45px [page-end gutter-end] 1fr [screen-end];\n grid-column-gap: 16px;\n }\n\n .grid {\n grid-column-gap: 16px;\n }\n}\n\n@media(min-width: 1000px) {\n .base-grid,\n distill-header,\n d-title,\n d-abstract,\n d-article,\n d-appendix,\n distill-appendix,\n d-byline,\n d-footnote-list,\n d-citation-list,\n distill-footer {\n grid-template-columns: [screen-start] 1fr [page-start kicker-start] 50px [middle-start] 50px [text-start kicker-end] 50px 50px 50px 50px 50px 50px 50px 50px [text-end gutter-start] 50px [middle-end] 50px [page-end gutter-end] 1fr [screen-end];\n grid-column-gap: 16px;\n }\n\n .grid {\n grid-column-gap: 16px;\n }\n}\n\n@media(min-width: 1180px) {\n .base-grid,\n distill-header,\n d-title,\n d-abstract,\n d-article,\n d-appendix,\n distill-appendix,\n d-byline,\n d-footnote-list,\n d-citation-list,\n distill-footer {\n grid-template-columns: [screen-start] 1fr [page-start kicker-start] 60px [middle-start] 60px [text-start kicker-end] 60px 60px 60px 60px 60px 60px 60px 60px [text-end gutter-start] 60px [middle-end] 60px [page-end gutter-end] 1fr [screen-end];\n grid-column-gap: 32px;\n }\n\n .grid {\n grid-column-gap: 32px;\n }\n}\n\n\n\n\n.base-grid {\n grid-column: screen;\n}\n\n/* .l-body,\nd-article > * {\n grid-column: text;\n}\n\n.l-page,\nd-title > *,\nd-figure {\n grid-column: page;\n} */\n\n.l-gutter {\n grid-column: gutter;\n}\n\n.l-text,\n.l-body {\n grid-column: text;\n}\n\n.l-page {\n grid-column: page;\n}\n\n.l-body-outset {\n grid-column: middle;\n}\n\n.l-page-outset {\n grid-column: page;\n}\n\n.l-screen {\n grid-column: screen;\n}\n\n.l-screen-inset {\n grid-column: screen;\n padding-left: 16px;\n padding-left: 16px;\n}\n\n\n/* Aside */\n\nd-article aside {\n grid-column: gutter;\n font-size: 12px;\n line-height: 1.6em;\n color: rgba(0, 0, 0, 0.6)\n}\n\n@media(min-width: 768px) {\n aside {\n grid-column: gutter;\n }\n\n .side {\n grid-column: gutter;\n }\n}\n"; - - var print = "/*\n * Copyright 2018 The Distill Template Authors\n *\n * Licensed under the Apache License, Version 2.0 (the \"License\");\n * you may not use this file except in compliance with the License.\n * You may obtain a copy of the License at\n *\n * http://www.apache.org/licenses/LICENSE-2.0\n *\n * Unless required by applicable law or agreed to in writing, software\n * distributed under the License is distributed on an \"AS IS\" BASIS,\n * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\n * See the License for the specific language governing permissions and\n * limitations under the License.\n */\n\n@media print {\n\n @page {\n size: 8in 11in;\n @bottom-right {\n content: counter(page) \" of \" counter(pages);\n }\n }\n\n html {\n /* no general margins -- CSS Grid takes care of those */\n }\n\n p, code {\n page-break-inside: avoid;\n }\n\n h2, h3 {\n page-break-after: avoid;\n }\n\n d-header {\n visibility: hidden;\n }\n\n d-footer {\n display: none!important;\n }\n\n}\n"; - - var byline = "/*\n * Copyright 2018 The Distill Template Authors\n *\n * Licensed under the Apache License, Version 2.0 (the \"License\");\n * you may not use this file except in compliance with the License.\n * You may obtain a copy of the License at\n *\n * http://www.apache.org/licenses/LICENSE-2.0\n *\n * Unless required by applicable law or agreed to in writing, software\n * distributed under the License is distributed on an \"AS IS\" BASIS,\n * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\n * See the License for the specific language governing permissions and\n * limitations under the License.\n */\n\nd-byline {\n contain: style;\n overflow: hidden;\n border-top: 1px solid rgba(0, 0, 0, 0.1);\n font-size: 0.8rem;\n line-height: 1.8em;\n padding: 1.5rem 0;\n min-height: 1.8em;\n}\n\n\nd-byline .byline {\n grid-template-columns: 1fr 1fr;\n grid-column: text;\n}\n\n@media(min-width: 768px) {\n d-byline .byline {\n grid-template-columns: 1fr 1fr 1fr 1fr;\n }\n}\n\nd-byline .authors-affiliations {\n grid-column-end: span 2;\n grid-template-columns: 1fr 1fr;\n margin-bottom: 1em;\n}\n\n@media(min-width: 768px) {\n d-byline .authors-affiliations {\n margin-bottom: 0;\n }\n}\n\nd-byline h3 {\n font-size: 0.6rem;\n font-weight: 400;\n color: rgba(0, 0, 0, 0.5);\n margin: 0;\n text-transform: uppercase;\n}\n\nd-byline p {\n margin: 0;\n}\n\nd-byline a,\nd-article d-byline a {\n color: rgba(0, 0, 0, 0.8);\n text-decoration: none;\n border-bottom: none;\n}\n\nd-article d-byline a:hover {\n text-decoration: underline;\n border-bottom: none;\n}\n\nd-byline p.author {\n font-weight: 500;\n}\n\nd-byline .affiliations {\n\n}\n"; - - var article = "/*\n * Copyright 2018 The Distill Template Authors\n *\n * Licensed under the Apache License, Version 2.0 (the \"License\");\n * you may not use this file except in compliance with the License.\n * You may obtain a copy of the License at\n *\n * http://www.apache.org/licenses/LICENSE-2.0\n *\n * Unless required by applicable law or agreed to in writing, software\n * distributed under the License is distributed on an \"AS IS\" BASIS,\n * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\n * See the License for the specific language governing permissions and\n * limitations under the License.\n */\n\nd-article {\n contain: layout style;\n overflow-x: hidden;\n border-top: 1px solid rgba(0, 0, 0, 0.1);\n padding-top: 2rem;\n color: rgba(0, 0, 0, 0.8);\n}\n\nd-article > * {\n grid-column: text;\n}\n\n@media(min-width: 768px) {\n d-article {\n font-size: 16px;\n }\n}\n\n@media(min-width: 1024px) {\n d-article {\n font-size: 1.06rem;\n line-height: 1.7em;\n }\n}\n\n\n/* H2 */\n\n\nd-article .marker {\n text-decoration: none;\n border: none;\n counter-reset: section;\n grid-column: kicker;\n line-height: 1.7em;\n}\n\nd-article .marker:hover {\n border: none;\n}\n\nd-article .marker span {\n padding: 0 3px 4px;\n border-bottom: 1px solid rgba(0, 0, 0, 0.2);\n position: relative;\n top: 4px;\n}\n\nd-article .marker:hover span {\n color: rgba(0, 0, 0, 0.7);\n border-bottom: 1px solid rgba(0, 0, 0, 0.7);\n}\n\nd-article h2 {\n font-weight: 600;\n font-size: 24px;\n line-height: 1.25em;\n margin: 2rem 0 1.5rem 0;\n border-bottom: 1px solid rgba(0, 0, 0, 0.1);\n padding-bottom: 1rem;\n}\n\n@media(min-width: 1024px) {\n d-article h2 {\n font-size: 36px;\n }\n}\n\n/* H3 */\n\nd-article h3 {\n font-weight: 700;\n font-size: 18px;\n line-height: 1.4em;\n margin-bottom: 1em;\n margin-top: 2em;\n}\n\n@media(min-width: 1024px) {\n d-article h3 {\n font-size: 20px;\n }\n}\n\n/* H4 */\n\nd-article h4 {\n font-weight: 600;\n text-transform: uppercase;\n font-size: 14px;\n line-height: 1.4em;\n}\n\nd-article a {\n color: inherit;\n}\n\nd-article p,\nd-article ul,\nd-article ol,\nd-article blockquote {\n margin-top: 0;\n margin-bottom: 1em;\n margin-left: 0;\n margin-right: 0;\n}\n\nd-article blockquote {\n border-left: 2px solid rgba(0, 0, 0, 0.2);\n padding-left: 2em;\n font-style: italic;\n color: rgba(0, 0, 0, 0.6);\n}\n\nd-article a {\n border-bottom: 1px solid rgba(0, 0, 0, 0.4);\n text-decoration: none;\n}\n\nd-article a:hover {\n border-bottom: 1px solid rgba(0, 0, 0, 0.8);\n}\n\nd-article .link {\n text-decoration: underline;\n cursor: pointer;\n}\n\nd-article ul,\nd-article ol {\n padding-left: 24px;\n}\n\nd-article li {\n margin-bottom: 1em;\n margin-left: 0;\n padding-left: 0;\n}\n\nd-article li:last-child {\n margin-bottom: 0;\n}\n\nd-article pre {\n font-size: 14px;\n margin-bottom: 20px;\n}\n\nd-article hr {\n grid-column: screen;\n width: 100%;\n border: none;\n border-bottom: 1px solid rgba(0, 0, 0, 0.1);\n margin-top: 60px;\n margin-bottom: 60px;\n}\n\nd-article section {\n margin-top: 60px;\n margin-bottom: 60px;\n}\n\nd-article span.equation-mimic {\n font-family: georgia;\n font-size: 115%;\n font-style: italic;\n}\n\nd-article > d-code,\nd-article section > d-code {\n display: block;\n}\n\nd-article > d-math[block],\nd-article section > d-math[block] {\n display: block;\n}\n\n@media (max-width: 768px) {\n d-article > d-code,\n d-article section > d-code,\n d-article > d-math[block],\n d-article section > d-math[block] {\n overflow-x: scroll;\n -ms-overflow-style: none; // IE 10+\n overflow: -moz-scrollbars-none; // Firefox\n }\n\n d-article > d-code::-webkit-scrollbar,\n d-article section > d-code::-webkit-scrollbar,\n d-article > d-math[block]::-webkit-scrollbar,\n d-article section > d-math[block]::-webkit-scrollbar {\n display: none; // Safari and Chrome\n }\n}\n\nd-article .citation {\n color: #668;\n cursor: pointer;\n}\n\nd-include {\n width: auto;\n display: block;\n}\n\nd-figure {\n contain: layout style;\n}\n\n/* KaTeX */\n\n.katex, .katex-prerendered {\n contain: style;\n display: inline-block;\n}\n\n/* Tables */\n\nd-article table {\n border-collapse: collapse;\n margin-bottom: 1.5rem;\n border-bottom: 1px solid rgba(0, 0, 0, 0.2);\n}\n\nd-article table th {\n border-bottom: 1px solid rgba(0, 0, 0, 0.2);\n}\n\nd-article table td {\n border-bottom: 1px solid rgba(0, 0, 0, 0.05);\n}\n\nd-article table tr:last-of-type td {\n border-bottom: none;\n}\n\nd-article table th,\nd-article table td {\n font-size: 15px;\n padding: 2px 8px;\n}\n\nd-article table tbody :first-child td {\n padding-top: 2px;\n}\n"; - - var title = "/*\n * Copyright 2018 The Distill Template Authors\n *\n * Licensed under the Apache License, Version 2.0 (the \"License\");\n * you may not use this file except in compliance with the License.\n * You may obtain a copy of the License at\n *\n * http://www.apache.org/licenses/LICENSE-2.0\n *\n * Unless required by applicable law or agreed to in writing, software\n * distributed under the License is distributed on an \"AS IS\" BASIS,\n * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\n * See the License for the specific language governing permissions and\n * limitations under the License.\n */\n\nd-title {\n padding: 2rem 0 1.5rem;\n contain: layout style;\n overflow-x: hidden;\n}\n\n@media(min-width: 768px) {\n d-title {\n padding: 4rem 0 1.5rem;\n }\n}\n\nd-title h1 {\n grid-column: text;\n font-size: 40px;\n font-weight: 700;\n line-height: 1.1em;\n margin: 0 0 0.5rem;\n}\n\n@media(min-width: 768px) {\n d-title h1 {\n font-size: 50px;\n }\n}\n\nd-title p {\n font-weight: 300;\n font-size: 1.2rem;\n line-height: 1.55em;\n grid-column: text;\n}\n\nd-title .status {\n margin-top: 0px;\n font-size: 12px;\n color: #009688;\n opacity: 0.8;\n grid-column: kicker;\n}\n\nd-title .status span {\n line-height: 1;\n display: inline-block;\n padding: 6px 0;\n border-bottom: 1px solid #80cbc4;\n font-size: 11px;\n text-transform: uppercase;\n}\n"; - - var math = "/*\n * Copyright 2018 The Distill Template Authors\n *\n * Licensed under the Apache License, Version 2.0 (the \"License\");\n * you may not use this file except in compliance with the License.\n * You may obtain a copy of the License at\n *\n * http://www.apache.org/licenses/LICENSE-2.0\n *\n * Unless required by applicable law or agreed to in writing, software\n * distributed under the License is distributed on an \"AS IS\" BASIS,\n * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\n * See the License for the specific language governing permissions and\n * limitations under the License.\n */\n\nspan.katex-display {\n text-align: left;\n padding: 8px 0 8px 0;\n margin: 0.5em 0 0.5em 1em;\n}\n\nspan.katex {\n -webkit-font-smoothing: antialiased;\n color: rgba(0, 0, 0, 0.8);\n font-size: 1.18em;\n}\n"; - - // Copyright 2018 The Distill Template Authors - - const styles = base + layout + title + byline + article + math + print; - - function makeStyleTag(dom) { - - const styleTagId = 'distill-prerendered-styles'; - const prerenderedTag = dom.getElementById(styleTagId); - if (!prerenderedTag) { - const styleTag = dom.createElement('style'); - styleTag.id = styleTagId; - styleTag.type = 'text/css'; - const cssTextTag = dom.createTextNode(styles); - styleTag.appendChild(cssTextTag); - const firstScriptTag = dom.head.querySelector('script'); - dom.head.insertBefore(styleTag, firstScriptTag); - } - - } - - // Copyright 2018 The Distill Template Authors - - function renderTOC(element, headings) { - - let ToC =` - - -

      Table of contents

      -
        `; - - for (const el of headings) { - // should element be included in TOC? - const isInTitle = el.parentElement.tagName == 'D-TITLE'; - const isException = el.getAttribute('no-toc'); - if (isInTitle || isException) continue; - // create TOC entry - const title = el.textContent; - const link = '#' + el.getAttribute('id'); - - let newLine = '
      • ' + '' + title + '' + '
        • '; - if (el.tagName == 'H3') { - newLine = '
          ' + newLine + '
        '; - } else { - newLine += '
        '; - } - ToC += newLine; - - } - - ToC += '
      '; - element.innerHTML = ToC; - } - - // Copyright 2018 The Distill Template Authors - - function TOC(dom) { - const article = dom.querySelector('d-article'); - const toc = dom.querySelector('d-toc'); - if (toc) { - const headings = article.querySelectorAll('h2, h3'); - renderTOC(toc, headings); - toc.setAttribute('prerendered', 'true'); - } - } - - // Copyright 2018 The Distill Template Authors - // - // Licensed under the Apache License, Version 2.0 (the "License"); - // you may not use this file except in compliance with the License. - // You may obtain a copy of the License at - // - // http://www.apache.org/licenses/LICENSE-2.0 - // - // Unless required by applicable law or agreed to in writing, software - // distributed under the License is distributed on an "AS IS" BASIS, - // WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - // See the License for the specific language governing permissions and - // limitations under the License. - - function Typeset(dom) { - - var textNodes = dom.createTreeWalker( - dom.body, - dom.defaultView.NodeFilter.SHOW_TEXT - ); - while (textNodes.nextNode()) { - var n = textNodes.currentNode, - text = n.nodeValue; - if (text && acceptNode(n)) { - text = quotes(text); - text = punctuation(text); - // TODO: Add back support for ligatures once their uppercased versions don't hang Chrome search anymore - // see: https://bugs.chromium.org/p/chromium/issues/detail?id=862648 - // text = ligatures(text); - n.nodeValue = text; - } - } - } - - // 2018-07-11 shancarter@ and ludwigschubert@ no longer know what this was meant to accomplish - // if it was trying to not replace text in any child nodes of those listed here, - // then it does not accomplish that. - function acceptNode(node) { - var parent = node.parentElement; - var isMath = (parent && parent.getAttribute && parent.getAttribute('class')) ? parent.getAttribute('class').includes('katex') || parent.getAttribute('class').includes('MathJax') : false; - return parent && - parent.nodeName !== 'SCRIPT' && - parent.nodeName !== 'STYLE' && - parent.nodeName !== 'CODE' && - parent.nodeName !== 'PRE' && - parent.nodeName !== 'SPAN' && - parent.nodeName !== 'D-HEADER' && - parent.nodeName !== 'D-BYLINE' && - parent.nodeName !== 'D-MATH' && - parent.nodeName !== 'D-CODE' && - parent.nodeName !== 'D-BIBLIOGRAPHY' && - parent.nodeName !== 'D-FOOTER' && - parent.nodeName !== 'D-APPENDIX' && - parent.nodeName !== 'D-FRONTMATTER' && - parent.nodeName !== 'D-TOC' && - parent.nodeType !== 8 && //comment nodes - !isMath; - } - - - /*! - * typeset - Typesetting for the web - * @version v0.1.6 - * @link https://github.com/davidmerfield/Typeset.js - * @author David Merfield - */ - // which has a CC0 license - // http://creativecommons.org/publicdomain/zero/1.0/ - - - function punctuation(text){ - - // Dashes - text = text.replace(/--/g, '\u2014'); - text = text.replace(/\s*\u2014\s*/g,'\u2009\u2014\u2009'); //this has thin spaces - - // Elipses - text = text.replace(/\.\.\./g,'…'); - - // Nbsp for punc with spaces - var NBSP = '\u00a0'; - var NBSP_PUNCTUATION_START = /([«¿¡]) /g; - var NBSP_PUNCTUATION_END = / ([!?:;.,‽»])/g; - - text = text.replace(NBSP_PUNCTUATION_START, '$1' + NBSP); - text = text.replace(NBSP_PUNCTUATION_END, NBSP + '$1'); - - return text; - } - - function quotes(text) { - - text = text - .replace(/(\W|^)"([^\s!?:;.,‽»])/g, '$1\u201c$2') // beginning " - .replace(/(\u201c[^"]*)"([^"]*$|[^\u201c"]*\u201c)/g, '$1\u201d$2') // ending " - .replace(/([^0-9])"/g,'$1\u201d') // remaining " at end of word - .replace(/(\W|^)'(\S)/g, '$1\u2018$2') // beginning ' - .replace(/([a-z])'([a-z])/ig, '$1\u2019$2') // conjunction's possession - .replace(/((\u2018[^']*)|[a-z])'([^0-9]|$)/ig, '$1\u2019$3') // ending ' - .replace(/(\u2018)([0-9]{2}[^\u2019]*)(\u2018([^0-9]|$)|$|\u2019[a-z])/ig, '\u2019$2$3') // abbrev. years like '93 - .replace(/(\B|^)\u2018(?=([^\u2019]*\u2019\b)*([^\u2019\u2018]*\W[\u2019\u2018]\b|[^\u2019\u2018]*$))/ig, '$1\u2019') // backwards apostrophe - .replace(/'''/g, '\u2034') // triple prime - .replace(/("|'')/g, '\u2033') // double prime - .replace(/'/g, '\u2032'); - - // Allow escaped quotes - text = text.replace(/\\“/, '"'); - text = text.replace(/\\”/, '"'); - text = text.replace(/\\’/, '\''); - text = text.replace(/\\‘/, '\''); - - return text; - } - - // Copyright 2018 The Distill Template Authors - - // const template = ` - // if ('IntersectionObserver' in window && - // 'IntersectionObserverEntry' in window && - // 'intersectionRatio' in IntersectionObserverEntry.prototype) { - // // Platform supports IntersectionObserver natively! :-) - // if (!('isIntersecting' in IntersectionObserverEntry.prototype)) { - // Object.defineProperty(IntersectionObserverEntry.prototype, - // 'isIntersecting', { - // get: function () { - // return this.intersectionRatio > 0; - // } - // }); - // } - // } else { - // // Platform does not support webcomponents--loading polyfills synchronously. - // const scriptTag = document.createElement('script'); - // scriptTag.src = '${intersectionObserverPath}'; - // scriptTag.async = false; - // document.currentScript.parentNode.insertBefore(scriptTag, document.currentScript.nextSibling); - // } - // - // if ('registerElement' in document && - // 'import' in document.createElement('link') && - // 'content' in document.createElement('template')) { - // // Platform supports webcomponents natively! :-) - // } else { - // // Platform does not support webcomponents--loading polyfills synchronously. - // const scriptTag = document.createElement('script'); - // scriptTag.src = '${webcomponentPath}'; - // scriptTag.async = false; - // document.currentScript.parentNode.insertBefore(scriptTag, document.currentScript.nextSibling); - // } - // - // - // `; - - - const addBackIn = ` -window.addEventListener('WebComponentsReady', function() { - console.warn('WebComponentsReady'); - const loaderTag = document.createElement('script'); - loaderTag.src = 'https://distill.pub/template.v2.js'; - document.head.insertBefore(loaderTag, document.head.firstChild); -}); -`; - - function render(dom) { - // pull out template script tag - const templateTag = dom.querySelector('script[src*="template.v2.js"]'); - if (templateTag) { - templateTag.parentNode.removeChild(templateTag); - } else { - console.debug('FYI: Did not find template tag when trying to remove it. You may not have added it. Be aware that our polyfills will add it.'); - } - - // add loader - const loaderTag = dom.createElement('script'); - loaderTag.src = 'https://cdnjs.cloudflare.com/ajax/libs/webcomponentsjs/1.0.17/webcomponents-loader.js'; - dom.head.insertBefore(loaderTag, dom.head.firstChild); - - // add loader event listener to add tempalrte back in - const addTag = dom.createElement('script'); - addTag.innerHTML = addBackIn; - dom.head.insertBefore(addTag, dom.head.firstChild); - - - // create polyfill script tag - // const polyfillScriptTag = dom.createElement('script'); - // polyfillScriptTag.innerHTML = template; - // polyfillScriptTag.id = 'polyfills'; - - // insert at appropriate position--before any other script tag - // const firstScriptTag = dom.head.querySelector('script'); - // dom.head.insertBefore(polyfillScriptTag, firstScriptTag); - } - - // Copyright 2018 The Distill Template Authors - - const styles$1 = ` -d-citation-list { - contain: style; -} - -d-citation-list .references { - grid-column: text; -} - -d-citation-list .references .title { - font-weight: 500; -} -`; - - function renderCitationList(element, entries, dom=document) { - if (entries.size > 0) { - element.style.display = ''; - let list = element.querySelector('.references'); - if (list) { - list.innerHTML = ''; - } else { - const stylesTag = dom.createElement('style'); - stylesTag.innerHTML = styles$1; - element.appendChild(stylesTag); - - const heading = dom.createElement('h3'); - heading.id = 'references'; - heading.textContent = 'References'; - element.appendChild(heading); - - list = dom.createElement('ol'); - list.id = 'references-list'; - list.className = 'references'; - element.appendChild(list); - } - - for (const [key, entry] of entries) { - const listItem = dom.createElement('li'); - listItem.id = key; - listItem.innerHTML = bibliography_cite(entry); - list.appendChild(listItem); - } - } else { - element.style.display = 'none'; - } - } - - // Copyright 2018 The Distill Template Authors - - function CitationList(dom, data) { - const citationListTag = dom.querySelector('d-citation-list'); - if (citationListTag) { - const entries = new Map(data.citations.map( citationKey => { - return [citationKey, data.bibliography.get(citationKey)]; - })); - renderCitationList(citationListTag, entries, dom); - citationListTag.setAttribute('distill-prerendered', 'true'); - } - } - - // Copyright 2018 The Distill Template Authors - // - // Licensed under the Apache License, Version 2.0 (the "License"); - // you may not use this file except in compliance with the License. - // You may obtain a copy of the License at - // - // http://www.apache.org/licenses/LICENSE-2.0 - // - // Unless required by applicable law or agreed to in writing, software - // distributed under the License is distributed on an "AS IS" BASIS, - // WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - // See the License for the specific language governing permissions and - // limitations under the License. - - /* - Try to only reorder things that MAY be user defined. - Try to use templates etc to define the order of our own tags. - */ - - function render$1(dom) { - const head = dom.head; - - const metaIE = head.querySelector('meta[http-equiv]'); - head.insertBefore(metaIE, head.firstChild); - - const metaViewport = head.querySelector('meta[name=viewport]'); - head.insertBefore(metaViewport, head.firstChild); - - const metaCharset = head.querySelector('meta[charset]'); - head.insertBefore(metaCharset, head.firstChild); - } - - var logo = "\n \n\n"; - - const headerTemplate = ` - -
      - - -
      -`; - - // Copyright 2018 The Distill Template Authors - - function DistillHeader(dom, data) { - const headerTag = dom.querySelector('distill-header'); - if (!headerTag) { - const header = dom.createElement('distill-header'); - header.innerHTML = headerTemplate; - header.setAttribute('distill-prerendered', ""); - const body = dom.querySelector('body'); - body.insertBefore(header, body.firstChild); - } - } - - // Copyright 2018 The Distill Template Authors - - const styles$2 = ` - -`; - - function appendixTemplate(frontMatter) { - let html = styles$2; - - if (typeof frontMatter.githubUrl !== 'undefined') { - html += ` -

      Updates and Corrections

      -

      `; - if (frontMatter.githubCompareUpdatesUrl) { - html += `View all changes to this article since it was first published.`; - } - html += ` - If you see mistakes or want to suggest changes, please create an issue on GitHub.

      - `; - } - - const journal = frontMatter.journal; - if (typeof journal !== 'undefined' && journal.title === 'Distill') { - html += ` -

      Reuse

      -

      Diagrams and text are licensed under Creative Commons Attribution CC-BY 4.0 with the source available on GitHub, unless noted otherwise. The figures that have been reused from other sources don’t fall under this license and can be recognized by a note in their caption: “Figure from …”.

      - `; - } - - if (typeof frontMatter.publishedDate !== 'undefined') { - html += ` -

      Citation

      -

      For attribution in academic contexts, please cite this work as

      - 
      ${frontMatter.concatenatedAuthors}, "${frontMatter.title}", Distill, ${frontMatter.publishedYear}.
      -

      BibTeX citation

      - 
      ${serializeFrontmatterToBibtex(frontMatter)}
      - `; - } - - return html; - } - - // Copyright 2018 The Distill Template Authors - - function DistillAppendix(dom, data) { - - const appendixTag = dom.querySelector('d-appendix'); - if (!appendixTag) { - console.warn('No appendix tag found!'); - return; - } - const distillAppendixTag = appendixTag.querySelector('distill-appendix'); - if (!distillAppendixTag) { - const distillAppendix = dom.createElement('distill-appendix'); - appendixTag.appendChild(distillAppendix); - distillAppendix.innerHTML = appendixTemplate(data); - } - - } - - const footerTemplate = ` - - -
      - - is dedicated to clear explanations of machine learning - -
      - About - Submit - Prize - Archive - RSS - GitHub - Twitter -      ISSN 2476-0757 -
      - -
      - -`; - - // Copyright 2018 The Distill Template Authors - - function DistillFooter(dom) { - const footerTag = dom.querySelector('distill-footer'); - if(!footerTag) { - const footer = dom.createElement('distill-footer'); - footer.innerHTML = footerTemplate; - const body = dom.querySelector('body'); - body.appendChild(footer); - } - } - - // Copyright 2018 The Distill Template Authors - - const extractors = new Map([ - ['ExtractFrontmatter', ExtractFrontmatter], - ['ExtractBibliography', ExtractBibliography], - ['ExtractCitations', ExtractCitations], - ]); - - const transforms = new Map([ - ['HTML', HTML], - ['makeStyleTag', makeStyleTag], - ['OptionalComponents', OptionalComponents], - ['TOC', TOC], - ['Byline', Byline], - ['Mathematics', Mathematics], - ['Meta', Meta], - ['Typeset', Typeset], - ['Polyfills', render], - ['CitationList', CitationList], - ['Reorder', render$1] // keep last - ]); - - const distillTransforms = new Map([ - ['DistillHeader', DistillHeader], - ['DistillAppendix', DistillAppendix], - ['DistillFooter', DistillFooter], - ]); - - /* Exported functions */ - - function render$2(dom, data, verbose=true) { - let frontMatter; - if (data instanceof FrontMatter) { - frontMatter = data; - } else { - frontMatter = FrontMatter.fromObject(data); - } - // first, we collect static data from the dom - for (const [name, extract] of extractors.entries()) { - if (verbose) console.warn('Running extractor: ' + name); - extract(dom, frontMatter, verbose); - } - // secondly we use it to transform parts of the dom - for (const [name, transform] of transforms.entries()) { - if (verbose) console.warn('Running transform: ' + name); - // console.warn('Running transform: ', transform); - transform(dom, frontMatter, verbose); - } - dom.body.setAttribute('distill-prerendered', ''); - // the function calling us can now use the transformed dom and filled data object - if (data instanceof FrontMatter) ; else { - frontMatter.assignToObject(data); - } - } - - function distillify(dom, data, verbose=true) { - // thirdly, we can use these additional transforms when publishing on the Distill website - for (const [name, transform] of distillTransforms.entries()) { - if (verbose) console.warn('Running distillify: ', name); - transform(dom, data, verbose); - } - } - - function usesTemplateV2(dom) { - const tags = dom.querySelectorAll('script'); - let usesV2 = undefined; - for (const tag of tags) { - const src = tag.src; - if (src.includes('template.v1.js')) { - usesV2 = false; - } else if (src.includes('template.v2.js')) { - usesV2 = true; - } else if (src.includes('template.')) { - throw new Error('Uses distill template, but unknown version?!'); - } - } - - if (usesV2 === undefined) { - throw new Error('Does not seem to use Distill template at all.'); - } else { - return usesV2; - } - } - - const testing = { - extractors: extractors, - transforms: transforms, - distillTransforms: distillTransforms - }; - - exports.FrontMatter = FrontMatter; - exports.distillify = distillify; - exports.render = render$2; - exports.testing = testing; - exports.usesTemplateV2 = usesTemplateV2; - - Object.defineProperty(exports, '__esModule', { value: true }); - -}))); -//# sourceMappingURL=transforms.v2.js.map +// Copyright 2018 The Distill Template Authors +const me='/*\n * Copyright 2018 The Distill Template Authors\n *\n * Licensed under the Apache License, Version 2.0 (the "License");\n * you may not use this file except in compliance with the License.\n * You may obtain a copy of the License at\n *\n * http://www.apache.org/licenses/LICENSE-2.0\n *\n * Unless required by applicable law or agreed to in writing, software\n * distributed under the License is distributed on an "AS IS" BASIS,\n * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\n * See the License for the specific language governing permissions and\n * limitations under the License.\n */\n\nhtml {\n font-size: 14px;\n\tline-height: 1.6em;\n /* font-family: "Libre Franklin", "Helvetica Neue", sans-serif; */\n font-family: -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, Oxygen, Ubuntu, Cantarell, "Fira Sans", "Droid Sans", "Helvetica Neue", Arial, sans-serif;\n /*, "Apple Color Emoji", "Segoe UI Emoji", "Segoe UI Symbol";*/\n text-size-adjust: 100%;\n -ms-text-size-adjust: 100%;\n -webkit-text-size-adjust: 100%;\n}\n\n@media(min-width: 768px) {\n html {\n font-size: 16px;\n }\n}\n\nbody {\n margin: 0;\n}\n\na {\n color: #004276;\n}\n\nfigure {\n margin: 0;\n}\n\ntable {\n\tborder-collapse: collapse;\n\tborder-spacing: 0;\n}\n\ntable th {\n\ttext-align: left;\n}\n\ntable thead {\n border-bottom: 1px solid rgba(0, 0, 0, 0.05);\n}\n\ntable thead th {\n padding-bottom: 0.5em;\n}\n\ntable tbody :first-child td {\n padding-top: 0.5em;\n}\n\npre {\n overflow: auto;\n max-width: 100%;\n}\n\np {\n margin-top: 0;\n margin-bottom: 1em;\n}\n\nsup, sub {\n vertical-align: baseline;\n position: relative;\n top: -0.4em;\n line-height: 1em;\n}\n\nsub {\n top: 0.4em;\n}\n\n.kicker,\n.marker {\n font-size: 15px;\n font-weight: 600;\n color: rgba(0, 0, 0, 0.5);\n}\n\n\n/* Headline */\n\n@media(min-width: 1024px) {\n d-title h1 span {\n display: block;\n }\n}\n\n/* Figure */\n\nfigure {\n position: relative;\n margin-bottom: 2.5em;\n margin-top: 1.5em;\n}\n\nfigcaption+figure {\n\n}\n\nfigure img {\n width: 100%;\n}\n\nfigure svg text,\nfigure svg tspan {\n}\n\nfigcaption,\n.figcaption {\n color: rgba(0, 0, 0, 0.6);\n font-size: 12px;\n line-height: 1.5em;\n}\n\n@media(min-width: 1024px) {\nfigcaption,\n.figcaption {\n font-size: 13px;\n }\n}\n\nfigure.external img {\n background: white;\n border: 1px solid rgba(0, 0, 0, 0.1);\n box-shadow: 0 1px 8px rgba(0, 0, 0, 0.1);\n padding: 18px;\n box-sizing: border-box;\n}\n\nfigcaption a {\n color: rgba(0, 0, 0, 0.6);\n}\n\nfigcaption b,\nfigcaption strong, {\n font-weight: 600;\n color: rgba(0, 0, 0, 1.0);\n}\n'+'/*\n * Copyright 2018 The Distill Template Authors\n *\n * Licensed under the Apache License, Version 2.0 (the "License");\n * you may not use this file except in compliance with the License.\n * You may obtain a copy of the License at\n *\n * http://www.apache.org/licenses/LICENSE-2.0\n *\n * Unless required by applicable law or agreed to in writing, software\n * distributed under the License is distributed on an "AS IS" BASIS,\n * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\n * See the License for the specific language governing permissions and\n * limitations under the License.\n */\n\n@supports not (display: grid) {\n .base-grid,\n distill-header,\n d-title,\n d-abstract,\n d-article,\n d-appendix,\n distill-appendix,\n d-byline,\n d-footnote-list,\n d-citation-list,\n distill-footer {\n display: block;\n padding: 8px;\n }\n}\n\n.base-grid,\ndistill-header,\nd-title,\nd-abstract,\nd-article,\nd-appendix,\ndistill-appendix,\nd-byline,\nd-footnote-list,\nd-citation-list,\ndistill-footer {\n display: grid;\n 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\ No newline at end of file diff --git a/assets/js/zoom.js b/assets/js/zoom.js index c8610d61..2a8bc1fb 100644 --- a/assets/js/zoom.js +++ b/assets/js/zoom.js @@ -1,8 +1 @@ -// Initialize medium zoom. -$(document).ready(function() { - medium_zoom = mediumZoom('[data-zoomable]', { - margin: 100, - background: getComputedStyle(document.documentElement) - .getPropertyValue('--global-bg-color') + 'ee', // + 'ee' for trasparency. - }) -}); +$(document).ready(function(){medium_zoom=mediumZoom("[data-zoomable]",{margin:100,background:getComputedStyle(document.documentElement).getPropertyValue("--global-bg-color")+"ee"})}); \ No newline at end of file diff --git a/atom.xml b/atom.xml index 15eed6ca..f45fe044 100644 --- a/atom.xml +++ b/atom.xml @@ -1,28 +1 @@ ---- -layout: null ---- - - - - - {{ site.title }} - - - {{ site.time | date_to_xmlschema }} - {{ site.url }} - - {{ site.author.name }} - {{ site.author.email }} - - - {% for post in site.posts %} - - {{ post.title }} - - {{ post.date | date_to_xmlschema }} - {{ site.url }}{{ site.baseurl }}{{ post.id }} - {{ post.content | xml_escape }} - - {% endfor %} - - + 6.S898 Deep Learning Blogs 2023 2023-10-19T16:53:28+00:00 https://deep-learning-mit.github.io A Match Made in Drug Discovery - Marrying Geometric and Diffusion Models 2023-02-17T00:00:00+00:00 https://deep-learning-mit.github.io/staging/blog/2023/test <h1 id="a-match-made-in-drug-discovery-marrying-geometric-and-diffusion-models">A Match Made in Drug Discovery: Marrying Geometric and Diffusion Models</h1> <h2 id="introduction">Introduction</h2> <p>With the initial breakthrough of the Denoising Diffusion <d-cite key="ho2020denoising"></d-cite>, diffusion models have evolved into a powerful tool for a wide range of applications in machine learning, including image generation and text generation. The rise and the recent release of Stable Diffusion <d-cite key="rombach2022high"></d-cite> in August 2022 has shown superior performance in a wide range of practical applications - from artistic and creative projects to scientific and industrial ones and has recently paved its way into the natural sciences, which includes the field of drug discovery <d-cite key="zhang2023sdegen,jing2022torsional"></d-cite>.</p> <p>Data-driven applications have increasingly been shown to accelerate solving diverse problems in the drug discovery pipeline <d-cite key="CHEN20181241"></d-cite> – from the use of predictive analytical methods for target identification and lead optimization, to the analysis of large-scale biological data for drug repurposing and personalized medicine. To limit the scope of the blog post, we will only focus on the use of generative methods in <strong>molecular conformation generation</strong>.</p> <h2 id="motivation">Motivation</h2> <p>Generating molecular conformations is a task fundamental to cheminformatics and drug discovery. The conformation of a molecule refers to the three-dimensional (3D) coordinates of all the atoms in a molecule in a 3D Euclidean space, which can be interconverted by rotations about formally single bonds <d-cite key="nature_def"></d-cite>. It allows for the prediction of the physical and chemical properties and interactions of molecules based on their possible 3D conformations, as well as their biological activity. In drug discovery, it is integral to obtain all the possible conformations of molecules for various tasks, such as three-dimensional quantitative structure-activity relationships (3D-QSAR), pharmacophore searching, molecular docking and thermodynamic calculations. Deep generative modelling, which aims to learn complex data distributions, is a recent promising approach to tackle the conformation generation problem <d-cite key="zhang2023sdegen"></d-cite>. When studying molecules it is important to understand them as three-dimensional structures formed by atoms bonded to each other. To encode the chemical properties, molecules could be represented as graphs where atoms (nodes) are connected by bonds (edges). Representing molecules as 3D molecular graphs captures the spatial arrangement of a molecule, which in turn determines its chemical property. A molecule could take up any conformation based on all possible permutations and combinations of spatial arrangements of atoms. However, some conformations may not occur physically, due to e.g steric hindrance, which arises when the spatial arrangement of atoms leads to unfavourable interactions/repulsive forces, leading to a higher energy state and less stable conformation.</p> <p>Therefore, we are only interested in conformations that fall in stable low-energy minima, as these low-energy conformations are the ones that the molecule will most likely adopt under natural conditions and play a crucial role in determining the molecule’s behaviour and properties. By identifying and characterizing the low-energy conformations, researchers gain insights into their stability, reactivity and interactions with other molecules.</p> <h2 id="formulating-the-conformation-generation-problem">Formulating the conformation generation problem</h2> <figure> <picture> <source class="responsive-img-srcset" media="(max-width: 480px)" srcset="/staging/assets/img/2022-12-01-test/formulation-480.webp" /> <source class="responsive-img-srcset" media="(max-width: 800px)" srcset="/staging/assets/img/2022-12-01-test/formulation-800.webp" /> <source class="responsive-img-srcset" media="(max-width: 1400px)" srcset="/staging/assets/img/2022-12-01-test/formulation-1400.webp" /> <!-- Fallback to the original file --> <img src="/staging/assets/img/2022-12-01-test/formulation.png" class="img-fluid" width="auto" height="auto" onerror="this.onerror=null; $('.responsive-img-srcset').remove();" /> </picture> </figure> <p>A formulation of the conformation generation problem, adapted from <d-cite key="xu2022geodiff"></d-cite></p> <table> <tbody> <tr> <td>We can formulate the problem of conformation generation as a conditional generative problem where we aim to generate stable conformations \(C\) from a molecule’s graph \(G\). For each \(G\) given its conformations \(C\) as i.i.d samples from an underlying Boltzmann distribution <d-cite key="noe2019boltzmann"></d-cite>, our goal is to learn a generative model $$p_\theta(C</td> <td>G)$$ to draw possible conformations from.</td> </tr> </tbody> </table> <h3 id="roto-translation-equivariance">Roto-translation equivariance</h3> <figure> <picture> <source class="responsive-img-srcset" media="(max-width: 480px)" srcset="/staging/assets/img/2022-12-01-test/roto-trans-480.webp" /> <source class="responsive-img-srcset" media="(max-width: 800px)" srcset="/staging/assets/img/2022-12-01-test/roto-trans-800.webp" /> <source class="responsive-img-srcset" media="(max-width: 1400px)" srcset="/staging/assets/img/2022-12-01-test/roto-trans-1400.webp" /> <!-- Fallback to the original file --> <img src="/staging/assets/img/2022-12-01-test/roto-trans.png" class="img-fluid" width="auto" height="auto" onerror="this.onerror=null; $('.responsive-img-srcset').remove();" /> </picture> </figure> <p>A visualisation of roto-translation equivariance, adapted from <d-cite key="xu2022geodiff"></d-cite></p> <p>To generate stable molecular conformations, we need an algorithm that preserves roto-translation equivariance of the conformations that previous work has not focused on. To explain this property, let us delve into what equivariance is. A representation \(φ\) is equivariant with a transformation \(g\) of the input if the transformation can be transferred to the representation output. Invariance is a special case of equivariance obtained when the transformation is the identity map <d-cite key="lenc2015understanding"></d-cite>.</p> <p>In the context of molecular conformations, we have to achieve the special case of equivariance in terms of rotation and translation, namely, roto-translation equivariance of the conformations which ensures that however the molecule is rotated or translated, the estimated (conditional) likelihood should be unaffected. GeoDiff considers the SE(3) Lie group which can be used to represent rotation and translation in 3D space <d-cite key="eade_2017"></d-cite>.</p> <h2 id="decomposing-geodiff">Decomposing GeoDiff</h2> <figure> <picture> <source class="responsive-img-srcset" media="(max-width: 480px)" srcset="/staging/assets/img/2022-12-01-test/geodiff_main-480.webp" /> <source class="responsive-img-srcset" media="(max-width: 800px)" srcset="/staging/assets/img/2022-12-01-test/geodiff_main-800.webp" /> <source class="responsive-img-srcset" media="(max-width: 1400px)" srcset="/staging/assets/img/2022-12-01-test/geodiff_main-1400.webp" /> <!-- Fallback to the original file --> <img src="/staging/assets/img/2022-12-01-test/geodiff_main.png" class="img-fluid" width="auto" height="auto" onerror="this.onerror=null; $('.responsive-img-srcset').remove();" /> </picture> </figure> <p>The diffusion model of GeoDiff, adapted from <d-cite key="xu2022geodiff"></d-cite></p> <p><strong>Legend</strong>:</p> <ul> <li>\(C^{0}\) denotes the ground truth conformations</li> <li>\(C^{t}\), where \(t = 1,···, T\) is the index for diffusion steps and \(C^{t}\), is the sequence of latent variables with the same dimension</li> <li>\(q(C^{t} \mid C^{t-1})\) is the fixed posterior distribution</li> <li>\(p_\theta(C^{t-1} \mid G, C^{t})\) are the Markov kernels through which the conformations are refined</li> </ul> <h3 id="a-primer-on-diffusion-models">A primer on Diffusion Models</h3> <p>A diffusion probabilistic model <d-cite key="sohl2015deep"></d-cite> can be described as a latent variable model with two processes: the forward and the reverse generative processes. Intuitively, the diffusion process progressively injects small noises into \(C^{0}\), while the generative process learns to revert the diffusion process by gradually eliminating the noise to recover the ground truth. Diffusion models are trained by adding noise to the input, which the model then learns how to remove.</p> <p>In this blog post, we use the GeoDiff implementation of diffusion models to explain how the diffusion model works and how it is being used for the geometric representation of molecules. The implementation of the diffusion model in GeoDiff is inspired by the DDPM paper <d-cite key="ho2020denoising"></d-cite>. To give a quick overview, the forward process \(q\) transforms the original input into complete noise over a certain number of timesteps and follows a normal distribution; the \(p_0\) involves denoising complete noise to the actual input using a neural network.</p> <h3 id="forward-process">Forward process</h3> <p>Let \(q(\mathbf{C}^0)\) be the real data distribution of molecular conformation. We can sample from this distribution to get a conformation, \(\mathbf{C}^0 \sim q(\mathbf{C}^0)\). We define the forward diffusion process which adds Gaussian noise at each time step \(t\), according to a known variance schedule \beta_t which can be linear, quadratic, cosine, etc. as follows:</p> \[\begin{align}\tag{1} q\left(\mathcal{C}^{1: T} \mid \mathcal{C}^0\right)=\prod_{t=1}^T q\left(\mathcal{C}^t \mid \mathcal{C}^{t-1}\right) \end{align}\] <p>where \(\quad q\left(\mathcal{C}^t \mid \mathcal{C}^{t-1}\right)=\mathcal{N}\left(\mathcal{C}^t ; \sqrt{1-\beta_t} \mathcal{C}^{t-1}, \beta_t I\right)\)</p> <p>Instead of having to compute \(q\left(\mathcal{C}^t \mid \mathcal{C}^{t-1}\right)\) at every timestep \(t\), we could compute at an arbitrary timestep in closed form:</p> \[\begin{equation}\tag{2} q\left(\mathcal{C}^t \mid \mathcal{C}^0\right)=\mathcal{N}\left(\mathcal{C}^t ; \sqrt{\bar{\alpha}_t} \mathcal{C}^0,\left(1-\bar{\alpha}_t\right) I\right) \end{equation}\] <p>where \(\alpha_t=1-\beta_t\) and \(\bar{\alpha}_t=\prod_{s=1}^t \alpha_s\)</p> <p>Thus with a sufficiently large number of timesteps, the forward process could convert \(\mathcal{C}^0\) to whitened isotropic Gaussian and so we could set \(p\left(\mathcal{C}^T\right)\) as a standard Gaussian distribution.</p> <h3 id="reverse-process">Reverse Process</h3> <p>The reverse process involved recovering the original conformation \(\mathcal{C}^0\) from the white noise \(\mathcal{C}^T\) . We need the conditional distribution \(p_\theta\left(\mathcal{C}^{t-1} \mid \mathcal{G}, \mathcal{C}^t\right)\) to sample some random Gaussian noise \(\mathcal{C}^t\), and “denoise” gradually to end up with a sample from the real distribution \(\mathcal{C}^0\).</p> <p>However, the conditional distribution of \(p_\theta\left(\mathcal{C}^{t-1} \mid \mathcal{G}, \mathcal{C}^t\right)\) is intractable as it requires knowing the distribution of all possible conformations in order to calculate this conditional probability. Hence, a neural network could be used to learn this conditional probability distribution, let’s call it \(p_\theta\), with \(\theta\) being the parameters of the neural network, updated by gradient descent. Thus, we formulate the reverse process as a conditional Markov chain with learnable transitions:</p> \[\begin{align*}\tag{3} p_\theta\left(\mathcal{C}^{0: T-1} \mid \mathcal{G}, \mathcal{C}^T\right)=\prod_{t=1}^T p_\theta\left(\mathcal{C}^{t-1} \mid \mathcal{G}, \mathcal{C}^t\right) \end{align*}\] <p>where \(\quad p_\theta\left(\mathcal{C}^{t-1} \mid \mathcal{G}, \mathcal{C}^t\right)=\mathcal{N}\left(\mathcal{C}^{t-1} ; \mu_\theta\left(\mathcal{G}, \mathcal{C}^t, t\right), \sigma_t^2 I\right)\)</p> <p>Hence, the neural network in the reverse process needs to learn/represent the mean and variance. However, just like the DDPM paper, GeoDiff also lets the variance be user-defined and fixed, and \(\mu_\theta\) is the neural network that estimates means.</p> <p>GeoDiff uses a parametrisation trick inspired by the diffusion model implementation from the DDPM paper such that this parametrisation resembles Langevin dynamics and simplifies the diffusion model’s variational bound to an objective that resembles denoising score matching. Moreover, in the context of molecular conformation generation, this parametrisation trick is analogous to the physical force fields <d-cite key="schutt2017schnet, zhang2018deep, hu2021forcenet, shuaibi2021rotation"></d-cite>, which also gradually push particles towards convergence around the equilibrium states, and is defined by the following equation:</p> \[\begin{align*}\tag{4} \mu_\theta\left(\mathcal{C}^t, t\right)=\frac{1}{\sqrt{\alpha_t}}\left(\mathcal{C}^t-\frac{\beta_t}{\sqrt{1-\bar{\alpha}_t}} \epsilon_\theta\left(\mathcal{G}, \mathcal{C}^t, t\right)\right) \end{align*}\] <p>where \(\epsilon_\theta\) are neural networks with trainable parameters \(\theta\).</p> <p>Now, we need to make \(\epsilon_\theta\) roto-translational equivariant which we elaborate on in the next section.</p> <h3 id="making-the-reverse-process-roto-translation-equivariant">Making the reverse process roto-translation equivariant</h3> <p>Firstly, we need to assume the prior distribution of the conformations and the intermediary conformations generated during the forward process are systems with zero centre of mass (CoM) or CoM-free systems <d-cite key="kohler2020equivariant"></d-cite>. By considering CoM-free systems, moving the particles to zero CoM can always ensure translational invariance in the Markov kernels.</p> <p>GeoDiff employs the use of an equivariant convolutional layer, named graph field network (GFN) inspired by <d-cite key="thomas2018tensor, satorras2021n"></d-cite>. In the \(l\)-th layer, GFN takes node embeddings \(h_l \in \mathbb{R}^{n \times b}\) (\(b\) denotes the feature dimension) and corresponding coordinate embeddings \(x_l \in \mathbb{R}^{n \times 3}\) as inputs, and outputs \(h_{l+1}\) and \(x_{l+1}\) as follows:</p> \[\begin{align} \tag{5} &amp; \mathbf{m}_{i j}=\Phi_m\left(\mathbf{h}_i^l, \mathbf{h}_j^l,\left\|\mathbf{x}_i^l-\mathbf{x}_j^l\right\|^2, e_{i j} ; \theta_m\right) \\ \tag{6} &amp; \mathbf{h}_i^{l+1}=\Phi_h\left(\mathbf{h}_i^l, \sum_{j \in \mathcal{N}(i)} \mathbf{m}_{i j} ; \theta_h\right) \\ &amp; \mathbf{x}_i^{l+1}=\sum_{j \in \mathcal{N}(i)} \frac{1}{d_{i j}}\left(\mathbf{c}_i-\mathbf{c}_j\right) \Phi_x\left(\mathbf{m}_{i j} ; \theta_x\right) \tag{7} \end{align}\] <p>where</p> <ul> <li>\(\Phi\) are feed-forward networks</li> <li>\(d_{ij}\) are interatomic distances</li> <li>\(\mathcal{N}(i)\) is the neighbourhood of the \(i\)-th node, which consists of both connected atoms and other ones within a radius threshold \(\tau\).</li> </ul> <p>By introducing the neighbourhood function, we enable the model to accurately represent distant interactions between atoms, as well as the ability to handle partially disconnected molecular graphs. Initial embeddings \(h_0\) are combinations of atom and timestep embeddings, and \(x_0\) are atomic coordinates. A key change in GFN compared to a vanilla GNN is \(x\) being updated as a combination of radial directions weighted by \(\Phi_x\): \(\mathbb{R}^b \rightarrow \mathbb{R}\) as seen in equation \((7)\). This allows the roto-translation equivariance property to be induced in the reverse process.</p> <h3 id="improved-training-objective">Improved Training Objective</h3> <p>Now, we need to set the training objective having considered the reverse process dynamics. We cannot compute the exact log-likelihood of the generative process, as it involves computing the likelihood of the observed molecular conformation given the parameters of the model. However, this likelihood is difficult to compute, as it would require integrating over all possible intermediate conformations, giving us a high-dimensional integral that cannot be solved analytically. Therefore, the authors have opted to maximize the variational lower bound (ELBO), as defined below:</p> \[\begin{aligned} \mathbb{E}\left[\log p_\theta\left(\mathcal{C}^0 \mid \mathcal{G}\right)\right] &amp; =\mathbb{E}\left[\log \mathbb{E}_{q\left(\mathcal{C}^{1: T} \mid \mathcal{C}^0\right)} \frac{p_\theta\left(\mathcal{C}^{0: T} \mid \mathcal{G}\right)}{q\left(\mathcal{C}^{1: T} \mid \mathcal{C}^0\right)}\right] \\ &amp; \geq-\mathbb{E}_q\left[\sum_{t=1}^T D_{\mathrm{KL}}\left(q\left(\mathcal{C}^{t-1} \mid \mathcal{C}^t, \mathcal{C}^0\right) \| p_\theta\left(\mathcal{C}^{t-1} \mid \mathcal{C}^t, \mathcal{G}\right)\right)\right]:=-\mathcal{L}_{\mathrm{ELBO}}\end{aligned}\] <p>where \(q\left(\mathcal{C}^{t-1} \mid \mathcal{C}^t, \mathcal{C}^0\right)\) is analytically tractable as \(\mathcal{N}\left(\frac{\sqrt{\bar{\alpha}_{t-1}} \beta_t}{1-\bar{\alpha}_t} \mathcal{C}^0+\frac{\sqrt{\alpha_t}\left(1-\bar{\alpha}_{t-1}\right)}{1-\bar{\alpha}_t} \mathcal{C}^t, \frac{1-\bar{\alpha}_{t-1}}{1-\bar{\alpha}_t} \beta_t\right)\).</p> <p>Using the parametrisation trick in the reverse process as seen in equation \((4)\), the ELBO could be simplified by taking the KL divergences between Gaussians as weighted \(\mathcal{L}_2\) distances between the means \(\epsilon_\theta\) and \(\epsilon^3\) as follows: \(\mathcal{L}_{\mathrm{ELBO}}=\sum_{t=1}^T \gamma_t \mathbb{E}_{\left\{\mathcal{C}^0, \mathcal{G}\right\} \sim q\left(\mathcal{C}^0, \mathcal{G}\right), \epsilon \sim \mathcal{N}(0, I)}\left[\left\|\epsilon-\epsilon_\theta\left(\mathcal{G}, \mathcal{C}^t, t\right)\right\|_2^2\right]\) where \(\mathcal{C}^t=\sqrt{\bar{\alpha}_t} \mathcal{C}^0+\sqrt{1-\bar{\alpha}_t} \epsilon\).</p> <p>The idea behind this objective is to independently sample chaotic conformations of different timesteps from \(q\left(C^{t-1} \mid C^t, C^0\right)\), and use \(\epsilon_\theta\) to approximate the noise vector \(\epsilon\).</p> <h3 id="sampling">Sampling</h3> <p>Now, we can generate stable molecular conformations via sampling. Given a graph \(\mathcal{G}\), its geometry \(\mathcal{C}^0\) is generated by first sampling chaotic particles \(\mathcal{C}^T \sim p\left(\mathcal{C}^T\right)\). For each timestep in the reverse process \(t=T, T-\) \(1, \cdots, 1\), we first shift the CoM of the conformation to zero, compute the transition means, \(\mu_\theta\left(\mathcal{G}, \mathcal{C}^t, t\right)\), using equation \((4)\) and sample \(\mathcal{C}^{t-1} \sim\) \(p_\theta\left(\mathcal{C}^{t-1} \mid \mathcal{G}, \mathcal{C}^t\right)\). The sampling algorithm is given in pseudo-code below:</p> <table> <thead> <tr> <th style="text-align: left">Algorithm 1 Sampling Algorithm of GEODIFF</th> </tr> </thead> <tbody> <tr> <td style="text-align: left">Input: the molecular graph \(\mathcal{G}\), the learned reverse model \(\epsilon_\theta\).</td> </tr> <tr> <td style="text-align: left">Output: the molecular conformation \(\mathcal{C}\).</td> </tr> <tr> <td style="text-align: left">1: Sample \(\mathcal{C}^T \sim p\left(\mathcal{C}^T\right)=\mathcal{N}(0, I)\)</td> </tr> <tr> <td style="text-align: left">2: for \(s=T, T-1, \cdots, 1\) do</td> </tr> <tr> <td style="text-align: left">3: \(\quad\) Shift \(\mathcal{C}^s\) to zero CoM</td> </tr> <tr> <td style="text-align: left">4: \(\quad\) Compute \(\mu_\theta\left(\mathcal{C}^s, \mathcal{G}, s\right)\) from \(\epsilon_\theta\left(\mathcal{C}^s, \mathcal{G}, s\right)\) using equation 4</td> </tr> <tr> <td style="text-align: left">5: \(\quad\) Sample \(\mathcal{C}^{s-1} \sim \mathcal{N}\left(\mathcal{C}^{s-1} ; \mu_\theta\left(\mathcal{C}^{\mathcal{s}}, \mathcal{G}, s\right), \sigma_t^2 I\right)\)</td> </tr> <tr> <td style="text-align: left">6: end for</td> </tr> <tr> <td style="text-align: left">7: return \(\mathcal{C}^0\) as $\mathcal{C}$$</td> </tr> </tbody> </table> <h2 id="but-why-generative-models">But why generative models?</h2> <p>The purpose of prediciting molecular conformations is to enable human experts to analyse the properties of the molecules and understand how these properties affect the viability of a molecule as a drug candidate. Therefore, it is important that the molecular conformations generated are diverse to capture the different possible conformations that could occur in nature but the conformations generated should not deviate significantly such that the analysis is affected. To set a threshold for the different possible conformations, the standard metric used has been selecting conformations that are within a certain root-mean-square deviation (RMSD), say a few ångströms, of the true structure.</p> <p>However, the objective of maximizing the proportion of predictions with RMSD within some tolerance \(\epsilon\) is not differentiable and thus, cannot be used for training with stochastic gradient descent. Instead, maximizing the expected proportion of predictions with RMSD &lt; \(\epsilon\) corresponds to maximizing the likelihood of the true structure under the model’s output distribution, in the limit as \(\epsilon\) goes to 0. This concept inspires the development of a generative model, whose objective is to minimize an upper bound on the negative log-likelihood of observed molecular structures under the distribution of the model. As a result, the problem of molecular docking is treated as a task of learning a distribution over possible positions of a ligand molecule conditioned on the protein structure and a diffusion generative model is developed to represent this space. Therefore, this observation has motivated several works on the use of generative models for molecular conformation generation, such as GeoDiff.</p> <h2 id="future-work">Future work</h2> <p>While diffusion models have shown promising results over the past months, there is still a need for further research and development to address some of the limitations and drawbacks of the use of diffusion models in conformer generation. As explained in our blog post, generative models are well-suited for molecular conformation generation. However, there are other kinds of established generative models, such as autoencoders that have been used for the same task <d-cite key="gomez2018automatic"></d-cite>. For instance, comparing diffusion models and autoencoders, diffusion models can handle all noise levels with a single set of parameters, without any bottlenecks, which an autoencoder would have <d-cite key="dieleman2022diffusion"></d-cite>. Thus, it is essential to study the advantages and disadvantages of different types and variants of generative models for conformation generation and understand what changes could be done to them to make them more suitable for molecular conformation.</p> <p>It must be noted that the experiments described in the study are done on benchmark geometric datasets, GEOM-QM9 <d-cite key="ramageom"></d-cite> and GEOM-Drugs <d-cite key="axelrod2022geom"></d-cite>, rather than industrial data, with a relatively small number of samples/drug/molecular compounds. Industry data may exhibit greater variability than standard geometric datasets, as they may be more diverse, complex and subject to greater fluctuations than these geometric datasets, which tend to be more standardized and more predictable.</p> <p>GeoDiff as a framework sets a precedent for future work that could marry the concepts of geometric deep learning and diffusion models across various domains. In the context of drug discovery, it would be interesting to extend this framework to more challenging structures, such as proteins, which may enable more accurate prediction of protein folding, protein-protein interactions and protein-ligand binding positions which would facilitate the design of new drugs and treatments. Additionally, this framework could potentially be applied to other complex systems beyond proteins, such as RNA molecules, to enable more efficient and accurate prediction of their behaviour and properties. Continued research in this area has the potential to revolutionize drug discovery and development, as well as advance our understanding of the fundamental principles governing the behaviour of complex biological systems.</p> <p>Research on the application of diffusion models in the life and natural sciences is still in its infancy, with great potential for improvement in terms of both theory as well as empirical testing. The GeoDiff model could be improved in terms of more efficient sampling and improved likelihood maximization methods. Traditionally, generating samples from diffusion models demand iterative approaches that involve a large number of evaluation steps. Recent work, such as the paper on Torsional Diffusion <d-cite key="jing2022torsional, satorras2021n"></d-cite> was able to speed up the sampling process, while also enhancing the quality of the resulting samples. Experimentally, Torsional Diffusion only takes 5 to 20 steps in comparison to GeoDiff which takes around 5000 steps <d-cite key="galkin_2022"></d-cite>.</p> <p>Looking ahead, GeoDiff has set a clear example for the use of diffusion models on geometric representations which could be extended to several problems, especially in the field of drug discovery. The novel contributions made by</p> <d-cite key="xu2022geodiff"></d-cite> <p>are motivated by the physical characteristics of the molecular conformation generation problem, which has resulted in a strong candidate method for conformation generation that could act as a springboard for even more effective and efficient methods that would eventually benefit the field of drug discovery as a whole.</p> A Match Made in Drug Discovery - Marrying Geometric and Diffusion Models 2023-02-17T00:00:00+00:00 https://deep-learning-mit.github.io/staging/blog/2023/diffusion-is-all-you-need <h1 id="a-match-made-in-drug-discovery-marrying-geometric-and-diffusion-models">A Match Made in Drug Discovery: Marrying Geometric and Diffusion Models</h1> <h2 id="introduction">Introduction</h2> <p>With the initial breakthrough of the Denoising Diffusion <d-cite key="ho2020denoising"></d-cite>, diffusion models have evolved into a powerful tool for a wide range of applications in machine learning, including image generation and text generation. The rise and the recent release of Stable Diffusion <d-cite key="rombach2022high"></d-cite> in August 2022 has shown superior performance in a wide range of practical applications - from artistic and creative projects to scientific and industrial ones and has recently paved its way into the natural sciences, which includes the field of drug discovery <d-cite key="zhang2023sdegen,jing2022torsional"></d-cite>.</p> <p>Data-driven applications have increasingly been shown to accelerate solving diverse problems in the drug discovery pipeline <d-cite key="CHEN20181241"></d-cite> – from the use of predictive analytical methods for target identification and lead optimization, to the analysis of large-scale biological data for drug repurposing and personalized medicine. To limit the scope of the blog post, we will only focus on the use of generative methods in <strong>molecular conformation generation</strong>.</p> <h2 id="motivation">Motivation</h2> <p>Generating molecular conformations is a task fundamental to cheminformatics and drug discovery. The conformation of a molecule refers to the three-dimensional (3D) coordinates of all the atoms in a molecule in a 3D Euclidean space, which can be interconverted by rotations about formally single bonds <d-cite key="nature_def"></d-cite>. It allows for the prediction of the physical and chemical properties and interactions of molecules based on their possible 3D conformations, as well as their biological activity. In drug discovery, it is integral to obtain all the possible conformations of molecules for various tasks, such as three-dimensional quantitative structure-activity relationships (3D-QSAR), pharmacophore searching, molecular docking and thermodynamic calculations. Deep generative modelling, which aims to learn complex data distributions, is a recent promising approach to tackle the conformation generation problem <d-cite key="zhang2023sdegen"></d-cite>. When studying molecules it is important to understand them as three-dimensional structures formed by atoms bonded to each other. To encode the chemical properties, molecules could be represented as graphs where atoms (nodes) are connected by bonds (edges). Representing molecules as 3D molecular graphs captures the spatial arrangement of a molecule, which in turn determines its chemical property. A molecule could take up any conformation based on all possible permutations and combinations of spatial arrangements of atoms. However, some conformations may not occur physically, due to e.g steric hindrance, which arises when the spatial arrangement of atoms leads to unfavourable interactions/repulsive forces, leading to a higher energy state and less stable conformation.</p> <p>Therefore, we are only interested in conformations that fall in stable low-energy minima, as these low-energy conformations are the ones that the molecule will most likely adopt under natural conditions and play a crucial role in determining the molecule’s behaviour and properties. By identifying and characterizing the low-energy conformations, researchers gain insights into their stability, reactivity and interactions with other molecules.</p> <h2 id="formulating-the-conformation-generation-problem">Formulating the conformation generation problem</h2> <figure> <picture> <source class="responsive-img-srcset" media="(max-width: 480px)" srcset="/staging/assets/img/2022-12-01-diffusion-is-all-you-need/formulation-480.webp" /> <source class="responsive-img-srcset" media="(max-width: 800px)" srcset="/staging/assets/img/2022-12-01-diffusion-is-all-you-need/formulation-800.webp" /> <source class="responsive-img-srcset" media="(max-width: 1400px)" srcset="/staging/assets/img/2022-12-01-diffusion-is-all-you-need/formulation-1400.webp" /> <!-- Fallback to the original file --> <img src="/staging/assets/img/2022-12-01-diffusion-is-all-you-need/formulation.png" class="img-fluid" width="auto" height="auto" onerror="this.onerror=null; $('.responsive-img-srcset').remove();" /> </picture> </figure> <p>A formulation of the conformation generation problem, adapted from <d-cite key="xu2022geodiff"></d-cite></p> <table> <tbody> <tr> <td>We can formulate the problem of conformation generation as a conditional generative problem where we aim to generate stable conformations \(C\) from a molecule’s graph \(G\). For each \(G\) given its conformations \(C\) as i.i.d samples from an underlying Boltzmann distribution <d-cite key="noe2019boltzmann"></d-cite>, our goal is to learn a generative model $$p_\theta(C</td> <td>G)$$ to draw possible conformations from.</td> </tr> </tbody> </table> <h3 id="roto-translation-equivariance">Roto-translation equivariance</h3> <figure> <picture> <source class="responsive-img-srcset" media="(max-width: 480px)" srcset="/staging/assets/img/2022-12-01-diffusion-is-all-you-need/roto-trans-480.webp" /> <source class="responsive-img-srcset" media="(max-width: 800px)" srcset="/staging/assets/img/2022-12-01-diffusion-is-all-you-need/roto-trans-800.webp" /> <source class="responsive-img-srcset" media="(max-width: 1400px)" srcset="/staging/assets/img/2022-12-01-diffusion-is-all-you-need/roto-trans-1400.webp" /> <!-- Fallback to the original file --> <img src="/staging/assets/img/2022-12-01-diffusion-is-all-you-need/roto-trans.png" class="img-fluid" width="auto" height="auto" onerror="this.onerror=null; $('.responsive-img-srcset').remove();" /> </picture> </figure> <p>A visualisation of roto-translation equivariance, adapted from <d-cite key="xu2022geodiff"></d-cite></p> <p>To generate stable molecular conformations, we need an algorithm that preserves roto-translation equivariance of the conformations that previous work has not focused on. To explain this property, let us delve into what equivariance is. A representation \(φ\) is equivariant with a transformation \(g\) of the input if the transformation can be transferred to the representation output. Invariance is a special case of equivariance obtained when the transformation is the identity map <d-cite key="lenc2015understanding"></d-cite>.</p> <p>In the context of molecular conformations, we have to achieve the special case of equivariance in terms of rotation and translation, namely, roto-translation equivariance of the conformations which ensures that however the molecule is rotated or translated, the estimated (conditional) likelihood should be unaffected. GeoDiff considers the SE(3) Lie group which can be used to represent rotation and translation in 3D space <d-cite key="eade_2017"></d-cite>.</p> <h2 id="decomposing-geodiff">Decomposing GeoDiff</h2> <figure> <picture> <source class="responsive-img-srcset" media="(max-width: 480px)" srcset="/staging/assets/img/2022-12-01-diffusion-is-all-you-need/geodiff_main-480.webp" /> <source class="responsive-img-srcset" media="(max-width: 800px)" srcset="/staging/assets/img/2022-12-01-diffusion-is-all-you-need/geodiff_main-800.webp" /> <source class="responsive-img-srcset" media="(max-width: 1400px)" srcset="/staging/assets/img/2022-12-01-diffusion-is-all-you-need/geodiff_main-1400.webp" /> <!-- Fallback to the original file --> <img src="/staging/assets/img/2022-12-01-diffusion-is-all-you-need/geodiff_main.png" class="img-fluid" width="auto" height="auto" onerror="this.onerror=null; $('.responsive-img-srcset').remove();" /> </picture> </figure> <p>The diffusion model of GeoDiff, adapted from <d-cite key="xu2022geodiff"></d-cite></p> <p><strong>Legend</strong>:</p> <ul> <li>\(C^{0}\) denotes the ground truth conformations</li> <li>\(C^{t}\), where \(t = 1,···, T\) is the index for diffusion steps and \(C^{t}\), is the sequence of latent variables with the same dimension</li> <li>\(q(C^{t} \mid C^{t-1})\) is the fixed posterior distribution</li> <li>\(p_\theta(C^{t-1} \mid G, C^{t})\) are the Markov kernels through which the conformations are refined</li> </ul> <h3 id="a-primer-on-diffusion-models">A primer on Diffusion Models</h3> <p>A diffusion probabilistic model <d-cite key="sohl2015deep"></d-cite> can be described as a latent variable model with two processes: the forward and the reverse generative processes. Intuitively, the diffusion process progressively injects small noises into \(C^{0}\), while the generative process learns to revert the diffusion process by gradually eliminating the noise to recover the ground truth. Diffusion models are trained by adding noise to the input, which the model then learns how to remove.</p> <p>In this blog post, we use the GeoDiff implementation of diffusion models to explain how the diffusion model works and how it is being used for the geometric representation of molecules. The implementation of the diffusion model in GeoDiff is inspired by the DDPM paper <d-cite key="ho2020denoising"></d-cite>. To give a quick overview, the forward process \(q\) transforms the original input into complete noise over a certain number of timesteps and follows a normal distribution; the \(p_0\) involves denoising complete noise to the actual input using a neural network.</p> <h3 id="forward-process">Forward process</h3> <p>Let \(q(\mathbf{C}^0)\) be the real data distribution of molecular conformation. We can sample from this distribution to get a conformation, \(\mathbf{C}^0 \sim q(\mathbf{C}^0)\). We define the forward diffusion process which adds Gaussian noise at each time step \(t\), according to a known variance schedule \beta_t which can be linear, quadratic, cosine, etc. as follows:</p> \[\begin{align}\tag{1} q\left(\mathcal{C}^{1: T} \mid \mathcal{C}^0\right)=\prod_{t=1}^T q\left(\mathcal{C}^t \mid \mathcal{C}^{t-1}\right) \end{align}\] <p>where \(\quad q\left(\mathcal{C}^t \mid \mathcal{C}^{t-1}\right)=\mathcal{N}\left(\mathcal{C}^t ; \sqrt{1-\beta_t} \mathcal{C}^{t-1}, \beta_t I\right)\)</p> <p>Instead of having to compute \(q\left(\mathcal{C}^t \mid \mathcal{C}^{t-1}\right)\) at every timestep \(t\), we could compute at an arbitrary timestep in closed form:</p> \[\begin{equation}\tag{2} q\left(\mathcal{C}^t \mid \mathcal{C}^0\right)=\mathcal{N}\left(\mathcal{C}^t ; \sqrt{\bar{\alpha}_t} \mathcal{C}^0,\left(1-\bar{\alpha}_t\right) I\right) \end{equation}\] <p>where \(\alpha_t=1-\beta_t\) and \(\bar{\alpha}_t=\prod_{s=1}^t \alpha_s\)</p> <p>Thus with a sufficiently large number of timesteps, the forward process could convert \(\mathcal{C}^0\) to whitened isotropic Gaussian and so we could set \(p\left(\mathcal{C}^T\right)\) as a standard Gaussian distribution.</p> <h3 id="reverse-process">Reverse Process</h3> <p>The reverse process involved recovering the original conformation \(\mathcal{C}^0\) from the white noise \(\mathcal{C}^T\) . We need the conditional distribution \(p_\theta\left(\mathcal{C}^{t-1} \mid \mathcal{G}, \mathcal{C}^t\right)\) to sample some random Gaussian noise \(\mathcal{C}^t\), and “denoise” gradually to end up with a sample from the real distribution \(\mathcal{C}^0\).</p> <p>However, the conditional distribution of \(p_\theta\left(\mathcal{C}^{t-1} \mid \mathcal{G}, \mathcal{C}^t\right)\) is intractable as it requires knowing the distribution of all possible conformations in order to calculate this conditional probability. Hence, a neural network could be used to learn this conditional probability distribution, let’s call it \(p_\theta\), with \(\theta\) being the parameters of the neural network, updated by gradient descent. Thus, we formulate the reverse process as a conditional Markov chain with learnable transitions:</p> \[\begin{align*}\tag{3} p_\theta\left(\mathcal{C}^{0: T-1} \mid \mathcal{G}, \mathcal{C}^T\right)=\prod_{t=1}^T p_\theta\left(\mathcal{C}^{t-1} \mid \mathcal{G}, \mathcal{C}^t\right) \end{align*}\] <p>where \(\quad p_\theta\left(\mathcal{C}^{t-1} \mid \mathcal{G}, \mathcal{C}^t\right)=\mathcal{N}\left(\mathcal{C}^{t-1} ; \mu_\theta\left(\mathcal{G}, \mathcal{C}^t, t\right), \sigma_t^2 I\right)\)</p> <p>Hence, the neural network in the reverse process needs to learn/represent the mean and variance. However, just like the DDPM paper, GeoDiff also lets the variance be user-defined and fixed, and \(\mu_\theta\) is the neural network that estimates means.</p> <p>GeoDiff uses a parametrisation trick inspired by the diffusion model implementation from the DDPM paper such that this parametrisation resembles Langevin dynamics and simplifies the diffusion model’s variational bound to an objective that resembles denoising score matching. Moreover, in the context of molecular conformation generation, this parametrisation trick is analogous to the physical force fields <d-cite key="schutt2017schnet, zhang2018deep, hu2021forcenet, shuaibi2021rotation"></d-cite>, which also gradually push particles towards convergence around the equilibrium states, and is defined by the following equation:</p> \[\begin{align*}\tag{4} \mu_\theta\left(\mathcal{C}^t, t\right)=\frac{1}{\sqrt{\alpha_t}}\left(\mathcal{C}^t-\frac{\beta_t}{\sqrt{1-\bar{\alpha}_t}} \epsilon_\theta\left(\mathcal{G}, \mathcal{C}^t, t\right)\right) \end{align*}\] <p>where \(\epsilon_\theta\) are neural networks with trainable parameters \(\theta\).</p> <p>Now, we need to make \(\epsilon_\theta\) roto-translational equivariant which we elaborate on in the next section.</p> <h3 id="making-the-reverse-process-roto-translation-equivariant">Making the reverse process roto-translation equivariant</h3> <p>Firstly, we need to assume the prior distribution of the conformations and the intermediary conformations generated during the forward process are systems with zero centre of mass (CoM) or CoM-free systems <d-cite key="kohler2020equivariant"></d-cite>. By considering CoM-free systems, moving the particles to zero CoM can always ensure translational invariance in the Markov kernels.</p> <p>GeoDiff employs the use of an equivariant convolutional layer, named graph field network (GFN) inspired by <d-cite key="thomas2018tensor, satorras2021n"></d-cite>. In the \(l\)-th layer, GFN takes node embeddings \(h_l \in \mathbb{R}^{n \times b}\) (\(b\) denotes the feature dimension) and corresponding coordinate embeddings \(x_l \in \mathbb{R}^{n \times 3}\) as inputs, and outputs \(h_{l+1}\) and \(x_{l+1}\) as follows:</p> \[\begin{align} \tag{5} &amp; \mathbf{m}_{i j}=\Phi_m\left(\mathbf{h}_i^l, \mathbf{h}_j^l,\left\|\mathbf{x}_i^l-\mathbf{x}_j^l\right\|^2, e_{i j} ; \theta_m\right) \\ \tag{6} &amp; \mathbf{h}_i^{l+1}=\Phi_h\left(\mathbf{h}_i^l, \sum_{j \in \mathcal{N}(i)} \mathbf{m}_{i j} ; \theta_h\right) \\ &amp; \mathbf{x}_i^{l+1}=\sum_{j \in \mathcal{N}(i)} \frac{1}{d_{i j}}\left(\mathbf{c}_i-\mathbf{c}_j\right) \Phi_x\left(\mathbf{m}_{i j} ; \theta_x\right) \tag{7} \end{align}\] <p>where</p> <ul> <li>\(\Phi\) are feed-forward networks</li> <li>\(d_{ij}\) are interatomic distances</li> <li>\(\mathcal{N}(i)\) is the neighbourhood of the \(i\)-th node, which consists of both connected atoms and other ones within a radius threshold \(\tau\).</li> </ul> <p>By introducing the neighbourhood function, we enable the model to accurately represent distant interactions between atoms, as well as the ability to handle partially disconnected molecular graphs. Initial embeddings \(h_0\) are combinations of atom and timestep embeddings, and \(x_0\) are atomic coordinates. A key change in GFN compared to a vanilla GNN is \(x\) being updated as a combination of radial directions weighted by \(\Phi_x\): \(\mathbb{R}^b \rightarrow \mathbb{R}\) as seen in equation \((7)\). This allows the roto-translation equivariance property to be induced in the reverse process.</p> <h3 id="improved-training-objective">Improved Training Objective</h3> <p>Now, we need to set the training objective having considered the reverse process dynamics. We cannot compute the exact log-likelihood of the generative process, as it involves computing the likelihood of the observed molecular conformation given the parameters of the model. However, this likelihood is difficult to compute, as it would require integrating over all possible intermediate conformations, giving us a high-dimensional integral that cannot be solved analytically. Therefore, the authors have opted to maximize the variational lower bound (ELBO), as defined below:</p> \[\begin{aligned} \mathbb{E}\left[\log p_\theta\left(\mathcal{C}^0 \mid \mathcal{G}\right)\right] &amp; =\mathbb{E}\left[\log \mathbb{E}_{q\left(\mathcal{C}^{1: T} \mid \mathcal{C}^0\right)} \frac{p_\theta\left(\mathcal{C}^{0: T} \mid \mathcal{G}\right)}{q\left(\mathcal{C}^{1: T} \mid \mathcal{C}^0\right)}\right] \\ &amp; \geq-\mathbb{E}_q\left[\sum_{t=1}^T D_{\mathrm{KL}}\left(q\left(\mathcal{C}^{t-1} \mid \mathcal{C}^t, \mathcal{C}^0\right) \| p_\theta\left(\mathcal{C}^{t-1} \mid \mathcal{C}^t, \mathcal{G}\right)\right)\right]:=-\mathcal{L}_{\mathrm{ELBO}}\end{aligned}\] <p>where \(q\left(\mathcal{C}^{t-1} \mid \mathcal{C}^t, \mathcal{C}^0\right)\) is analytically tractable as \(\mathcal{N}\left(\frac{\sqrt{\bar{\alpha}_{t-1}} \beta_t}{1-\bar{\alpha}_t} \mathcal{C}^0+\frac{\sqrt{\alpha_t}\left(1-\bar{\alpha}_{t-1}\right)}{1-\bar{\alpha}_t} \mathcal{C}^t, \frac{1-\bar{\alpha}_{t-1}}{1-\bar{\alpha}_t} \beta_t\right)\).</p> <p>Using the parametrisation trick in the reverse process as seen in equation \((4)\), the ELBO could be simplified by taking the KL divergences between Gaussians as weighted \(\mathcal{L}_2\) distances between the means \(\epsilon_\theta\) and \(\epsilon^3\) as follows: \(\mathcal{L}_{\mathrm{ELBO}}=\sum_{t=1}^T \gamma_t \mathbb{E}_{\left\{\mathcal{C}^0, \mathcal{G}\right\} \sim q\left(\mathcal{C}^0, \mathcal{G}\right), \epsilon \sim \mathcal{N}(0, I)}\left[\left\|\epsilon-\epsilon_\theta\left(\mathcal{G}, \mathcal{C}^t, t\right)\right\|_2^2\right]\) where \(\mathcal{C}^t=\sqrt{\bar{\alpha}_t} \mathcal{C}^0+\sqrt{1-\bar{\alpha}_t} \epsilon\).</p> <p>The idea behind this objective is to independently sample chaotic conformations of different timesteps from \(q\left(C^{t-1} \mid C^t, C^0\right)\), and use \(\epsilon_\theta\) to approximate the noise vector \(\epsilon\).</p> <h3 id="sampling">Sampling</h3> <p>Now, we can generate stable molecular conformations via sampling. Given a graph \(\mathcal{G}\), its geometry \(\mathcal{C}^0\) is generated by first sampling chaotic particles \(\mathcal{C}^T \sim p\left(\mathcal{C}^T\right)\). For each timestep in the reverse process \(t=T, T-\) \(1, \cdots, 1\), we first shift the CoM of the conformation to zero, compute the transition means, \(\mu_\theta\left(\mathcal{G}, \mathcal{C}^t, t\right)\), using equation \((4)\) and sample \(\mathcal{C}^{t-1} \sim\) \(p_\theta\left(\mathcal{C}^{t-1} \mid \mathcal{G}, \mathcal{C}^t\right)\). The sampling algorithm is given in pseudo-code below:</p> <table> <thead> <tr> <th style="text-align: left">Algorithm 1 Sampling Algorithm of GEODIFF</th> </tr> </thead> <tbody> <tr> <td style="text-align: left">Input: the molecular graph \(\mathcal{G}\), the learned reverse model \(\epsilon_\theta\).</td> </tr> <tr> <td style="text-align: left">Output: the molecular conformation \(\mathcal{C}\).</td> </tr> <tr> <td style="text-align: left">1: Sample \(\mathcal{C}^T \sim p\left(\mathcal{C}^T\right)=\mathcal{N}(0, I)\)</td> </tr> <tr> <td style="text-align: left">2: for \(s=T, T-1, \cdots, 1\) do</td> </tr> <tr> <td style="text-align: left">3: \(\quad\) Shift \(\mathcal{C}^s\) to zero CoM</td> </tr> <tr> <td style="text-align: left">4: \(\quad\) Compute \(\mu_\theta\left(\mathcal{C}^s, \mathcal{G}, s\right)\) from \(\epsilon_\theta\left(\mathcal{C}^s, \mathcal{G}, s\right)\) using equation 4</td> </tr> <tr> <td style="text-align: left">5: \(\quad\) Sample \(\mathcal{C}^{s-1} \sim \mathcal{N}\left(\mathcal{C}^{s-1} ; \mu_\theta\left(\mathcal{C}^{\mathcal{s}}, \mathcal{G}, s\right), \sigma_t^2 I\right)\)</td> </tr> <tr> <td style="text-align: left">6: end for</td> </tr> <tr> <td style="text-align: left">7: return \(\mathcal{C}^0\) as $\mathcal{C}$$</td> </tr> </tbody> </table> <h2 id="but-why-generative-models">But why generative models?</h2> <p>The purpose of prediciting molecular conformations is to enable human experts to analyse the properties of the molecules and understand how these properties affect the viability of a molecule as a drug candidate. Therefore, it is important that the molecular conformations generated are diverse to capture the different possible conformations that could occur in nature but the conformations generated should not deviate significantly such that the analysis is affected. To set a threshold for the different possible conformations, the standard metric used has been selecting conformations that are within a certain root-mean-square deviation (RMSD), say a few ångströms, of the true structure.</p> <p>However, the objective of maximizing the proportion of predictions with RMSD within some tolerance \(\epsilon\) is not differentiable and thus, cannot be used for training with stochastic gradient descent. Instead, maximizing the expected proportion of predictions with RMSD &lt; \(\epsilon\) corresponds to maximizing the likelihood of the true structure under the model’s output distribution, in the limit as \(\epsilon\) goes to 0. This concept inspires the development of a generative model, whose objective is to minimize an upper bound on the negative log-likelihood of observed molecular structures under the distribution of the model. As a result, the problem of molecular docking is treated as a task of learning a distribution over possible positions of a ligand molecule conditioned on the protein structure and a diffusion generative model is developed to represent this space. Therefore, this observation has motivated several works on the use of generative models for molecular conformation generation, such as GeoDiff.</p> <h2 id="future-work">Future work</h2> <p>While diffusion models have shown promising results over the past months, there is still a need for further research and development to address some of the limitations and drawbacks of the use of diffusion models in conformer generation. As explained in our blog post, generative models are well-suited for molecular conformation generation. However, there are other kinds of established generative models, such as autoencoders that have been used for the same task <d-cite key="gomez2018automatic"></d-cite>. For instance, comparing diffusion models and autoencoders, diffusion models can handle all noise levels with a single set of parameters, without any bottlenecks, which an autoencoder would have <d-cite key="dieleman2022diffusion"></d-cite>. Thus, it is essential to study the advantages and disadvantages of different types and variants of generative models for conformation generation and understand what changes could be done to them to make them more suitable for molecular conformation.</p> <p>It must be noted that the experiments described in the study are done on benchmark geometric datasets, GEOM-QM9 <d-cite key="ramageom"></d-cite> and GEOM-Drugs <d-cite key="axelrod2022geom"></d-cite>, rather than industrial data, with a relatively small number of samples/drug/molecular compounds. Industry data may exhibit greater variability than standard geometric datasets, as they may be more diverse, complex and subject to greater fluctuations than these geometric datasets, which tend to be more standardized and more predictable.</p> <p>GeoDiff as a framework sets a precedent for future work that could marry the concepts of geometric deep learning and diffusion models across various domains. In the context of drug discovery, it would be interesting to extend this framework to more challenging structures, such as proteins, which may enable more accurate prediction of protein folding, protein-protein interactions and protein-ligand binding positions which would facilitate the design of new drugs and treatments. Additionally, this framework could potentially be applied to other complex systems beyond proteins, such as RNA molecules, to enable more efficient and accurate prediction of their behaviour and properties. Continued research in this area has the potential to revolutionize drug discovery and development, as well as advance our understanding of the fundamental principles governing the behaviour of complex biological systems.</p> <p>Research on the application of diffusion models in the life and natural sciences is still in its infancy, with great potential for improvement in terms of both theory as well as empirical testing. The GeoDiff model could be improved in terms of more efficient sampling and improved likelihood maximization methods. Traditionally, generating samples from diffusion models demand iterative approaches that involve a large number of evaluation steps. Recent work, such as the paper on Torsional Diffusion <d-cite key="jing2022torsional, satorras2021n"></d-cite> was able to speed up the sampling process, while also enhancing the quality of the resulting samples. Experimentally, Torsional Diffusion only takes 5 to 20 steps in comparison to GeoDiff which takes around 5000 steps <d-cite key="galkin_2022"></d-cite>.</p> <p>Looking ahead, GeoDiff has set a clear example for the use of diffusion models on geometric representations which could be extended to several problems, especially in the field of drug discovery. The novel contributions made by</p> <d-cite key="xu2022geodiff"></d-cite> <p>are motivated by the physical characteristics of the molecular conformation generation problem, which has resulted in a strong candidate method for conformation generation that could act as a springboard for even more effective and efficient methods that would eventually benefit the field of drug discovery as a whole.</p> Sample Blog Post 2022-12-01T00:00:00+00:00 https://deep-learning-mit.github.io/staging/blog/2022/distill-example <h2 id="equations">Equations</h2> <p>This theme supports rendering beautiful math in inline and display modes using <a href="https://www.mathjax.org/">MathJax 3</a> engine. You just need to surround your math expression with <code class="language-plaintext highlighter-rouge">$$</code>, like <code class="language-plaintext highlighter-rouge">$$ E = mc^2 $$</code>. If you leave it inside a paragraph, it will produce an inline expression, just like \(E = mc^2\).</p> <p>To use display mode, again surround your expression with <code class="language-plaintext highlighter-rouge">$$</code> and place it as a separate paragraph. Here is an example:</p> \[\left( \sum_{k=1}^n a_k b_k \right)^2 \leq \left( \sum_{k=1}^n a_k^2 \right) \left( \sum_{k=1}^n b_k^2 \right)\] <p>Note that MathJax 3 is <a href="https://docs.mathjax.org/en/latest/upgrading/whats-new-3.0.html">a major re-write of MathJax</a> that brought a significant improvement to the loading and rendering speed, which is now <a href="http://www.intmath.com/cg5/katex-mathjax-comparison.php">on par with KaTeX</a>.</p> <h2 id="images-and-figures">Images and Figures</h2> <p>Its generally a better idea to avoid linking to images hosted elsewhere - links can break and you might face losing important information in your blog post. To include images in your submission in this way, you must do something like the following:</p> <div class="language-markdown highlighter-rouge"><div class="highlight"><pre class="highlight"><code>{% include figure.html path="assets/img/2022-12-01-distill-example/iclr.png" class="img-fluid" %} </code></pre></div></div> <p>which results in the following image:</p> <figure> <picture> <source class="responsive-img-srcset" media="(max-width: 480px)" srcset="/staging/assets/img/2022-12-01-distill-example/iclr-480.webp" /> <source class="responsive-img-srcset" media="(max-width: 800px)" srcset="/staging/assets/img/2022-12-01-distill-example/iclr-800.webp" /> <source class="responsive-img-srcset" media="(max-width: 1400px)" srcset="/staging/assets/img/2022-12-01-distill-example/iclr-1400.webp" /> <!-- Fallback to the original file --> <img src="/staging/assets/img/2022-12-01-distill-example/iclr.png" class="img-fluid" width="auto" height="auto" onerror="this.onerror=null; $('.responsive-img-srcset').remove();" /> </picture> </figure> <p>To ensure that there are no namespace conflicts, you must save your asset to your unique directory <code class="language-plaintext highlighter-rouge">/assets/img/2023-05-01-[SUBMISSION NAME]</code> within your submission.</p> <p>Please avoid using the direct markdown method of embedding images; they may not be properly resized. Some more complex ways to load images (note the different styles of the shapes/shadows):</p> <div class="row mt-3"> <div class="col-sm mt-3 mt-md-0"> <figure> <picture> <source class="responsive-img-srcset" media="(max-width: 480px)" srcset="/staging/assets/img/2022-12-01-distill-example/9-480.webp" /> <source class="responsive-img-srcset" media="(max-width: 800px)" srcset="/staging/assets/img/2022-12-01-distill-example/9-800.webp" /> <source class="responsive-img-srcset" media="(max-width: 1400px)" srcset="/staging/assets/img/2022-12-01-distill-example/9-1400.webp" /> <!-- Fallback to the original file --> <img src="/staging/assets/img/2022-12-01-distill-example/9.jpg" class="img-fluid rounded z-depth-1" width="auto" height="auto" onerror="this.onerror=null; $('.responsive-img-srcset').remove();" /> </picture> </figure> </div> <div class="col-sm mt-3 mt-md-0"> <figure> <picture> <source class="responsive-img-srcset" media="(max-width: 480px)" srcset="/staging/assets/img/2022-12-01-distill-example/7-480.webp" /> <source class="responsive-img-srcset" media="(max-width: 800px)" srcset="/staging/assets/img/2022-12-01-distill-example/7-800.webp" /> <source class="responsive-img-srcset" media="(max-width: 1400px)" srcset="/staging/assets/img/2022-12-01-distill-example/7-1400.webp" /> <!-- Fallback to the original file --> <img src="/staging/assets/img/2022-12-01-distill-example/7.jpg" class="img-fluid rounded z-depth-1" width="auto" height="auto" onerror="this.onerror=null; $('.responsive-img-srcset').remove();" /> </picture> </figure> </div> </div> <div class="caption"> A simple, elegant caption looks good between image rows, after each row, or doesn't have to be there at all. </div> <div class="row mt-3"> <div class="col-sm mt-3 mt-md-0"> <figure> <picture> <source class="responsive-img-srcset" media="(max-width: 480px)" srcset="/staging/assets/img/2022-12-01-distill-example/8-480.webp" /> <source class="responsive-img-srcset" media="(max-width: 800px)" srcset="/staging/assets/img/2022-12-01-distill-example/8-800.webp" /> <source class="responsive-img-srcset" media="(max-width: 1400px)" srcset="/staging/assets/img/2022-12-01-distill-example/8-1400.webp" /> <!-- Fallback to the original file --> <img src="/staging/assets/img/2022-12-01-distill-example/8.jpg" class="img-fluid z-depth-2" width="auto" height="auto" onerror="this.onerror=null; $('.responsive-img-srcset').remove();" /> </picture> </figure> </div> <div class="col-sm mt-3 mt-md-0"> <figure> <picture> <source class="responsive-img-srcset" media="(max-width: 480px)" srcset="/staging/assets/img/2022-12-01-distill-example/10-480.webp" /> <source class="responsive-img-srcset" media="(max-width: 800px)" srcset="/staging/assets/img/2022-12-01-distill-example/10-800.webp" /> <source class="responsive-img-srcset" media="(max-width: 1400px)" srcset="/staging/assets/img/2022-12-01-distill-example/10-1400.webp" /> <!-- Fallback to the original file --> <img src="/staging/assets/img/2022-12-01-distill-example/10.jpg" class="img-fluid z-depth-2" width="auto" height="auto" onerror="this.onerror=null; $('.responsive-img-srcset').remove();" /> </picture> </figure> </div> </div> <div class="row mt-3"> <div class="col-sm mt-3 mt-md-0"> <figure> <picture> <source class="responsive-img-srcset" media="(max-width: 480px)" srcset="/staging/assets/img/2022-12-01-distill-example/11-480.webp" /> <source class="responsive-img-srcset" media="(max-width: 800px)" srcset="/staging/assets/img/2022-12-01-distill-example/11-800.webp" /> <source class="responsive-img-srcset" media="(max-width: 1400px)" srcset="/staging/assets/img/2022-12-01-distill-example/11-1400.webp" /> <!-- Fallback to the original file --> <img src="/staging/assets/img/2022-12-01-distill-example/11.jpg" class="img-fluid" width="auto" height="auto" onerror="this.onerror=null; $('.responsive-img-srcset').remove();" /> </picture> </figure> </div> <div class="col-sm mt-3 mt-md-0"> <figure> <picture> <source class="responsive-img-srcset" media="(max-width: 480px)" srcset="/staging/assets/img/2022-12-01-distill-example/12-480.webp" /> <source class="responsive-img-srcset" media="(max-width: 800px)" srcset="/staging/assets/img/2022-12-01-distill-example/12-800.webp" /> <source class="responsive-img-srcset" media="(max-width: 1400px)" srcset="/staging/assets/img/2022-12-01-distill-example/12-1400.webp" /> <!-- Fallback to the original file --> <img src="/staging/assets/img/2022-12-01-distill-example/12.jpg" class="img-fluid" width="auto" height="auto" onerror="this.onerror=null; $('.responsive-img-srcset').remove();" /> </picture> </figure> </div> <div class="col-sm mt-3 mt-md-0"> <figure> <picture> <source class="responsive-img-srcset" media="(max-width: 480px)" srcset="/staging/assets/img/2022-12-01-distill-example/7-480.webp" /> <source class="responsive-img-srcset" media="(max-width: 800px)" srcset="/staging/assets/img/2022-12-01-distill-example/7-800.webp" /> <source class="responsive-img-srcset" media="(max-width: 1400px)" srcset="/staging/assets/img/2022-12-01-distill-example/7-1400.webp" /> <!-- Fallback to the original file --> <img src="/staging/assets/img/2022-12-01-distill-example/7.jpg" class="img-fluid" width="auto" height="auto" onerror="this.onerror=null; $('.responsive-img-srcset').remove();" /> </picture> </figure> </div> </div> <h3 id="interactive-figures">Interactive Figures</h3> <p>Here’s how you could embed interactive figures that have been exported as HTML files. Note that we will be using plotly for this demo, but anything built off of HTML should work (<strong>no extra javascript is allowed!</strong>). All that’s required is for you to export your figure into HTML format, and make sure that the file exists in the <code class="language-plaintext highlighter-rouge">assets/html/[SUBMISSION NAME]/</code> directory in this repository’s root directory. To embed it into any page, simply insert the following code anywhere into your page.</p> <div class="language-markdown highlighter-rouge"><div class="highlight"><pre class="highlight"><code>{% include [FIGURE_NAME].html %} </code></pre></div></div> <p>For example, the following code can be used to generate the figure underneath it.</p> <div class="language-python highlighter-rouge"><div class="highlight"><pre class="highlight"><code><span class="kn">import</span> <span class="n">pandas</span> <span class="k">as</span> <span class="n">pd</span> <span class="kn">import</span> <span class="n">plotly.express</span> <span class="k">as</span> <span class="n">px</span> <span class="n">df</span> <span class="o">=</span> <span class="n">pd</span><span class="p">.</span><span class="nf">read_csv</span><span class="p">(</span><span class="sh">'</span><span class="s">https://raw.githubusercontent.com/plotly/datasets/master/earthquakes-23k.csv</span><span class="sh">'</span><span class="p">)</span> <span class="n">fig</span> <span class="o">=</span> <span class="n">px</span><span class="p">.</span><span class="nf">density_mapbox</span><span class="p">(</span> <span class="n">df</span><span class="p">,</span> <span class="n">lat</span><span class="o">=</span><span class="sh">'</span><span class="s">Latitude</span><span class="sh">'</span><span class="p">,</span> <span class="n">lon</span><span class="o">=</span><span class="sh">'</span><span class="s">Longitude</span><span class="sh">'</span><span class="p">,</span> <span class="n">z</span><span class="o">=</span><span class="sh">'</span><span class="s">Magnitude</span><span class="sh">'</span><span class="p">,</span> <span class="n">radius</span><span class="o">=</span><span class="mi">10</span><span class="p">,</span> <span class="n">center</span><span class="o">=</span><span class="nf">dict</span><span class="p">(</span><span class="n">lat</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">lon</span><span class="o">=</span><span class="mi">180</span><span class="p">),</span> <span class="n">zoom</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">mapbox_style</span><span class="o">=</span><span class="sh">"</span><span class="s">stamen-terrain</span><span class="sh">"</span><span class="p">)</span> <span class="n">fig</span><span class="p">.</span><span class="nf">show</span><span class="p">()</span> <span class="n">fig</span><span class="p">.</span><span class="nf">write_html</span><span class="p">(</span><span class="sh">'</span><span class="s">./assets/html/2022-12-01-distill-example/plotly_demo_1.html</span><span class="sh">'</span><span class="p">)</span> </code></pre></div></div> <p>And then include it with the following:</p> <div class="language-html highlighter-rouge"><div class="highlight"><pre class="highlight"><code><span class="nt">&lt;div</span> <span class="na">class=</span><span class="s">"l-page"</span><span class="nt">&gt;</span> <span class="nt">&lt;iframe</span> <span class="na">src=</span><span class="s">"{{ 'assets/html/2022-12-01-distill-example/plotly_demo_1.html' | relative_url }}"</span> <span class="na">frameborder=</span><span class="s">'0'</span> <span class="na">scrolling=</span><span class="s">'no'</span> <span class="na">height=</span><span class="s">"600px"</span> <span class="na">width=</span><span class="s">"100%"</span><span class="nt">&gt;&lt;/iframe&gt;</span> <span class="nt">&lt;/div&gt;</span> </code></pre></div></div> <p>Voila!</p> <div class="l-page"> <iframe src="/staging/assets/html/2022-12-01-distill-example/plotly_demo_1.html" frameborder="0" scrolling="no" height="600px" width="100%"></iframe> </div> <h2 id="citations">Citations</h2> <p>Citations are then used in the article body with the <code class="language-plaintext highlighter-rouge">&lt;d-cite&gt;</code> tag. The key attribute is a reference to the id provided in the bibliography. The key attribute can take multiple ids, separated by commas.</p> <p>The citation is presented inline like this: <d-cite key="gregor2015draw"></d-cite> (a number that displays more information on hover). If you have an appendix, a bibliography is automatically created and populated in it.</p> <p>Distill chose a numerical inline citation style to improve readability of citation dense articles and because many of the benefits of longer citations are obviated by displaying more information on hover. However, we consider it good style to mention author last names if you discuss something at length and it fits into the flow well — the authors are human and it’s nice for them to have the community associate them with their work.</p> <hr /> <h2 id="footnotes">Footnotes</h2> <p>Just wrap the text you would like to show up in a footnote in a <code class="language-plaintext highlighter-rouge">&lt;d-footnote&gt;</code> tag. The number of the footnote will be automatically generated.<d-footnote>This will become a hoverable footnote.</d-footnote></p> <hr /> <h2 id="code-blocks">Code Blocks</h2> <p>This theme implements a built-in Jekyll feature, the use of Rouge, for syntax highlighting. It supports more than 100 languages. This example is in C++. All you have to do is wrap your code in a liquid tag:</p> <p>{% highlight c++ linenos %} <br /> code code code <br /> {% endhighlight %}</p> <p>The keyword <code class="language-plaintext highlighter-rouge">linenos</code> triggers display of line numbers. You can try toggling it on or off yourself below:</p> <figure class="highlight"><pre><code class="language-c--" data-lang="c++"><span class="kt">int</span> <span class="nf">main</span><span class="p">(</span><span class="kt">int</span> <span class="n">argc</span><span class="p">,</span> <span class="kt">char</span> <span class="k">const</span> <span class="err">\</span><span class="o">*</span><span class="n">argv</span><span class="p">[])</span> <span class="p">{</span> <span class="n">string</span> <span class="n">myString</span><span class="p">;</span> <span class="n">cout</span> <span class="o">&lt;&lt;</span> <span class="s">"input a string: "</span><span class="p">;</span> <span class="n">getline</span><span class="p">(</span><span class="n">cin</span><span class="p">,</span> <span class="n">myString</span><span class="p">);</span> <span class="kt">int</span> <span class="n">length</span> <span class="o">=</span> <span class="n">myString</span><span class="p">.</span><span class="n">length</span><span class="p">();</span> <span class="kt">char</span> <span class="n">charArray</span> <span class="o">=</span> <span class="k">new</span> <span class="kt">char</span> <span class="o">*</span> <span class="p">[</span><span class="n">length</span><span class="p">];</span> <span class="n">charArray</span> <span class="o">=</span> <span class="n">myString</span><span class="p">;</span> <span class="k">for</span><span class="p">(</span><span class="kt">int</span> <span class="n">i</span> <span class="o">=</span> <span class="mi">0</span><span class="p">;</span> <span class="n">i</span> <span class="o">&lt;</span> <span class="n">length</span><span class="p">;</span> <span class="o">++</span><span class="n">i</span><span class="p">){</span> <span class="n">cout</span> <span class="o">&lt;&lt;</span> <span class="n">charArray</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">&lt;&lt;</span> <span class="s">" "</span><span class="p">;</span> <span class="p">}</span> <span class="k">return</span> <span class="mi">0</span><span class="p">;</span> <span class="p">}</span></code></pre></figure> <hr /> <h2 id="diagrams">Diagrams</h2> <p>This theme supports generating various diagrams from a text description using <a href="https://github.com/zhustec/jekyll-diagrams" target="\_blank">jekyll-diagrams</a> plugin. Below, we generate a few examples of such diagrams using languages such as <a href="https://mermaid-js.github.io/mermaid/" target="\_blank">mermaid</a>, <a href="https://plantuml.com/" target="\_blank">plantuml</a>, <a href="https://vega.github.io/vega-lite/" target="\_blank">vega-lite</a>, etc.</p> <p><strong>Note:</strong> different diagram-generation packages require external dependencies to be installed on your machine. Also, be mindful of that because of diagram generation the fist time you build your Jekyll website after adding new diagrams will be SLOW. For any other details, please refer to <a href="https://github.com/zhustec/jekyll-diagrams" target="\_blank">jekyll-diagrams</a> README.</p> <p><strong>Note:</strong> This is not supported for local rendering!</p> <p>The diagram below was generated by the following code:</p> <div class="language-plaintext highlighter-rouge"><div class="highlight"><pre class="highlight"><code>{% mermaid %} sequenceDiagram participant John participant Alice Alice-&gt;&gt;John: Hello John, how are you? 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#aggregationEnd,#mermaid-1697734447192 #aggregationStart{fill:#ececff;stroke:#9370db;stroke-width:1}#mermaid-1697734447192 #dependencyEnd,#mermaid-1697734447192 #dependencyStart,#mermaid-1697734447192 #extensionEnd,#mermaid-1697734447192 #extensionStart{fill:#9370db;stroke:#9370db;stroke-width:1}#mermaid-1697734447192 .branch-label,#mermaid-1697734447192 .commit-id,#mermaid-1697734447192 .commit-msg{fill:#d3d3d3;color:#d3d3d3}</style><style>#mermaid-1697734447192 { color: rgb(0, 0, 0); font: normal normal 400 normal 16px / normal "Times New Roman"; }</style><g></g><g><line id="actor0" x1="75" y1="5" x2="75" y2="220" class="actor-line" stroke-width="0.5px" stroke="#999"></line><rect x="0" y="0" fill="#eaeaea" stroke="#666" width="150" height="65" rx="3" ry="3" class="actor"></rect><text x="75" y="32.5" dominant-baseline="central" alignment-baseline="central" class="actor" style="text-anchor: middle;"><tspan x="75" dy="0">John</tspan></text></g><g><line id="actor1" x1="275" y1="5" x2="275" y2="220" class="actor-line" stroke-width="0.5px" stroke="#999"></line><rect x="200" y="0" fill="#eaeaea" stroke="#666" width="150" height="65" rx="3" ry="3" class="actor"></rect><text x="275" y="32.5" dominant-baseline="central" alignment-baseline="central" class="actor" style="text-anchor: middle;"><tspan x="275" dy="0">Alice</tspan></text></g><defs><marker id="arrowhead" refX="5" refY="2" markerWidth="6" markerHeight="4" orient="auto"><path d="M 0,0 V 4 L6,2 Z"></path></marker></defs><defs><marker id="crosshead" markerWidth="15" markerHeight="8" orient="auto" refX="16" refY="4"><path fill="black" stroke="#000000" stroke-width="1px" d="M 9,2 V 6 L16,4 Z" style="stroke-dasharray: 0, 0;"></path><path fill="none" stroke="#000000" stroke-width="1px" d="M 0,1 L 6,7 M 6,1 L 0,7" style="stroke-dasharray: 0, 0;"></path></marker></defs><g><text x="175" y="93" class="messageText" style="text-anchor: middle;">Hello John, how are you?</text><line x1="275" y1="100" x2="75" y2="100" class="messageLine0" stroke-width="2" stroke="black" marker-end="url(#arrowhead)" style="fill: none;"></line></g><g><text x="175" y="128" class="messageText" style="text-anchor: middle;">Great!</text><line x1="75" y1="135" x2="275" y2="135" class="messageLine1" stroke-width="2" stroke="black" marker-end="url(#arrowhead)" style="stroke-dasharray: 3, 3; fill: none;"></line></g><g><rect x="0" y="155" fill="#eaeaea" stroke="#666" width="150" height="65" rx="3" ry="3" class="actor"></rect><text x="75" y="187.5" dominant-baseline="central" alignment-baseline="central" class="actor" style="text-anchor: middle;"><tspan x="75" dy="0">John</tspan></text></g><g><rect x="200" y="155" fill="#eaeaea" stroke="#666" width="150" height="65" rx="3" ry="3" class="actor"></rect><text x="275" y="187.5" dominant-baseline="central" alignment-baseline="central" class="actor" style="text-anchor: middle;"><tspan x="275" dy="0">Alice</tspan></text></g></svg> </div> <hr /> <h2 id="blockquotes">Blockquotes</h2> <blockquote> We do not grow absolutely, chronologically. We grow sometimes in one dimension, and not in another, unevenly. We grow partially. We are relative. We are mature in one realm, childish in another. —Anais Nin </blockquote> <hr /> <h2 id="layouts">Layouts</h2> <p>The main text column is referred to as the body. It is the assumed layout of any direct descendants of the <code class="language-plaintext highlighter-rouge">d-article</code> element.</p> <div class="fake-img l-body"> <p>.l-body</p> </div> <p>For images you want to display a little larger, try <code class="language-plaintext highlighter-rouge">.l-page</code>:</p> <div class="fake-img l-page"> <p>.l-page</p> </div> <p>All of these have an outset variant if you want to poke out from the body text a little bit. For instance:</p> <div class="fake-img l-body-outset"> <p>.l-body-outset</p> </div> <div class="fake-img l-page-outset"> <p>.l-page-outset</p> </div> <p>Occasionally you’ll want to use the full browser width. For this, use <code class="language-plaintext highlighter-rouge">.l-screen</code>. You can also inset the element a little from the edge of the browser by using the inset variant.</p> <div class="fake-img l-screen"> <p>.l-screen</p> </div> <div class="fake-img l-screen-inset"> <p>.l-screen-inset</p> </div> <p>The final layout is for marginalia, asides, and footnotes. It does not interrupt the normal flow of <code class="language-plaintext highlighter-rouge">.l-body</code> sized text except on mobile screen sizes.</p> <div class="fake-img l-gutter"> <p>.l-gutter</p> </div> <hr /> <h2 id="other-typography">Other Typography?</h2> <p>Emphasis, aka italics, with <em>asterisks</em> (<code class="language-plaintext highlighter-rouge">*asterisks*</code>) or <em>underscores</em> (<code class="language-plaintext highlighter-rouge">_underscores_</code>).</p> <p>Strong emphasis, aka bold, with <strong>asterisks</strong> or <strong>underscores</strong>.</p> <p>Combined emphasis with <strong>asterisks and <em>underscores</em></strong>.</p> <p>Strikethrough uses two tildes. <del>Scratch this.</del></p> <ol> <li>First ordered list item</li> <li>Another item ⋅⋅* Unordered sub-list.</li> <li>Actual numbers don’t matter, just that it’s a number ⋅⋅1. Ordered sub-list</li> <li>And another item.</li> </ol> <p>⋅⋅⋅You can have properly indented paragraphs within list items. Notice the blank line above, and the leading spaces (at least one, but we’ll use three here to also align the raw Markdown).</p> <p>⋅⋅⋅To have a line break without a paragraph, you will need to use two trailing spaces.⋅⋅ ⋅⋅⋅Note that this line is separate, but within the same paragraph.⋅⋅ ⋅⋅⋅(This is contrary to the typical GFM line break behaviour, where trailing spaces are not required.)</p> <ul> <li>Unordered list can use asterisks</li> <li>Or minuses</li> <li>Or pluses</li> </ul> <p><a href="https://www.google.com">I’m an inline-style link</a></p> <p><a href="https://www.google.com" title="Google's Homepage">I’m an inline-style link with title</a></p> <p><a href="https://www.mozilla.org">I’m a reference-style link</a></p> <p><a href="../blob/master/LICENSE">I’m a relative reference to a repository file</a></p> <p><a href="http://slashdot.org">You can use numbers for reference-style link definitions</a></p> <p>Or leave it empty and use the <a href="http://www.reddit.com">link text itself</a>.</p> <p>URLs and URLs in angle brackets will automatically get turned into links. http://www.example.com or <a href="http://www.example.com">http://www.example.com</a> and sometimes example.com (but not on Github, for example).</p> <p>Some text to show that the reference links can follow later.</p> <p>Here’s our logo (hover to see the title text):</p> <p>Inline-style: <img src="https://github.com/adam-p/markdown-here/raw/master/src/common/images/icon48.png" alt="alt text" title="Logo Title Text 1" /></p> <p>Reference-style: <img src="https://github.com/adam-p/markdown-here/raw/master/src/common/images/icon48.png" alt="alt text" title="Logo Title Text 2" /></p> <p>Inline <code class="language-plaintext highlighter-rouge">code</code> has <code class="language-plaintext highlighter-rouge">back-ticks around</code> it.</p> <div class="language-javascript highlighter-rouge"><div class="highlight"><pre class="highlight"><code><span class="kd">var</span> <span class="nx">s</span> <span class="o">=</span> <span class="dl">"</span><span class="s2">JavaScript syntax highlighting</span><span class="dl">"</span><span class="p">;</span> <span class="nf">alert</span><span class="p">(</span><span class="nx">s</span><span class="p">);</span> </code></pre></div></div> <div class="language-python highlighter-rouge"><div class="highlight"><pre class="highlight"><code><span class="n">s</span> <span class="o">=</span> <span class="sh">"</span><span class="s">Python syntax highlighting</span><span class="sh">"</span> <span class="k">print</span> <span class="n">s</span> </code></pre></div></div> <div class="language-plaintext highlighter-rouge"><div class="highlight"><pre class="highlight"><code>No language indicated, so no syntax highlighting. But let's throw in a &lt;b&gt;tag&lt;/b&gt;. </code></pre></div></div> <p>Colons can be used to align columns.</p> <table> <thead> <tr> <th>Tables</th> <th style="text-align: center">Are</th> <th style="text-align: right">Cool</th> </tr> </thead> <tbody> <tr> <td>col 3 is</td> <td style="text-align: center">right-aligned</td> <td style="text-align: right">$1600</td> </tr> <tr> <td>col 2 is</td> <td style="text-align: center">centered</td> <td style="text-align: right">$12</td> </tr> <tr> <td>zebra stripes</td> <td style="text-align: center">are neat</td> <td style="text-align: right">$1</td> </tr> </tbody> </table> <p>There must be at least 3 dashes separating each header cell. The outer pipes (|) are optional, and you don’t need to make the raw Markdown line up prettily. You can also use inline Markdown.</p> <table> <thead> <tr> <th>Markdown</th> <th>Less</th> <th>Pretty</th> </tr> </thead> <tbody> <tr> <td><em>Still</em></td> <td><code class="language-plaintext highlighter-rouge">renders</code></td> <td><strong>nicely</strong></td> </tr> <tr> <td>1</td> <td>2</td> <td>3</td> </tr> </tbody> </table> <blockquote> <p>Blockquotes are very handy in email to emulate reply text. This line is part of the same quote.</p> </blockquote> <p>Quote break.</p> <blockquote> <p>This is a very long line that will still be quoted properly when it wraps. Oh boy let’s keep writing to make sure this is long enough to actually wrap for everyone. Oh, you can <em>put</em> <strong>Markdown</strong> into a blockquote.</p> </blockquote> <p>Here’s a line for us to start with.</p> <p>This line is separated from the one above by two newlines, so it will be a <em>separate paragraph</em>.</p> <p>This line is also a separate paragraph, but… This line is only separated by a single newline, so it’s a separate line in the <em>same paragraph</em>.</p> \ No newline at end of file diff --git a/bin/cibuild b/bin/cibuild deleted file mode 100755 index d5c9e195..00000000 --- a/bin/cibuild +++ /dev/null @@ -1 +0,0 @@ -bundle exec jekyll build diff --git a/bin/deploy b/bin/deploy deleted file mode 100755 index 2953d787..00000000 --- a/bin/deploy +++ /dev/null @@ -1,118 +0,0 @@ -#!/usr/bin/env bash - -# Run this script to deploy the app to Github Pages - -# Parse cmd arguments - -SRC_BRANCH="master" -DEPLOY_BRANCH="gh-pages" - -USAGE_MSG="usage: deploy [-h|--help] [-u|--user] [-s|--src SRC_BRANCH] [-d|--deploy DEPLOY_BRANCH] [--verbose] [--no-push]" - -while [[ $# > 0 ]]; do - key="$1" - - case $key in - -h|--help) - echo $USAGE_MSG - exit 0 - ;; - -u|--user) - SRC_BRANCH="source" - DEPLOY_BRANCH="master" - ;; - -s|--src) - SRC_BRANCH="$2" - shift - ;; - -d|--deploy) - DEPLOY_BRANCH="$2" - shift - ;; - --verbose) - set -x - ;; - --no-push) - NO_PUSH="--no-push" - ;; - *) - echo "Option $1 is unknown." >&2 - echo $USAGE_MSG >&2 - exit 1 - ;; - esac - shift -done - -# Exit if any subcommand fails -set -e - -echo "Deploying..." -echo "Source branch: $SRC_BRANCH" -echo "Deploy branch: $DEPLOY_BRANCH" - -read -r -p "Do you want to proceed? [y/N] " response -if [[ ! $response =~ ^([yY][eE][sS]|[yY])+$ ]] -then - echo "Aborting." - [[ "$0" = "$BASH_SOURCE" ]] && exit 1 || return 1 -fi - -# Check if there are any uncommitted changes -if ! git diff-index --quiet HEAD --; then - echo "Changes to the following files are uncommitted:" - git diff-index --name-only HEAD -- - echo "Please commit the changes before proceeding." - echo "Aborting." - [[ "$0" = "$BASH_SOURCE" ]] && exit 1 || return 1 -fi - -# Check if there are any untracked files -if ! test -z "$(git ls-files --exclude-standard --others)"; then - echo "There are untracked files:" - git ls-files --exclude-standard --others - echo "Please commit those files or stash them before proceeding." - echo "Aborting." - [[ "$0" = "$BASH_SOURCE" ]] && exit 1 || return 1 -fi - -# Switch to source branch (creates it if necessary from the current branch) -if [ `git branch | grep $SRC_BRANCH | tr ' ' '\n' | tail -1` ] -then - git checkout $SRC_BRANCH -else - git checkout -b $SRC_BRANCH -fi - -# Checkout DEPLOY_BRANCH branch -if [ `git branch | grep $DEPLOY_BRANCH` ] -then - git branch -D $DEPLOY_BRANCH -fi -git checkout -b $DEPLOY_BRANCH - -# Export JEKYLL_ENV=production -export JEKYLL_ENV=production - -# Build site -bundle exec jekyll build - -# Delete and move files -find . -maxdepth 1 ! -name '_site' ! -name '.git' ! -name 'CNAME' ! -name '.gitignore' -exec rm -rf {} \; -mv _site/* . -rm -R _site/ - -# Create `.nojekyll` file (bypass GitHub Pages Jekyll processing) -touch .nojekyll - -# Push to DEPLOY_BRANCH -git add -fA -git commit --allow-empty -m "$(git log -1 --pretty=%B) [ci skip]" -[[ ${NO_PUSH} ]] || git push -f -q origin $DEPLOY_BRANCH - -# Move back to SRC_BRANCH -git checkout $SRC_BRANCH - -echo "Deployed successfully!" - -exit 0 diff --git a/bin/docker_build_image.sh b/bin/docker_build_image.sh deleted file mode 100755 index fe208afb..00000000 --- a/bin/docker_build_image.sh +++ /dev/null @@ -1,5 +0,0 @@ - FILE=Gemfile.lock -if [ -f "$FILE" ]; then - rm $FILE -fi - docker build -t "al-folio:latest" . \ No newline at end of file diff --git a/bin/docker_run.sh b/bin/docker_run.sh deleted file mode 100755 index a59a44ba..00000000 --- a/bin/docker_run.sh +++ /dev/null @@ -1,7 +0,0 @@ -FILE=Gemfile.lock -if [ -f "$FILE" ]; then - rm $FILE -fi -docker run --rm -v "$PWD:/srv/jekyll/" -p "8080:8080" \ - -it al-folio:latest bundler \ - exec jekyll serve --watch --port=8080 --host=0.0.0.0 \ No newline at end of file diff --git a/bin/dockerhub_run.sh b/bin/dockerhub_run.sh deleted file mode 100755 index 738a04c7..00000000 --- a/bin/dockerhub_run.sh +++ /dev/null @@ -1,7 +0,0 @@ -FILE=Gemfile.lock -if [ -f "$FILE" ]; then - rm $FILE -fi -docker run --rm -v "$PWD:/srv/jekyll/" -p "8080:8080" \ - -it amirpourmand/al-folio:v0.7.0 bundler \ - exec jekyll serve --watch --port=8080 --host=0.0.0.0 diff --git a/bin/entry_point.sh b/bin/entry_point.sh deleted file mode 100644 index 062f2c64..00000000 --- a/bin/entry_point.sh +++ /dev/null @@ -1,22 +0,0 @@ -#!/bin/bash - -CONFIG_FILE=_config.yml - -/bin/bash -c "rm -f Gemfile.lock && exec jekyll serve --watch --port=8080 --host=0.0.0.0 --livereload --verbose --trace --force_polling"& - -while true; do - - inotifywait -q -e modify,move,create,delete $CONFIG_FILE - - if [ $? -eq 0 ]; then - - echo "Change detected to $CONFIG_FILE, restarting Jekyll" - - jekyll_pid=$(pgrep -f jekyll) - kill -KILL $jekyll_pid - - /bin/bash -c "rm -f Gemfile.lock && exec jekyll serve --watch --port=8080 --host=0.0.0.0 --livereload --verbose --trace --force_polling"& - - fi - -done \ No newline at end of file diff --git a/blog/2022/distill-example/index.html b/blog/2022/distill-example/index.html new file mode 100644 index 00000000..c1cba804 --- /dev/null +++ b/blog/2022/distill-example/index.html @@ -0,0 +1,98 @@ + Sample Blog Post | 6.S898 Deep Learning Blogs 2023

      Sample Blog Post

      Your blog post's abstract. This is an example of a distill-style blog post and the main elements it supports.

      Equations

      This theme supports rendering beautiful math in inline and display modes using MathJax 3 engine. You just need to surround your math expression with $$, like $$ E = mc^2 $$. If you leave it inside a paragraph, it will produce an inline expression, just like \(E = mc^2\).

      To use display mode, again surround your expression with $$ and place it as a separate paragraph. Here is an example:

      \[\left( \sum_{k=1}^n a_k b_k \right)^2 \leq \left( \sum_{k=1}^n a_k^2 \right) \left( \sum_{k=1}^n b_k^2 \right)\]

      Note that MathJax 3 is a major re-write of MathJax that brought a significant improvement to the loading and rendering speed, which is now on par with KaTeX.

      Images and Figures

      Its generally a better idea to avoid linking to images hosted elsewhere - links can break and you might face losing important information in your blog post. To include images in your submission in this way, you must do something like the following:

      {% include figure.html path="assets/img/2022-12-01-distill-example/iclr.png" class="img-fluid" %}
+

      which results in the following image:

      To ensure that there are no namespace conflicts, you must save your asset to your unique directory /assets/img/2023-05-01-[SUBMISSION NAME] within your submission.

      Please avoid using the direct markdown method of embedding images; they may not be properly resized. Some more complex ways to load images (note the different styles of the shapes/shadows):

      A simple, elegant caption looks good between image rows, after each row, or doesn't have to be there at all.

      Interactive Figures

      Here’s how you could embed interactive figures that have been exported as HTML files. Note that we will be using plotly for this demo, but anything built off of HTML should work (no extra javascript is allowed!). All that’s required is for you to export your figure into HTML format, and make sure that the file exists in the assets/html/[SUBMISSION NAME]/ directory in this repository’s root directory. To embed it into any page, simply insert the following code anywhere into your page.

      {% include [FIGURE_NAME].html %} 
+

      For example, the following code can be used to generate the figure underneath it.

      import pandas as pd
+import plotly.express as px
+
+df = pd.read_csv('https://raw.githubusercontent.com/plotly/datasets/master/earthquakes-23k.csv')
+
+fig = px.density_mapbox(
+    df, lat='Latitude', lon='Longitude', z='Magnitude', radius=10,
+    center=dict(lat=0, lon=180), zoom=0, mapbox_style="stamen-terrain")
+fig.show()
+
+fig.write_html('./assets/html/2022-12-01-distill-example/plotly_demo_1.html')
+

      And then include it with the following:

      <div class="l-page">
+  <iframe src="{{ 'assets/html/2022-12-01-distill-example/plotly_demo_1.html' | relative_url }}" frameborder='0' scrolling='no' height="600px" width="100%"></iframe>
+</div>
+

      Voila!

      Citations

      Citations are then used in the article body with the <d-cite> tag. The key attribute is a reference to the id provided in the bibliography. The key attribute can take multiple ids, separated by commas.

      The citation is presented inline like this: (a number that displays more information on hover). If you have an appendix, a bibliography is automatically created and populated in it.

      Distill chose a numerical inline citation style to improve readability of citation dense articles and because many of the benefits of longer citations are obviated by displaying more information on hover. However, we consider it good style to mention author last names if you discuss something at length and it fits into the flow well — the authors are human and it’s nice for them to have the community associate them with their work.

      Footnotes

      Just wrap the text you would like to show up in a footnote in a <d-footnote> tag. The number of the footnote will be automatically generated.This will become a hoverable footnote.

      Code Blocks

      This theme implements a built-in Jekyll feature, the use of Rouge, for syntax highlighting. It supports more than 100 languages. This example is in C++. All you have to do is wrap your code in a liquid tag:

      {% highlight c++ linenos %}
      code code code
      {% endhighlight %}

      The keyword linenos triggers display of line numbers. You can try toggling it on or off yourself below:

      int main(int argc, char const \*argv[])
+{
+string myString;
+
+    cout << "input a string: ";
+    getline(cin, myString);
+    int length = myString.length();
+
+    char charArray = new char * [length];
+
+    charArray = myString;
+    for(int i = 0; i < length; ++i){
+        cout << charArray[i] << " ";
+    }
+
+    return 0;
+}

      Diagrams

      This theme supports generating various diagrams from a text description using jekyll-diagrams plugin. Below, we generate a few examples of such diagrams using languages such as mermaid, plantuml, vega-lite, etc.

      Note: different diagram-generation packages require external dependencies to be installed on your machine. Also, be mindful of that because of diagram generation the fist time you build your Jekyll website after adding new diagrams will be SLOW. For any other details, please refer to jekyll-diagrams README.

      Note: This is not supported for local rendering!

      The diagram below was generated by the following code:

      {% mermaid %}
+sequenceDiagram
+    participant John
+    participant Alice
+    Alice->>John: Hello John, how are you?
+    John-->>Alice: Great!
+{% endmermaid %}
+
      JohnAliceHello John, how are you?Great!JohnAlice

      Blockquotes

      We do not grow absolutely, chronologically. We grow sometimes in one dimension, and not in another, unevenly. We grow partially. We are relative. We are mature in one realm, childish in another. —Anais Nin

      Layouts

      The main text column is referred to as the body. It is the assumed layout of any direct descendants of the d-article element.

      .l-body

      For images you want to display a little larger, try .l-page:

      .l-page

      All of these have an outset variant if you want to poke out from the body text a little bit. For instance:

      .l-body-outset

      .l-page-outset

      Occasionally you’ll want to use the full browser width. For this, use .l-screen. You can also inset the element a little from the edge of the browser by using the inset variant.

      .l-screen

      .l-screen-inset

      The final layout is for marginalia, asides, and footnotes. It does not interrupt the normal flow of .l-body sized text except on mobile screen sizes.

      .l-gutter

      Other Typography?

      Emphasis, aka italics, with asterisks (*asterisks*) or underscores (_underscores_).

      Strong emphasis, aka bold, with asterisks or underscores.

      Combined emphasis with asterisks and underscores.

      Strikethrough uses two tildes. Scratch this.

      1. First ordered list item
      2. Another item ⋅⋅* Unordered sub-list.
      3. Actual numbers don’t matter, just that it’s a number ⋅⋅1. Ordered sub-list
      4. And another item.

      ⋅⋅⋅You can have properly indented paragraphs within list items. Notice the blank line above, and the leading spaces (at least one, but we’ll use three here to also align the raw Markdown).

      ⋅⋅⋅To have a line break without a paragraph, you will need to use two trailing spaces.⋅⋅ ⋅⋅⋅Note that this line is separate, but within the same paragraph.⋅⋅ ⋅⋅⋅(This is contrary to the typical GFM line break behaviour, where trailing spaces are not required.)

      • Unordered list can use asterisks
      • Or minuses
      • Or pluses

      I’m an inline-style link

      I’m an inline-style link with title

      I’m a reference-style link

      I’m a relative reference to a repository file

      You can use numbers for reference-style link definitions

      Or leave it empty and use the link text itself.

      URLs and URLs in angle brackets will automatically get turned into links. http://www.example.com or http://www.example.com and sometimes example.com (but not on Github, for example).

      Some text to show that the reference links can follow later.

      Here’s our logo (hover to see the title text):

      Inline-style: alt text

      Reference-style: alt text

      Inline code has back-ticks around it.

      var s = "JavaScript syntax highlighting";
+alert(s);
+
      s = "Python syntax highlighting"
+print s
+
      No language indicated, so no syntax highlighting. 
+But let's throw in a <b>tag</b>.
+

      Colons can be used to align columns.

      Tables Are Cool
      col 3 is right-aligned $1600
      col 2 is centered $12
      zebra stripes are neat $1

      There must be at least 3 dashes separating each header cell. The outer pipes (|) are optional, and you don’t need to make the raw Markdown line up prettily. You can also use inline Markdown.

      Markdown Less Pretty
      Still renders nicely
      1 2 3

      Blockquotes are very handy in email to emulate reply text. This line is part of the same quote.

      Quote break.

      This is a very long line that will still be quoted properly when it wraps. Oh boy let’s keep writing to make sure this is long enough to actually wrap for everyone. Oh, you can put Markdown into a blockquote.

      Here’s a line for us to start with.

      This line is separated from the one above by two newlines, so it will be a separate paragraph.

      This line is also a separate paragraph, but… This line is only separated by a single newline, so it’s a separate line in the same paragraph.
      \ No newline at end of file diff --git a/blog/2022/index.html b/blog/2022/index.html new file mode 100644 index 00000000..bb33e7f9 --- /dev/null +++ b/blog/2022/index.html @@ -0,0 +1 @@ + 2022 | 6.S898 Deep Learning Blogs 2023

      2022

      an archive of posts from this year

      \ No newline at end of file diff --git a/blog/2023/diffusion-is-all-you-need/index.html b/blog/2023/diffusion-is-all-you-need/index.html new file mode 100644 index 00000000..284732c8 --- /dev/null +++ b/blog/2023/diffusion-is-all-you-need/index.html @@ -0,0 +1,32 @@ + A Match Made in Drug Discovery - Marrying Geometric and Diffusion Models | 6.S898 Deep Learning Blogs 2023

      A Match Made in Drug Discovery - Marrying Geometric and Diffusion Models

      The chemical space of molecular candidates is vast, and within this space, interesting and powerful drugs are waiting to be found. The use of machine learning has shown to be an effective method to speed up the process of discovering novel compounds, especially the use of (deep) generative models. The recent surge in graph generative models have opened up new avenues for exploring the chemical space of molecular candidates, enabling a more efficient and systematic exploration of the chemical space, increasing the chances of finding novel and potent molecules. One of the recent breakthroughs includes the use of diffusion models, which have proven to yield superior performance in molecular conformation tasks, among others. In this blog post, we aim to highlight one of them, which is the 'GeoDiff - A Geometric Diffusion Model for Molecular Conformation Generation' paper by Xu et al. (2022). We aim to distill the paper in semi-layman terms, to provide researchers and practitioners with a deeper understanding of the (i) methodology and results and (ii) (societal) implications of this breakthrough in the field of drug discovery and (iii) discuss future applications in the field of (bio)medicine.

      A Match Made in Drug Discovery: Marrying Geometric and Diffusion Models

      Introduction

      With the initial breakthrough of the Denoising Diffusion , diffusion models have evolved into a powerful tool for a wide range of applications in machine learning, including image generation and text generation. The rise and the recent release of Stable Diffusion in August 2022 has shown superior performance in a wide range of practical applications - from artistic and creative projects to scientific and industrial ones and has recently paved its way into the natural sciences, which includes the field of drug discovery .

      Data-driven applications have increasingly been shown to accelerate solving diverse problems in the drug discovery pipeline – from the use of predictive analytical methods for target identification and lead optimization, to the analysis of large-scale biological data for drug repurposing and personalized medicine. To limit the scope of the blog post, we will only focus on the use of generative methods in molecular conformation generation.

      Motivation

      Generating molecular conformations is a task fundamental to cheminformatics and drug discovery. The conformation of a molecule refers to the three-dimensional (3D) coordinates of all the atoms in a molecule in a 3D Euclidean space, which can be interconverted by rotations about formally single bonds . It allows for the prediction of the physical and chemical properties and interactions of molecules based on their possible 3D conformations, as well as their biological activity. In drug discovery, it is integral to obtain all the possible conformations of molecules for various tasks, such as three-dimensional quantitative structure-activity relationships (3D-QSAR), pharmacophore searching, molecular docking and thermodynamic calculations. Deep generative modelling, which aims to learn complex data distributions, is a recent promising approach to tackle the conformation generation problem . When studying molecules it is important to understand them as three-dimensional structures formed by atoms bonded to each other. To encode the chemical properties, molecules could be represented as graphs where atoms (nodes) are connected by bonds (edges). Representing molecules as 3D molecular graphs captures the spatial arrangement of a molecule, which in turn determines its chemical property. A molecule could take up any conformation based on all possible permutations and combinations of spatial arrangements of atoms. However, some conformations may not occur physically, due to e.g steric hindrance, which arises when the spatial arrangement of atoms leads to unfavourable interactions/repulsive forces, leading to a higher energy state and less stable conformation.

      Therefore, we are only interested in conformations that fall in stable low-energy minima, as these low-energy conformations are the ones that the molecule will most likely adopt under natural conditions and play a crucial role in determining the molecule’s behaviour and properties. By identifying and characterizing the low-energy conformations, researchers gain insights into their stability, reactivity and interactions with other molecules.

      Formulating the conformation generation problem

      A formulation of the conformation generation problem, adapted from

      We can formulate the problem of conformation generation as a conditional generative problem where we aim to generate stable conformations \(C\) from a molecule’s graph \(G\). For each \(G\) given its conformations \(C\) as i.i.d samples from an underlying Boltzmann distribution , our goal is to learn a generative model $$p_\theta(C G)$$ to draw possible conformations from.

      Roto-translation equivariance

      A visualisation of roto-translation equivariance, adapted from

      To generate stable molecular conformations, we need an algorithm that preserves roto-translation equivariance of the conformations that previous work has not focused on. To explain this property, let us delve into what equivariance is. A representation \(φ\) is equivariant with a transformation \(g\) of the input if the transformation can be transferred to the representation output. Invariance is a special case of equivariance obtained when the transformation is the identity map .

      In the context of molecular conformations, we have to achieve the special case of equivariance in terms of rotation and translation, namely, roto-translation equivariance of the conformations which ensures that however the molecule is rotated or translated, the estimated (conditional) likelihood should be unaffected. GeoDiff considers the SE(3) Lie group which can be used to represent rotation and translation in 3D space .

      Decomposing GeoDiff

      The diffusion model of GeoDiff, adapted from

      Legend:

      • \(C^{0}\) denotes the ground truth conformations
      • \(C^{t}\), where \(t = 1,···, T\) is the index for diffusion steps and \(C^{t}\), is the sequence of latent variables with the same dimension
      • \(q(C^{t} \mid C^{t-1})\) is the fixed posterior distribution
      • \(p_\theta(C^{t-1} \mid G, C^{t})\) are the Markov kernels through which the conformations are refined

      A primer on Diffusion Models

      A diffusion probabilistic model can be described as a latent variable model with two processes: the forward and the reverse generative processes. Intuitively, the diffusion process progressively injects small noises into \(C^{0}\), while the generative process learns to revert the diffusion process by gradually eliminating the noise to recover the ground truth. Diffusion models are trained by adding noise to the input, which the model then learns how to remove.

      In this blog post, we use the GeoDiff implementation of diffusion models to explain how the diffusion model works and how it is being used for the geometric representation of molecules. The implementation of the diffusion model in GeoDiff is inspired by the DDPM paper . To give a quick overview, the forward process \(q\) transforms the original input into complete noise over a certain number of timesteps and follows a normal distribution; the \(p_0\) involves denoising complete noise to the actual input using a neural network.

      Forward process

      Let \(q(\mathbf{C}^0)\) be the real data distribution of molecular conformation. We can sample from this distribution to get a conformation, \(\mathbf{C}^0 \sim q(\mathbf{C}^0)\). We define the forward diffusion process which adds Gaussian noise at each time step \(t\), according to a known variance schedule \beta_t which can be linear, quadratic, cosine, etc. as follows:

      \[\begin{align}\tag{1} q\left(\mathcal{C}^{1: T} \mid \mathcal{C}^0\right)=\prod_{t=1}^T q\left(\mathcal{C}^t \mid \mathcal{C}^{t-1}\right) \end{align}\]

      where \(\quad q\left(\mathcal{C}^t \mid \mathcal{C}^{t-1}\right)=\mathcal{N}\left(\mathcal{C}^t ; \sqrt{1-\beta_t} \mathcal{C}^{t-1}, \beta_t I\right)\)

      Instead of having to compute \(q\left(\mathcal{C}^t \mid \mathcal{C}^{t-1}\right)\) at every timestep \(t\), we could compute at an arbitrary timestep in closed form:

      \[\begin{equation}\tag{2} q\left(\mathcal{C}^t \mid \mathcal{C}^0\right)=\mathcal{N}\left(\mathcal{C}^t ; \sqrt{\bar{\alpha}_t} \mathcal{C}^0,\left(1-\bar{\alpha}_t\right) I\right) \end{equation}\]

      where \(\alpha_t=1-\beta_t\) and \(\bar{\alpha}_t=\prod_{s=1}^t \alpha_s\)

      Thus with a sufficiently large number of timesteps, the forward process could convert \(\mathcal{C}^0\) to whitened isotropic Gaussian and so we could set \(p\left(\mathcal{C}^T\right)\) as a standard Gaussian distribution.

      Reverse Process

      The reverse process involved recovering the original conformation \(\mathcal{C}^0\) from the white noise \(\mathcal{C}^T\) . We need the conditional distribution \(p_\theta\left(\mathcal{C}^{t-1} \mid \mathcal{G}, \mathcal{C}^t\right)\) to sample some random Gaussian noise \(\mathcal{C}^t\), and “denoise” gradually to end up with a sample from the real distribution \(\mathcal{C}^0\).

      However, the conditional distribution of \(p_\theta\left(\mathcal{C}^{t-1} \mid \mathcal{G}, \mathcal{C}^t\right)\) is intractable as it requires knowing the distribution of all possible conformations in order to calculate this conditional probability. Hence, a neural network could be used to learn this conditional probability distribution, let’s call it \(p_\theta\), with \(\theta\) being the parameters of the neural network, updated by gradient descent. Thus, we formulate the reverse process as a conditional Markov chain with learnable transitions:

      \[\begin{align*}\tag{3} p_\theta\left(\mathcal{C}^{0: T-1} \mid \mathcal{G}, \mathcal{C}^T\right)=\prod_{t=1}^T p_\theta\left(\mathcal{C}^{t-1} \mid \mathcal{G}, \mathcal{C}^t\right) \end{align*}\]

      where \(\quad p_\theta\left(\mathcal{C}^{t-1} \mid \mathcal{G}, \mathcal{C}^t\right)=\mathcal{N}\left(\mathcal{C}^{t-1} ; \mu_\theta\left(\mathcal{G}, \mathcal{C}^t, t\right), \sigma_t^2 I\right)\)

      Hence, the neural network in the reverse process needs to learn/represent the mean and variance. However, just like the DDPM paper, GeoDiff also lets the variance be user-defined and fixed, and \(\mu_\theta\) is the neural network that estimates means.

      GeoDiff uses a parametrisation trick inspired by the diffusion model implementation from the DDPM paper such that this parametrisation resembles Langevin dynamics and simplifies the diffusion model’s variational bound to an objective that resembles denoising score matching. Moreover, in the context of molecular conformation generation, this parametrisation trick is analogous to the physical force fields , which also gradually push particles towards convergence around the equilibrium states, and is defined by the following equation:

      \[\begin{align*}\tag{4} \mu_\theta\left(\mathcal{C}^t, t\right)=\frac{1}{\sqrt{\alpha_t}}\left(\mathcal{C}^t-\frac{\beta_t}{\sqrt{1-\bar{\alpha}_t}} \epsilon_\theta\left(\mathcal{G}, \mathcal{C}^t, t\right)\right) \end{align*}\]

      where \(\epsilon_\theta\) are neural networks with trainable parameters \(\theta\).

      Now, we need to make \(\epsilon_\theta\) roto-translational equivariant which we elaborate on in the next section.

      Making the reverse process roto-translation equivariant

      Firstly, we need to assume the prior distribution of the conformations and the intermediary conformations generated during the forward process are systems with zero centre of mass (CoM) or CoM-free systems . By considering CoM-free systems, moving the particles to zero CoM can always ensure translational invariance in the Markov kernels.

      GeoDiff employs the use of an equivariant convolutional layer, named graph field network (GFN) inspired by . In the \(l\)-th layer, GFN takes node embeddings \(h_l \in \mathbb{R}^{n \times b}\) (\(b\) denotes the feature dimension) and corresponding coordinate embeddings \(x_l \in \mathbb{R}^{n \times 3}\) as inputs, and outputs \(h_{l+1}\) and \(x_{l+1}\) as follows:

      \[\begin{align} \tag{5} & \mathbf{m}_{i j}=\Phi_m\left(\mathbf{h}_i^l, \mathbf{h}_j^l,\left\|\mathbf{x}_i^l-\mathbf{x}_j^l\right\|^2, e_{i j} ; \theta_m\right) \\ \tag{6} & \mathbf{h}_i^{l+1}=\Phi_h\left(\mathbf{h}_i^l, \sum_{j \in \mathcal{N}(i)} \mathbf{m}_{i j} ; \theta_h\right) \\ & \mathbf{x}_i^{l+1}=\sum_{j \in \mathcal{N}(i)} \frac{1}{d_{i j}}\left(\mathbf{c}_i-\mathbf{c}_j\right) \Phi_x\left(\mathbf{m}_{i j} ; \theta_x\right) \tag{7} \end{align}\]

      where

      • \(\Phi\) are feed-forward networks
      • \(d_{ij}\) are interatomic distances
      • \(\mathcal{N}(i)\) is the neighbourhood of the \(i\)-th node, which consists of both connected atoms and other ones within a radius threshold \(\tau\).

      By introducing the neighbourhood function, we enable the model to accurately represent distant interactions between atoms, as well as the ability to handle partially disconnected molecular graphs. Initial embeddings \(h_0\) are combinations of atom and timestep embeddings, and \(x_0\) are atomic coordinates. A key change in GFN compared to a vanilla GNN is \(x\) being updated as a combination of radial directions weighted by \(\Phi_x\): \(\mathbb{R}^b \rightarrow \mathbb{R}\) as seen in equation \((7)\). This allows the roto-translation equivariance property to be induced in the reverse process.

      Improved Training Objective

      Now, we need to set the training objective having considered the reverse process dynamics. We cannot compute the exact log-likelihood of the generative process, as it involves computing the likelihood of the observed molecular conformation given the parameters of the model. However, this likelihood is difficult to compute, as it would require integrating over all possible intermediate conformations, giving us a high-dimensional integral that cannot be solved analytically. Therefore, the authors have opted to maximize the variational lower bound (ELBO), as defined below:

      \[\begin{aligned} \mathbb{E}\left[\log p_\theta\left(\mathcal{C}^0 \mid \mathcal{G}\right)\right] & =\mathbb{E}\left[\log \mathbb{E}_{q\left(\mathcal{C}^{1: T} \mid \mathcal{C}^0\right)} \frac{p_\theta\left(\mathcal{C}^{0: T} \mid \mathcal{G}\right)}{q\left(\mathcal{C}^{1: T} \mid \mathcal{C}^0\right)}\right] \\ & \geq-\mathbb{E}_q\left[\sum_{t=1}^T D_{\mathrm{KL}}\left(q\left(\mathcal{C}^{t-1} \mid \mathcal{C}^t, \mathcal{C}^0\right) \| p_\theta\left(\mathcal{C}^{t-1} \mid \mathcal{C}^t, \mathcal{G}\right)\right)\right]:=-\mathcal{L}_{\mathrm{ELBO}}\end{aligned}\]

      where \(q\left(\mathcal{C}^{t-1} \mid \mathcal{C}^t, \mathcal{C}^0\right)\) is analytically tractable as \(\mathcal{N}\left(\frac{\sqrt{\bar{\alpha}_{t-1}} \beta_t}{1-\bar{\alpha}_t} \mathcal{C}^0+\frac{\sqrt{\alpha_t}\left(1-\bar{\alpha}_{t-1}\right)}{1-\bar{\alpha}_t} \mathcal{C}^t, \frac{1-\bar{\alpha}_{t-1}}{1-\bar{\alpha}_t} \beta_t\right)\).

      Using the parametrisation trick in the reverse process as seen in equation \((4)\), the ELBO could be simplified by taking the KL divergences between Gaussians as weighted \(\mathcal{L}_2\) distances between the means \(\epsilon_\theta\) and \(\epsilon^3\) as follows: \(\mathcal{L}_{\mathrm{ELBO}}=\sum_{t=1}^T \gamma_t \mathbb{E}_{\left\{\mathcal{C}^0, \mathcal{G}\right\} \sim q\left(\mathcal{C}^0, \mathcal{G}\right), \epsilon \sim \mathcal{N}(0, I)}\left[\left\|\epsilon-\epsilon_\theta\left(\mathcal{G}, \mathcal{C}^t, t\right)\right\|_2^2\right]\) where \(\mathcal{C}^t=\sqrt{\bar{\alpha}_t} \mathcal{C}^0+\sqrt{1-\bar{\alpha}_t} \epsilon\).

      The idea behind this objective is to independently sample chaotic conformations of different timesteps from \(q\left(C^{t-1} \mid C^t, C^0\right)\), and use \(\epsilon_\theta\) to approximate the noise vector \(\epsilon\).

      Sampling

      Now, we can generate stable molecular conformations via sampling. Given a graph \(\mathcal{G}\), its geometry \(\mathcal{C}^0\) is generated by first sampling chaotic particles \(\mathcal{C}^T \sim p\left(\mathcal{C}^T\right)\). For each timestep in the reverse process \(t=T, T-\) \(1, \cdots, 1\), we first shift the CoM of the conformation to zero, compute the transition means, \(\mu_\theta\left(\mathcal{G}, \mathcal{C}^t, t\right)\), using equation \((4)\) and sample \(\mathcal{C}^{t-1} \sim\) \(p_\theta\left(\mathcal{C}^{t-1} \mid \mathcal{G}, \mathcal{C}^t\right)\). The sampling algorithm is given in pseudo-code below:

      Algorithm 1 Sampling Algorithm of GEODIFF
      Input: the molecular graph \(\mathcal{G}\), the learned reverse model \(\epsilon_\theta\).
      Output: the molecular conformation \(\mathcal{C}\).
      1: Sample \(\mathcal{C}^T \sim p\left(\mathcal{C}^T\right)=\mathcal{N}(0, I)\)
      2: for \(s=T, T-1, \cdots, 1\) do
      3: \(\quad\) Shift \(\mathcal{C}^s\) to zero CoM
      4: \(\quad\) Compute \(\mu_\theta\left(\mathcal{C}^s, \mathcal{G}, s\right)\) from \(\epsilon_\theta\left(\mathcal{C}^s, \mathcal{G}, s\right)\) using equation 4
      5: \(\quad\) Sample \(\mathcal{C}^{s-1} \sim \mathcal{N}\left(\mathcal{C}^{s-1} ; \mu_\theta\left(\mathcal{C}^{\mathcal{s}}, \mathcal{G}, s\right), \sigma_t^2 I\right)\)
      6: end for
      7: return \(\mathcal{C}^0\) as $\mathcal{C}$$

      But why generative models?

      The purpose of prediciting molecular conformations is to enable human experts to analyse the properties of the molecules and understand how these properties affect the viability of a molecule as a drug candidate. Therefore, it is important that the molecular conformations generated are diverse to capture the different possible conformations that could occur in nature but the conformations generated should not deviate significantly such that the analysis is affected. To set a threshold for the different possible conformations, the standard metric used has been selecting conformations that are within a certain root-mean-square deviation (RMSD), say a few ångströms, of the true structure.

      However, the objective of maximizing the proportion of predictions with RMSD within some tolerance \(\epsilon\) is not differentiable and thus, cannot be used for training with stochastic gradient descent. Instead, maximizing the expected proportion of predictions with RMSD < \(\epsilon\) corresponds to maximizing the likelihood of the true structure under the model’s output distribution, in the limit as \(\epsilon\) goes to 0. This concept inspires the development of a generative model, whose objective is to minimize an upper bound on the negative log-likelihood of observed molecular structures under the distribution of the model. As a result, the problem of molecular docking is treated as a task of learning a distribution over possible positions of a ligand molecule conditioned on the protein structure and a diffusion generative model is developed to represent this space. Therefore, this observation has motivated several works on the use of generative models for molecular conformation generation, such as GeoDiff.

      Future work

      While diffusion models have shown promising results over the past months, there is still a need for further research and development to address some of the limitations and drawbacks of the use of diffusion models in conformer generation. As explained in our blog post, generative models are well-suited for molecular conformation generation. However, there are other kinds of established generative models, such as autoencoders that have been used for the same task . For instance, comparing diffusion models and autoencoders, diffusion models can handle all noise levels with a single set of parameters, without any bottlenecks, which an autoencoder would have . Thus, it is essential to study the advantages and disadvantages of different types and variants of generative models for conformation generation and understand what changes could be done to them to make them more suitable for molecular conformation.

      It must be noted that the experiments described in the study are done on benchmark geometric datasets, GEOM-QM9 and GEOM-Drugs , rather than industrial data, with a relatively small number of samples/drug/molecular compounds. Industry data may exhibit greater variability than standard geometric datasets, as they may be more diverse, complex and subject to greater fluctuations than these geometric datasets, which tend to be more standardized and more predictable.

      GeoDiff as a framework sets a precedent for future work that could marry the concepts of geometric deep learning and diffusion models across various domains. In the context of drug discovery, it would be interesting to extend this framework to more challenging structures, such as proteins, which may enable more accurate prediction of protein folding, protein-protein interactions and protein-ligand binding positions which would facilitate the design of new drugs and treatments. Additionally, this framework could potentially be applied to other complex systems beyond proteins, such as RNA molecules, to enable more efficient and accurate prediction of their behaviour and properties. Continued research in this area has the potential to revolutionize drug discovery and development, as well as advance our understanding of the fundamental principles governing the behaviour of complex biological systems.

      Research on the application of diffusion models in the life and natural sciences is still in its infancy, with great potential for improvement in terms of both theory as well as empirical testing. The GeoDiff model could be improved in terms of more efficient sampling and improved likelihood maximization methods. Traditionally, generating samples from diffusion models demand iterative approaches that involve a large number of evaluation steps. Recent work, such as the paper on Torsional Diffusion was able to speed up the sampling process, while also enhancing the quality of the resulting samples. Experimentally, Torsional Diffusion only takes 5 to 20 steps in comparison to GeoDiff which takes around 5000 steps .

      Looking ahead, GeoDiff has set a clear example for the use of diffusion models on geometric representations which could be extended to several problems, especially in the field of drug discovery. The novel contributions made by

      are motivated by the physical characteristics of the molecular conformation generation problem, which has resulted in a strong candidate method for conformation generation that could act as a springboard for even more effective and efficient methods that would eventually benefit the field of drug discovery as a whole.
      \ No newline at end of file diff --git a/blog/2023/index.html b/blog/2023/index.html new file mode 100644 index 00000000..cc84d71f --- /dev/null +++ b/blog/2023/index.html @@ -0,0 +1 @@ + 2023 | 6.S898 Deep Learning Blogs 2023

      2023

      an archive of posts from this year

      \ No newline at end of file diff --git a/blog/2023/test/index.html b/blog/2023/test/index.html new file mode 100644 index 00000000..f07c706c --- /dev/null +++ b/blog/2023/test/index.html @@ -0,0 +1,32 @@ + A Match Made in Drug Discovery - Marrying Geometric and Diffusion Models | 6.S898 Deep Learning Blogs 2023

      A Match Made in Drug Discovery - Marrying Geometric and Diffusion Models

      The chemical space of molecular candidates is vast, and within this space, interesting and powerful drugs are waiting to be found. The use of machine learning has shown to be an effective method to speed up the process of discovering novel compounds, especially the use of (deep) generative models. The recent surge in graph generative models have opened up new avenues for exploring the chemical space of molecular candidates, enabling a more efficient and systematic exploration of the chemical space, increasing the chances of finding novel and potent molecules. One of the recent breakthroughs includes the use of diffusion models, which have proven to yield superior performance in molecular conformation tasks, among others. In this blog post, we aim to highlight one of them, which is the 'GeoDiff - A Geometric Diffusion Model for Molecular Conformation Generation' paper by Xu et al. (2022). We aim to distill the paper in semi-layman terms, to provide researchers and practitioners with a deeper understanding of the (i) methodology and results and (ii) (societal) implications of this breakthrough in the field of drug discovery and (iii) discuss future applications in the field of (bio)medicine.

      A Match Made in Drug Discovery: Marrying Geometric and Diffusion Models

      Introduction

      With the initial breakthrough of the Denoising Diffusion , diffusion models have evolved into a powerful tool for a wide range of applications in machine learning, including image generation and text generation. The rise and the recent release of Stable Diffusion in August 2022 has shown superior performance in a wide range of practical applications - from artistic and creative projects to scientific and industrial ones and has recently paved its way into the natural sciences, which includes the field of drug discovery .

      Data-driven applications have increasingly been shown to accelerate solving diverse problems in the drug discovery pipeline – from the use of predictive analytical methods for target identification and lead optimization, to the analysis of large-scale biological data for drug repurposing and personalized medicine. To limit the scope of the blog post, we will only focus on the use of generative methods in molecular conformation generation.

      Motivation

      Generating molecular conformations is a task fundamental to cheminformatics and drug discovery. The conformation of a molecule refers to the three-dimensional (3D) coordinates of all the atoms in a molecule in a 3D Euclidean space, which can be interconverted by rotations about formally single bonds . It allows for the prediction of the physical and chemical properties and interactions of molecules based on their possible 3D conformations, as well as their biological activity. In drug discovery, it is integral to obtain all the possible conformations of molecules for various tasks, such as three-dimensional quantitative structure-activity relationships (3D-QSAR), pharmacophore searching, molecular docking and thermodynamic calculations. Deep generative modelling, which aims to learn complex data distributions, is a recent promising approach to tackle the conformation generation problem . When studying molecules it is important to understand them as three-dimensional structures formed by atoms bonded to each other. To encode the chemical properties, molecules could be represented as graphs where atoms (nodes) are connected by bonds (edges). Representing molecules as 3D molecular graphs captures the spatial arrangement of a molecule, which in turn determines its chemical property. A molecule could take up any conformation based on all possible permutations and combinations of spatial arrangements of atoms. However, some conformations may not occur physically, due to e.g steric hindrance, which arises when the spatial arrangement of atoms leads to unfavourable interactions/repulsive forces, leading to a higher energy state and less stable conformation.

      Therefore, we are only interested in conformations that fall in stable low-energy minima, as these low-energy conformations are the ones that the molecule will most likely adopt under natural conditions and play a crucial role in determining the molecule’s behaviour and properties. By identifying and characterizing the low-energy conformations, researchers gain insights into their stability, reactivity and interactions with other molecules.

      Formulating the conformation generation problem

      A formulation of the conformation generation problem, adapted from

      We can formulate the problem of conformation generation as a conditional generative problem where we aim to generate stable conformations \(C\) from a molecule’s graph \(G\). For each \(G\) given its conformations \(C\) as i.i.d samples from an underlying Boltzmann distribution , our goal is to learn a generative model $$p_\theta(C G)$$ to draw possible conformations from.

      Roto-translation equivariance

      A visualisation of roto-translation equivariance, adapted from

      To generate stable molecular conformations, we need an algorithm that preserves roto-translation equivariance of the conformations that previous work has not focused on. To explain this property, let us delve into what equivariance is. A representation \(φ\) is equivariant with a transformation \(g\) of the input if the transformation can be transferred to the representation output. Invariance is a special case of equivariance obtained when the transformation is the identity map .

      In the context of molecular conformations, we have to achieve the special case of equivariance in terms of rotation and translation, namely, roto-translation equivariance of the conformations which ensures that however the molecule is rotated or translated, the estimated (conditional) likelihood should be unaffected. GeoDiff considers the SE(3) Lie group which can be used to represent rotation and translation in 3D space .

      Decomposing GeoDiff

      The diffusion model of GeoDiff, adapted from

      Legend:

      • \(C^{0}\) denotes the ground truth conformations
      • \(C^{t}\), where \(t = 1,···, T\) is the index for diffusion steps and \(C^{t}\), is the sequence of latent variables with the same dimension
      • \(q(C^{t} \mid C^{t-1})\) is the fixed posterior distribution
      • \(p_\theta(C^{t-1} \mid G, C^{t})\) are the Markov kernels through which the conformations are refined

      A primer on Diffusion Models

      A diffusion probabilistic model can be described as a latent variable model with two processes: the forward and the reverse generative processes. Intuitively, the diffusion process progressively injects small noises into \(C^{0}\), while the generative process learns to revert the diffusion process by gradually eliminating the noise to recover the ground truth. Diffusion models are trained by adding noise to the input, which the model then learns how to remove.

      In this blog post, we use the GeoDiff implementation of diffusion models to explain how the diffusion model works and how it is being used for the geometric representation of molecules. The implementation of the diffusion model in GeoDiff is inspired by the DDPM paper . To give a quick overview, the forward process \(q\) transforms the original input into complete noise over a certain number of timesteps and follows a normal distribution; the \(p_0\) involves denoising complete noise to the actual input using a neural network.

      Forward process

      Let \(q(\mathbf{C}^0)\) be the real data distribution of molecular conformation. We can sample from this distribution to get a conformation, \(\mathbf{C}^0 \sim q(\mathbf{C}^0)\). We define the forward diffusion process which adds Gaussian noise at each time step \(t\), according to a known variance schedule \beta_t which can be linear, quadratic, cosine, etc. as follows:

      \[\begin{align}\tag{1} q\left(\mathcal{C}^{1: T} \mid \mathcal{C}^0\right)=\prod_{t=1}^T q\left(\mathcal{C}^t \mid \mathcal{C}^{t-1}\right) \end{align}\]

      where \(\quad q\left(\mathcal{C}^t \mid \mathcal{C}^{t-1}\right)=\mathcal{N}\left(\mathcal{C}^t ; \sqrt{1-\beta_t} \mathcal{C}^{t-1}, \beta_t I\right)\)

      Instead of having to compute \(q\left(\mathcal{C}^t \mid \mathcal{C}^{t-1}\right)\) at every timestep \(t\), we could compute at an arbitrary timestep in closed form:

      \[\begin{equation}\tag{2} q\left(\mathcal{C}^t \mid \mathcal{C}^0\right)=\mathcal{N}\left(\mathcal{C}^t ; \sqrt{\bar{\alpha}_t} \mathcal{C}^0,\left(1-\bar{\alpha}_t\right) I\right) \end{equation}\]

      where \(\alpha_t=1-\beta_t\) and \(\bar{\alpha}_t=\prod_{s=1}^t \alpha_s\)

      Thus with a sufficiently large number of timesteps, the forward process could convert \(\mathcal{C}^0\) to whitened isotropic Gaussian and so we could set \(p\left(\mathcal{C}^T\right)\) as a standard Gaussian distribution.

      Reverse Process

      The reverse process involved recovering the original conformation \(\mathcal{C}^0\) from the white noise \(\mathcal{C}^T\) . We need the conditional distribution \(p_\theta\left(\mathcal{C}^{t-1} \mid \mathcal{G}, \mathcal{C}^t\right)\) to sample some random Gaussian noise \(\mathcal{C}^t\), and “denoise” gradually to end up with a sample from the real distribution \(\mathcal{C}^0\).

      However, the conditional distribution of \(p_\theta\left(\mathcal{C}^{t-1} \mid \mathcal{G}, \mathcal{C}^t\right)\) is intractable as it requires knowing the distribution of all possible conformations in order to calculate this conditional probability. Hence, a neural network could be used to learn this conditional probability distribution, let’s call it \(p_\theta\), with \(\theta\) being the parameters of the neural network, updated by gradient descent. Thus, we formulate the reverse process as a conditional Markov chain with learnable transitions:

      \[\begin{align*}\tag{3} p_\theta\left(\mathcal{C}^{0: T-1} \mid \mathcal{G}, \mathcal{C}^T\right)=\prod_{t=1}^T p_\theta\left(\mathcal{C}^{t-1} \mid \mathcal{G}, \mathcal{C}^t\right) \end{align*}\]

      where \(\quad p_\theta\left(\mathcal{C}^{t-1} \mid \mathcal{G}, \mathcal{C}^t\right)=\mathcal{N}\left(\mathcal{C}^{t-1} ; \mu_\theta\left(\mathcal{G}, \mathcal{C}^t, t\right), \sigma_t^2 I\right)\)

      Hence, the neural network in the reverse process needs to learn/represent the mean and variance. However, just like the DDPM paper, GeoDiff also lets the variance be user-defined and fixed, and \(\mu_\theta\) is the neural network that estimates means.

      GeoDiff uses a parametrisation trick inspired by the diffusion model implementation from the DDPM paper such that this parametrisation resembles Langevin dynamics and simplifies the diffusion model’s variational bound to an objective that resembles denoising score matching. Moreover, in the context of molecular conformation generation, this parametrisation trick is analogous to the physical force fields , which also gradually push particles towards convergence around the equilibrium states, and is defined by the following equation:

      \[\begin{align*}\tag{4} \mu_\theta\left(\mathcal{C}^t, t\right)=\frac{1}{\sqrt{\alpha_t}}\left(\mathcal{C}^t-\frac{\beta_t}{\sqrt{1-\bar{\alpha}_t}} \epsilon_\theta\left(\mathcal{G}, \mathcal{C}^t, t\right)\right) \end{align*}\]

      where \(\epsilon_\theta\) are neural networks with trainable parameters \(\theta\).

      Now, we need to make \(\epsilon_\theta\) roto-translational equivariant which we elaborate on in the next section.

      Making the reverse process roto-translation equivariant

      Firstly, we need to assume the prior distribution of the conformations and the intermediary conformations generated during the forward process are systems with zero centre of mass (CoM) or CoM-free systems . By considering CoM-free systems, moving the particles to zero CoM can always ensure translational invariance in the Markov kernels.

      GeoDiff employs the use of an equivariant convolutional layer, named graph field network (GFN) inspired by . In the \(l\)-th layer, GFN takes node embeddings \(h_l \in \mathbb{R}^{n \times b}\) (\(b\) denotes the feature dimension) and corresponding coordinate embeddings \(x_l \in \mathbb{R}^{n \times 3}\) as inputs, and outputs \(h_{l+1}\) and \(x_{l+1}\) as follows:

      \[\begin{align} \tag{5} & \mathbf{m}_{i j}=\Phi_m\left(\mathbf{h}_i^l, \mathbf{h}_j^l,\left\|\mathbf{x}_i^l-\mathbf{x}_j^l\right\|^2, e_{i j} ; \theta_m\right) \\ \tag{6} & \mathbf{h}_i^{l+1}=\Phi_h\left(\mathbf{h}_i^l, \sum_{j \in \mathcal{N}(i)} \mathbf{m}_{i j} ; \theta_h\right) \\ & \mathbf{x}_i^{l+1}=\sum_{j \in \mathcal{N}(i)} \frac{1}{d_{i j}}\left(\mathbf{c}_i-\mathbf{c}_j\right) \Phi_x\left(\mathbf{m}_{i j} ; \theta_x\right) \tag{7} \end{align}\]

      where

      • \(\Phi\) are feed-forward networks
      • \(d_{ij}\) are interatomic distances
      • \(\mathcal{N}(i)\) is the neighbourhood of the \(i\)-th node, which consists of both connected atoms and other ones within a radius threshold \(\tau\).

      By introducing the neighbourhood function, we enable the model to accurately represent distant interactions between atoms, as well as the ability to handle partially disconnected molecular graphs. Initial embeddings \(h_0\) are combinations of atom and timestep embeddings, and \(x_0\) are atomic coordinates. A key change in GFN compared to a vanilla GNN is \(x\) being updated as a combination of radial directions weighted by \(\Phi_x\): \(\mathbb{R}^b \rightarrow \mathbb{R}\) as seen in equation \((7)\). This allows the roto-translation equivariance property to be induced in the reverse process.

      Improved Training Objective

      Now, we need to set the training objective having considered the reverse process dynamics. We cannot compute the exact log-likelihood of the generative process, as it involves computing the likelihood of the observed molecular conformation given the parameters of the model. However, this likelihood is difficult to compute, as it would require integrating over all possible intermediate conformations, giving us a high-dimensional integral that cannot be solved analytically. Therefore, the authors have opted to maximize the variational lower bound (ELBO), as defined below:

      \[\begin{aligned} \mathbb{E}\left[\log p_\theta\left(\mathcal{C}^0 \mid \mathcal{G}\right)\right] & =\mathbb{E}\left[\log \mathbb{E}_{q\left(\mathcal{C}^{1: T} \mid \mathcal{C}^0\right)} \frac{p_\theta\left(\mathcal{C}^{0: T} \mid \mathcal{G}\right)}{q\left(\mathcal{C}^{1: T} \mid \mathcal{C}^0\right)}\right] \\ & \geq-\mathbb{E}_q\left[\sum_{t=1}^T D_{\mathrm{KL}}\left(q\left(\mathcal{C}^{t-1} \mid \mathcal{C}^t, \mathcal{C}^0\right) \| p_\theta\left(\mathcal{C}^{t-1} \mid \mathcal{C}^t, \mathcal{G}\right)\right)\right]:=-\mathcal{L}_{\mathrm{ELBO}}\end{aligned}\]

      where \(q\left(\mathcal{C}^{t-1} \mid \mathcal{C}^t, \mathcal{C}^0\right)\) is analytically tractable as \(\mathcal{N}\left(\frac{\sqrt{\bar{\alpha}_{t-1}} \beta_t}{1-\bar{\alpha}_t} \mathcal{C}^0+\frac{\sqrt{\alpha_t}\left(1-\bar{\alpha}_{t-1}\right)}{1-\bar{\alpha}_t} \mathcal{C}^t, \frac{1-\bar{\alpha}_{t-1}}{1-\bar{\alpha}_t} \beta_t\right)\).

      Using the parametrisation trick in the reverse process as seen in equation \((4)\), the ELBO could be simplified by taking the KL divergences between Gaussians as weighted \(\mathcal{L}_2\) distances between the means \(\epsilon_\theta\) and \(\epsilon^3\) as follows: \(\mathcal{L}_{\mathrm{ELBO}}=\sum_{t=1}^T \gamma_t \mathbb{E}_{\left\{\mathcal{C}^0, \mathcal{G}\right\} \sim q\left(\mathcal{C}^0, \mathcal{G}\right), \epsilon \sim \mathcal{N}(0, I)}\left[\left\|\epsilon-\epsilon_\theta\left(\mathcal{G}, \mathcal{C}^t, t\right)\right\|_2^2\right]\) where \(\mathcal{C}^t=\sqrt{\bar{\alpha}_t} \mathcal{C}^0+\sqrt{1-\bar{\alpha}_t} \epsilon\).

      The idea behind this objective is to independently sample chaotic conformations of different timesteps from \(q\left(C^{t-1} \mid C^t, C^0\right)\), and use \(\epsilon_\theta\) to approximate the noise vector \(\epsilon\).

      Sampling

      Now, we can generate stable molecular conformations via sampling. Given a graph \(\mathcal{G}\), its geometry \(\mathcal{C}^0\) is generated by first sampling chaotic particles \(\mathcal{C}^T \sim p\left(\mathcal{C}^T\right)\). For each timestep in the reverse process \(t=T, T-\) \(1, \cdots, 1\), we first shift the CoM of the conformation to zero, compute the transition means, \(\mu_\theta\left(\mathcal{G}, \mathcal{C}^t, t\right)\), using equation \((4)\) and sample \(\mathcal{C}^{t-1} \sim\) \(p_\theta\left(\mathcal{C}^{t-1} \mid \mathcal{G}, \mathcal{C}^t\right)\). The sampling algorithm is given in pseudo-code below:

      Algorithm 1 Sampling Algorithm of GEODIFF
      Input: the molecular graph \(\mathcal{G}\), the learned reverse model \(\epsilon_\theta\).
      Output: the molecular conformation \(\mathcal{C}\).
      1: Sample \(\mathcal{C}^T \sim p\left(\mathcal{C}^T\right)=\mathcal{N}(0, I)\)
      2: for \(s=T, T-1, \cdots, 1\) do
      3: \(\quad\) Shift \(\mathcal{C}^s\) to zero CoM
      4: \(\quad\) Compute \(\mu_\theta\left(\mathcal{C}^s, \mathcal{G}, s\right)\) from \(\epsilon_\theta\left(\mathcal{C}^s, \mathcal{G}, s\right)\) using equation 4
      5: \(\quad\) Sample \(\mathcal{C}^{s-1} \sim \mathcal{N}\left(\mathcal{C}^{s-1} ; \mu_\theta\left(\mathcal{C}^{\mathcal{s}}, \mathcal{G}, s\right), \sigma_t^2 I\right)\)
      6: end for
      7: return \(\mathcal{C}^0\) as $\mathcal{C}$$

      But why generative models?

      The purpose of prediciting molecular conformations is to enable human experts to analyse the properties of the molecules and understand how these properties affect the viability of a molecule as a drug candidate. Therefore, it is important that the molecular conformations generated are diverse to capture the different possible conformations that could occur in nature but the conformations generated should not deviate significantly such that the analysis is affected. To set a threshold for the different possible conformations, the standard metric used has been selecting conformations that are within a certain root-mean-square deviation (RMSD), say a few ångströms, of the true structure.

      However, the objective of maximizing the proportion of predictions with RMSD within some tolerance \(\epsilon\) is not differentiable and thus, cannot be used for training with stochastic gradient descent. Instead, maximizing the expected proportion of predictions with RMSD < \(\epsilon\) corresponds to maximizing the likelihood of the true structure under the model’s output distribution, in the limit as \(\epsilon\) goes to 0. This concept inspires the development of a generative model, whose objective is to minimize an upper bound on the negative log-likelihood of observed molecular structures under the distribution of the model. As a result, the problem of molecular docking is treated as a task of learning a distribution over possible positions of a ligand molecule conditioned on the protein structure and a diffusion generative model is developed to represent this space. Therefore, this observation has motivated several works on the use of generative models for molecular conformation generation, such as GeoDiff.

      Future work

      While diffusion models have shown promising results over the past months, there is still a need for further research and development to address some of the limitations and drawbacks of the use of diffusion models in conformer generation. As explained in our blog post, generative models are well-suited for molecular conformation generation. However, there are other kinds of established generative models, such as autoencoders that have been used for the same task . For instance, comparing diffusion models and autoencoders, diffusion models can handle all noise levels with a single set of parameters, without any bottlenecks, which an autoencoder would have . Thus, it is essential to study the advantages and disadvantages of different types and variants of generative models for conformation generation and understand what changes could be done to them to make them more suitable for molecular conformation.

      It must be noted that the experiments described in the study are done on benchmark geometric datasets, GEOM-QM9 and GEOM-Drugs , rather than industrial data, with a relatively small number of samples/drug/molecular compounds. Industry data may exhibit greater variability than standard geometric datasets, as they may be more diverse, complex and subject to greater fluctuations than these geometric datasets, which tend to be more standardized and more predictable.

      GeoDiff as a framework sets a precedent for future work that could marry the concepts of geometric deep learning and diffusion models across various domains. In the context of drug discovery, it would be interesting to extend this framework to more challenging structures, such as proteins, which may enable more accurate prediction of protein folding, protein-protein interactions and protein-ligand binding positions which would facilitate the design of new drugs and treatments. Additionally, this framework could potentially be applied to other complex systems beyond proteins, such as RNA molecules, to enable more efficient and accurate prediction of their behaviour and properties. Continued research in this area has the potential to revolutionize drug discovery and development, as well as advance our understanding of the fundamental principles governing the behaviour of complex biological systems.

      Research on the application of diffusion models in the life and natural sciences is still in its infancy, with great potential for improvement in terms of both theory as well as empirical testing. The GeoDiff model could be improved in terms of more efficient sampling and improved likelihood maximization methods. Traditionally, generating samples from diffusion models demand iterative approaches that involve a large number of evaluation steps. Recent work, such as the paper on Torsional Diffusion was able to speed up the sampling process, while also enhancing the quality of the resulting samples. Experimentally, Torsional Diffusion only takes 5 to 20 steps in comparison to GeoDiff which takes around 5000 steps .

      Looking ahead, GeoDiff has set a clear example for the use of diffusion models on geometric representations which could be extended to several problems, especially in the field of drug discovery. The novel contributions made by

      are motivated by the physical characteristics of the molecular conformation generation problem, which has resulted in a strong candidate method for conformation generation that could act as a springboard for even more effective and efficient methods that would eventually benefit the field of drug discovery as a whole.
      \ No newline at end of file diff --git a/blog/index.html b/blog/index.html index e1230a92..f173e1e7 100644 --- a/blog/index.html +++ b/blog/index.html @@ -1,103 +1 @@ ---- -layout: default -title: blog -nav: true -nav_order: 9 -permalink: /blog -pagination: - enabled: true - collection: posts - permalink: /page/:num/ - per_page: 30 - sort_field: date - sort_reverse: true - trail: - before: 1 # The number of links before the current page - after: 3 # The number of links after the current page ---- - -
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      + blog | 6.S898 Deep Learning Blogs 2023

      6.S898 Deep Learning Blogs

      Fall 2023

      • A Match Made in Drug Discovery - Marrying Geometric and Diffusion Models

        The chemical space of molecular candidates is vast, and within this space, interesting and powerful drugs are waiting to be found. The use of machine learning has shown to be an effective method to speed up the process of discovering novel compounds, especially the use of (deep) generative models. The recent surge in graph generative models have opened up new avenues for exploring the chemical space of molecular candidates, enabling a more efficient and systematic exploration of the chemical space, increasing the chances of finding novel and potent molecules. One of the recent breakthroughs includes the use of diffusion models, which have proven to yield superior performance in molecular conformation tasks, among others. In this blog post, we aim to highlight one of them, which is the 'GeoDiff - A Geometric Diffusion Model for Molecular Conformation Generation' paper by Xu et al. (2022). We aim to distill the paper in semi-layman terms, to provide researchers and practitioners with a deeper understanding of the (i) methodology and results and (ii) (societal) implications of this breakthrough in the field of drug discovery and (iii) discuss future applications in the field of (bio)medicine.

        17 min read   ·   February 17, 2023

        2023

      • A Match Made in Drug Discovery - Marrying Geometric and Diffusion Models

        The chemical space of molecular candidates is vast, and within this space, interesting and powerful drugs are waiting to be found. The use of machine learning has shown to be an effective method to speed up the process of discovering novel compounds, especially the use of (deep) generative models. The recent surge in graph generative models have opened up new avenues for exploring the chemical space of molecular candidates, enabling a more efficient and systematic exploration of the chemical space, increasing the chances of finding novel and potent molecules. One of the recent breakthroughs includes the use of diffusion models, which have proven to yield superior performance in molecular conformation tasks, among others. In this blog post, we aim to highlight one of them, which is the 'GeoDiff - A Geometric Diffusion Model for Molecular Conformation Generation' paper by Xu et al. (2022). We aim to distill the paper in semi-layman terms, to provide researchers and practitioners with a deeper understanding of the (i) methodology and results and (ii) (societal) implications of this breakthrough in the field of drug discovery and (iii) discuss future applications in the field of (bio)medicine.

        17 min read   ·   February 17, 2023

        2023

      • Sample Blog Post

        Your blog post's abstract. This is an example of a distill-style blog post and the main elements it supports.

        14 min read   ·   December 1, 2022

        2022

      \ No newline at end of file diff --git a/docker/.gitignore b/docker/.gitignore deleted file mode 100644 index 2ca86829..00000000 --- a/docker/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -_site/ -.sass-cache/ -.jekyll-cache/ -.jekyll-metadata diff --git a/feed.xml b/feed.xml new file mode 100644 index 00000000..480e7008 --- /dev/null +++ b/feed.xml @@ -0,0 +1,47 @@ +Jekyll2023-10-19T16:53:28+00:00https://deep-learning-mit.github.io/staging/feed.xml6.S898 Deep Learning Blogs 2023Staging website for the 2023 ICLR Blogposts track A Match Made in Drug Discovery - Marrying Geometric and Diffusion Models2023-02-17T00:00:00+00:002023-02-17T00:00:00+00:00https://deep-learning-mit.github.io/staging/blog/2023/diffusion-is-all-you-needA Match Made in Drug Discovery: Marrying Geometric and Diffusion Models

      Introduction

      With the initial breakthrough of the Denoising Diffusion , diffusion models have evolved into a powerful tool for a wide range of applications in machine learning, including image generation and text generation. The rise and the recent release of Stable Diffusion in August 2022 has shown superior performance in a wide range of practical applications - from artistic and creative projects to scientific and industrial ones and has recently paved its way into the natural sciences, which includes the field of drug discovery .

      Data-driven applications have increasingly been shown to accelerate solving diverse problems in the drug discovery pipeline – from the use of predictive analytical methods for target identification and lead optimization, to the analysis of large-scale biological data for drug repurposing and personalized medicine. To limit the scope of the blog post, we will only focus on the use of generative methods in molecular conformation generation.

      Motivation

      Generating molecular conformations is a task fundamental to cheminformatics and drug discovery. The conformation of a molecule refers to the three-dimensional (3D) coordinates of all the atoms in a molecule in a 3D Euclidean space, which can be interconverted by rotations about formally single bonds . It allows for the prediction of the physical and chemical properties and interactions of molecules based on their possible 3D conformations, as well as their biological activity. In drug discovery, it is integral to obtain all the possible conformations of molecules for various tasks, such as three-dimensional quantitative structure-activity relationships (3D-QSAR), pharmacophore searching, molecular docking and thermodynamic calculations. Deep generative modelling, which aims to learn complex data distributions, is a recent promising approach to tackle the conformation generation problem . When studying molecules it is important to understand them as three-dimensional structures formed by atoms bonded to each other. To encode the chemical properties, molecules could be represented as graphs where atoms (nodes) are connected by bonds (edges). Representing molecules as 3D molecular graphs captures the spatial arrangement of a molecule, which in turn determines its chemical property. A molecule could take up any conformation based on all possible permutations and combinations of spatial arrangements of atoms. However, some conformations may not occur physically, due to e.g steric hindrance, which arises when the spatial arrangement of atoms leads to unfavourable interactions/repulsive forces, leading to a higher energy state and less stable conformation.

      Therefore, we are only interested in conformations that fall in stable low-energy minima, as these low-energy conformations are the ones that the molecule will most likely adopt under natural conditions and play a crucial role in determining the molecule’s behaviour and properties. By identifying and characterizing the low-energy conformations, researchers gain insights into their stability, reactivity and interactions with other molecules.

      Formulating the conformation generation problem

      A formulation of the conformation generation problem, adapted from

      We can formulate the problem of conformation generation as a conditional generative problem where we aim to generate stable conformations \(C\) from a molecule’s graph \(G\). For each \(G\) given its conformations \(C\) as i.i.d samples from an underlying Boltzmann distribution , our goal is to learn a generative model $$p_\theta(C G)$$ to draw possible conformations from.

      Roto-translation equivariance

      A visualisation of roto-translation equivariance, adapted from

      To generate stable molecular conformations, we need an algorithm that preserves roto-translation equivariance of the conformations that previous work has not focused on. To explain this property, let us delve into what equivariance is. A representation \(φ\) is equivariant with a transformation \(g\) of the input if the transformation can be transferred to the representation output. Invariance is a special case of equivariance obtained when the transformation is the identity map .

      In the context of molecular conformations, we have to achieve the special case of equivariance in terms of rotation and translation, namely, roto-translation equivariance of the conformations which ensures that however the molecule is rotated or translated, the estimated (conditional) likelihood should be unaffected. GeoDiff considers the SE(3) Lie group which can be used to represent rotation and translation in 3D space .

      Decomposing GeoDiff

      The diffusion model of GeoDiff, adapted from

      Legend:

      • \(C^{0}\) denotes the ground truth conformations
      • \(C^{t}\), where \(t = 1,···, T\) is the index for diffusion steps and \(C^{t}\), is the sequence of latent variables with the same dimension
      • \(q(C^{t} \mid C^{t-1})\) is the fixed posterior distribution
      • \(p_\theta(C^{t-1} \mid G, C^{t})\) are the Markov kernels through which the conformations are refined

      A primer on Diffusion Models

      A diffusion probabilistic model can be described as a latent variable model with two processes: the forward and the reverse generative processes. Intuitively, the diffusion process progressively injects small noises into \(C^{0}\), while the generative process learns to revert the diffusion process by gradually eliminating the noise to recover the ground truth. Diffusion models are trained by adding noise to the input, which the model then learns how to remove.

      In this blog post, we use the GeoDiff implementation of diffusion models to explain how the diffusion model works and how it is being used for the geometric representation of molecules. The implementation of the diffusion model in GeoDiff is inspired by the DDPM paper . To give a quick overview, the forward process \(q\) transforms the original input into complete noise over a certain number of timesteps and follows a normal distribution; the \(p_0\) involves denoising complete noise to the actual input using a neural network.

      Forward process

      Let \(q(\mathbf{C}^0)\) be the real data distribution of molecular conformation. We can sample from this distribution to get a conformation, \(\mathbf{C}^0 \sim q(\mathbf{C}^0)\). We define the forward diffusion process which adds Gaussian noise at each time step \(t\), according to a known variance schedule \beta_t which can be linear, quadratic, cosine, etc. as follows:

      \[\begin{align}\tag{1} q\left(\mathcal{C}^{1: T} \mid \mathcal{C}^0\right)=\prod_{t=1}^T q\left(\mathcal{C}^t \mid \mathcal{C}^{t-1}\right) \end{align}\]

      where \(\quad q\left(\mathcal{C}^t \mid \mathcal{C}^{t-1}\right)=\mathcal{N}\left(\mathcal{C}^t ; \sqrt{1-\beta_t} \mathcal{C}^{t-1}, \beta_t I\right)\)

      Instead of having to compute \(q\left(\mathcal{C}^t \mid \mathcal{C}^{t-1}\right)\) at every timestep \(t\), we could compute at an arbitrary timestep in closed form:

      \[\begin{equation}\tag{2} q\left(\mathcal{C}^t \mid \mathcal{C}^0\right)=\mathcal{N}\left(\mathcal{C}^t ; \sqrt{\bar{\alpha}_t} \mathcal{C}^0,\left(1-\bar{\alpha}_t\right) I\right) \end{equation}\]

      where \(\alpha_t=1-\beta_t\) and \(\bar{\alpha}_t=\prod_{s=1}^t \alpha_s\)

      Thus with a sufficiently large number of timesteps, the forward process could convert \(\mathcal{C}^0\) to whitened isotropic Gaussian and so we could set \(p\left(\mathcal{C}^T\right)\) as a standard Gaussian distribution.

      Reverse Process

      The reverse process involved recovering the original conformation \(\mathcal{C}^0\) from the white noise \(\mathcal{C}^T\) . We need the conditional distribution \(p_\theta\left(\mathcal{C}^{t-1} \mid \mathcal{G}, \mathcal{C}^t\right)\) to sample some random Gaussian noise \(\mathcal{C}^t\), and “denoise” gradually to end up with a sample from the real distribution \(\mathcal{C}^0\).

      However, the conditional distribution of \(p_\theta\left(\mathcal{C}^{t-1} \mid \mathcal{G}, \mathcal{C}^t\right)\) is intractable as it requires knowing the distribution of all possible conformations in order to calculate this conditional probability. Hence, a neural network could be used to learn this conditional probability distribution, let’s call it \(p_\theta\), with \(\theta\) being the parameters of the neural network, updated by gradient descent. Thus, we formulate the reverse process as a conditional Markov chain with learnable transitions:

      \[\begin{align*}\tag{3} p_\theta\left(\mathcal{C}^{0: T-1} \mid \mathcal{G}, \mathcal{C}^T\right)=\prod_{t=1}^T p_\theta\left(\mathcal{C}^{t-1} \mid \mathcal{G}, \mathcal{C}^t\right) \end{align*}\]

      where \(\quad p_\theta\left(\mathcal{C}^{t-1} \mid \mathcal{G}, \mathcal{C}^t\right)=\mathcal{N}\left(\mathcal{C}^{t-1} ; \mu_\theta\left(\mathcal{G}, \mathcal{C}^t, t\right), \sigma_t^2 I\right)\)

      Hence, the neural network in the reverse process needs to learn/represent the mean and variance. However, just like the DDPM paper, GeoDiff also lets the variance be user-defined and fixed, and \(\mu_\theta\) is the neural network that estimates means.

      GeoDiff uses a parametrisation trick inspired by the diffusion model implementation from the DDPM paper such that this parametrisation resembles Langevin dynamics and simplifies the diffusion model’s variational bound to an objective that resembles denoising score matching. Moreover, in the context of molecular conformation generation, this parametrisation trick is analogous to the physical force fields , which also gradually push particles towards convergence around the equilibrium states, and is defined by the following equation:

      \[\begin{align*}\tag{4} \mu_\theta\left(\mathcal{C}^t, t\right)=\frac{1}{\sqrt{\alpha_t}}\left(\mathcal{C}^t-\frac{\beta_t}{\sqrt{1-\bar{\alpha}_t}} \epsilon_\theta\left(\mathcal{G}, \mathcal{C}^t, t\right)\right) \end{align*}\]

      where \(\epsilon_\theta\) are neural networks with trainable parameters \(\theta\).

      Now, we need to make \(\epsilon_\theta\) roto-translational equivariant which we elaborate on in the next section.

      Making the reverse process roto-translation equivariant

      Firstly, we need to assume the prior distribution of the conformations and the intermediary conformations generated during the forward process are systems with zero centre of mass (CoM) or CoM-free systems . By considering CoM-free systems, moving the particles to zero CoM can always ensure translational invariance in the Markov kernels.

      GeoDiff employs the use of an equivariant convolutional layer, named graph field network (GFN) inspired by . In the \(l\)-th layer, GFN takes node embeddings \(h_l \in \mathbb{R}^{n \times b}\) (\(b\) denotes the feature dimension) and corresponding coordinate embeddings \(x_l \in \mathbb{R}^{n \times 3}\) as inputs, and outputs \(h_{l+1}\) and \(x_{l+1}\) as follows:

      \[\begin{align} \tag{5} & \mathbf{m}_{i j}=\Phi_m\left(\mathbf{h}_i^l, \mathbf{h}_j^l,\left\|\mathbf{x}_i^l-\mathbf{x}_j^l\right\|^2, e_{i j} ; \theta_m\right) \\ \tag{6} & \mathbf{h}_i^{l+1}=\Phi_h\left(\mathbf{h}_i^l, \sum_{j \in \mathcal{N}(i)} \mathbf{m}_{i j} ; \theta_h\right) \\ & \mathbf{x}_i^{l+1}=\sum_{j \in \mathcal{N}(i)} \frac{1}{d_{i j}}\left(\mathbf{c}_i-\mathbf{c}_j\right) \Phi_x\left(\mathbf{m}_{i j} ; \theta_x\right) \tag{7} \end{align}\]

      where

      • \(\Phi\) are feed-forward networks
      • \(d_{ij}\) are interatomic distances
      • \(\mathcal{N}(i)\) is the neighbourhood of the \(i\)-th node, which consists of both connected atoms and other ones within a radius threshold \(\tau\).

      By introducing the neighbourhood function, we enable the model to accurately represent distant interactions between atoms, as well as the ability to handle partially disconnected molecular graphs. Initial embeddings \(h_0\) are combinations of atom and timestep embeddings, and \(x_0\) are atomic coordinates. A key change in GFN compared to a vanilla GNN is \(x\) being updated as a combination of radial directions weighted by \(\Phi_x\): \(\mathbb{R}^b \rightarrow \mathbb{R}\) as seen in equation \((7)\). This allows the roto-translation equivariance property to be induced in the reverse process.

      Improved Training Objective

      Now, we need to set the training objective having considered the reverse process dynamics. We cannot compute the exact log-likelihood of the generative process, as it involves computing the likelihood of the observed molecular conformation given the parameters of the model. However, this likelihood is difficult to compute, as it would require integrating over all possible intermediate conformations, giving us a high-dimensional integral that cannot be solved analytically. Therefore, the authors have opted to maximize the variational lower bound (ELBO), as defined below:

      \[\begin{aligned} \mathbb{E}\left[\log p_\theta\left(\mathcal{C}^0 \mid \mathcal{G}\right)\right] & =\mathbb{E}\left[\log \mathbb{E}_{q\left(\mathcal{C}^{1: T} \mid \mathcal{C}^0\right)} \frac{p_\theta\left(\mathcal{C}^{0: T} \mid \mathcal{G}\right)}{q\left(\mathcal{C}^{1: T} \mid \mathcal{C}^0\right)}\right] \\ & \geq-\mathbb{E}_q\left[\sum_{t=1}^T D_{\mathrm{KL}}\left(q\left(\mathcal{C}^{t-1} \mid \mathcal{C}^t, \mathcal{C}^0\right) \| p_\theta\left(\mathcal{C}^{t-1} \mid \mathcal{C}^t, \mathcal{G}\right)\right)\right]:=-\mathcal{L}_{\mathrm{ELBO}}\end{aligned}\]

      where \(q\left(\mathcal{C}^{t-1} \mid \mathcal{C}^t, \mathcal{C}^0\right)\) is analytically tractable as \(\mathcal{N}\left(\frac{\sqrt{\bar{\alpha}_{t-1}} \beta_t}{1-\bar{\alpha}_t} \mathcal{C}^0+\frac{\sqrt{\alpha_t}\left(1-\bar{\alpha}_{t-1}\right)}{1-\bar{\alpha}_t} \mathcal{C}^t, \frac{1-\bar{\alpha}_{t-1}}{1-\bar{\alpha}_t} \beta_t\right)\).

      Using the parametrisation trick in the reverse process as seen in equation \((4)\), the ELBO could be simplified by taking the KL divergences between Gaussians as weighted \(\mathcal{L}_2\) distances between the means \(\epsilon_\theta\) and \(\epsilon^3\) as follows: \(\mathcal{L}_{\mathrm{ELBO}}=\sum_{t=1}^T \gamma_t \mathbb{E}_{\left\{\mathcal{C}^0, \mathcal{G}\right\} \sim q\left(\mathcal{C}^0, \mathcal{G}\right), \epsilon \sim \mathcal{N}(0, I)}\left[\left\|\epsilon-\epsilon_\theta\left(\mathcal{G}, \mathcal{C}^t, t\right)\right\|_2^2\right]\) where \(\mathcal{C}^t=\sqrt{\bar{\alpha}_t} \mathcal{C}^0+\sqrt{1-\bar{\alpha}_t} \epsilon\).

      The idea behind this objective is to independently sample chaotic conformations of different timesteps from \(q\left(C^{t-1} \mid C^t, C^0\right)\), and use \(\epsilon_\theta\) to approximate the noise vector \(\epsilon\).

      Sampling

      Now, we can generate stable molecular conformations via sampling. Given a graph \(\mathcal{G}\), its geometry \(\mathcal{C}^0\) is generated by first sampling chaotic particles \(\mathcal{C}^T \sim p\left(\mathcal{C}^T\right)\). For each timestep in the reverse process \(t=T, T-\) \(1, \cdots, 1\), we first shift the CoM of the conformation to zero, compute the transition means, \(\mu_\theta\left(\mathcal{G}, \mathcal{C}^t, t\right)\), using equation \((4)\) and sample \(\mathcal{C}^{t-1} \sim\) \(p_\theta\left(\mathcal{C}^{t-1} \mid \mathcal{G}, \mathcal{C}^t\right)\). The sampling algorithm is given in pseudo-code below:

      Algorithm 1 Sampling Algorithm of GEODIFF
      Input: the molecular graph \(\mathcal{G}\), the learned reverse model \(\epsilon_\theta\).
      Output: the molecular conformation \(\mathcal{C}\).
      1: Sample \(\mathcal{C}^T \sim p\left(\mathcal{C}^T\right)=\mathcal{N}(0, I)\)
      2: for \(s=T, T-1, \cdots, 1\) do
      3: \(\quad\) Shift \(\mathcal{C}^s\) to zero CoM
      4: \(\quad\) Compute \(\mu_\theta\left(\mathcal{C}^s, \mathcal{G}, s\right)\) from \(\epsilon_\theta\left(\mathcal{C}^s, \mathcal{G}, s\right)\) using equation 4
      5: \(\quad\) Sample \(\mathcal{C}^{s-1} \sim \mathcal{N}\left(\mathcal{C}^{s-1} ; \mu_\theta\left(\mathcal{C}^{\mathcal{s}}, \mathcal{G}, s\right), \sigma_t^2 I\right)\)
      6: end for
      7: return \(\mathcal{C}^0\) as $\mathcal{C}$$

      But why generative models?

      The purpose of prediciting molecular conformations is to enable human experts to analyse the properties of the molecules and understand how these properties affect the viability of a molecule as a drug candidate. Therefore, it is important that the molecular conformations generated are diverse to capture the different possible conformations that could occur in nature but the conformations generated should not deviate significantly such that the analysis is affected. To set a threshold for the different possible conformations, the standard metric used has been selecting conformations that are within a certain root-mean-square deviation (RMSD), say a few ångströms, of the true structure.

      However, the objective of maximizing the proportion of predictions with RMSD within some tolerance \(\epsilon\) is not differentiable and thus, cannot be used for training with stochastic gradient descent. Instead, maximizing the expected proportion of predictions with RMSD < \(\epsilon\) corresponds to maximizing the likelihood of the true structure under the model’s output distribution, in the limit as \(\epsilon\) goes to 0. This concept inspires the development of a generative model, whose objective is to minimize an upper bound on the negative log-likelihood of observed molecular structures under the distribution of the model. As a result, the problem of molecular docking is treated as a task of learning a distribution over possible positions of a ligand molecule conditioned on the protein structure and a diffusion generative model is developed to represent this space. Therefore, this observation has motivated several works on the use of generative models for molecular conformation generation, such as GeoDiff.

      Future work

      While diffusion models have shown promising results over the past months, there is still a need for further research and development to address some of the limitations and drawbacks of the use of diffusion models in conformer generation. As explained in our blog post, generative models are well-suited for molecular conformation generation. However, there are other kinds of established generative models, such as autoencoders that have been used for the same task . For instance, comparing diffusion models and autoencoders, diffusion models can handle all noise levels with a single set of parameters, without any bottlenecks, which an autoencoder would have . Thus, it is essential to study the advantages and disadvantages of different types and variants of generative models for conformation generation and understand what changes could be done to them to make them more suitable for molecular conformation.

      It must be noted that the experiments described in the study are done on benchmark geometric datasets, GEOM-QM9 and GEOM-Drugs , rather than industrial data, with a relatively small number of samples/drug/molecular compounds. Industry data may exhibit greater variability than standard geometric datasets, as they may be more diverse, complex and subject to greater fluctuations than these geometric datasets, which tend to be more standardized and more predictable.

      GeoDiff as a framework sets a precedent for future work that could marry the concepts of geometric deep learning and diffusion models across various domains. In the context of drug discovery, it would be interesting to extend this framework to more challenging structures, such as proteins, which may enable more accurate prediction of protein folding, protein-protein interactions and protein-ligand binding positions which would facilitate the design of new drugs and treatments. Additionally, this framework could potentially be applied to other complex systems beyond proteins, such as RNA molecules, to enable more efficient and accurate prediction of their behaviour and properties. Continued research in this area has the potential to revolutionize drug discovery and development, as well as advance our understanding of the fundamental principles governing the behaviour of complex biological systems.

      Research on the application of diffusion models in the life and natural sciences is still in its infancy, with great potential for improvement in terms of both theory as well as empirical testing. The GeoDiff model could be improved in terms of more efficient sampling and improved likelihood maximization methods. Traditionally, generating samples from diffusion models demand iterative approaches that involve a large number of evaluation steps. Recent work, such as the paper on Torsional Diffusion was able to speed up the sampling process, while also enhancing the quality of the resulting samples. Experimentally, Torsional Diffusion only takes 5 to 20 steps in comparison to GeoDiff which takes around 5000 steps .

      Looking ahead, GeoDiff has set a clear example for the use of diffusion models on geometric representations which could be extended to several problems, especially in the field of drug discovery. The novel contributions made by

      are motivated by the physical characteristics of the molecular conformation generation problem, which has resulted in a strong candidate method for conformation generation that could act as a springboard for even more effective and efficient methods that would eventually benefit the field of drug discovery as a whole.

      ]]>      Anonymous      A Match Made in Drug Discovery - Marrying Geometric and Diffusion Models2023-02-17T00:00:00+00:002023-02-17T00:00:00+00:00https://deep-learning-mit.github.io/staging/blog/2023/testA Match Made in Drug Discovery: Marrying Geometric and Diffusion Models

      Introduction

      With the initial breakthrough of the Denoising Diffusion , diffusion models have evolved into a powerful tool for a wide range of applications in machine learning, including image generation and text generation. The rise and the recent release of Stable Diffusion in August 2022 has shown superior performance in a wide range of practical applications - from artistic and creative projects to scientific and industrial ones and has recently paved its way into the natural sciences, which includes the field of drug discovery .

      Data-driven applications have increasingly been shown to accelerate solving diverse problems in the drug discovery pipeline – from the use of predictive analytical methods for target identification and lead optimization, to the analysis of large-scale biological data for drug repurposing and personalized medicine. To limit the scope of the blog post, we will only focus on the use of generative methods in molecular conformation generation.

      Motivation

      Generating molecular conformations is a task fundamental to cheminformatics and drug discovery. The conformation of a molecule refers to the three-dimensional (3D) coordinates of all the atoms in a molecule in a 3D Euclidean space, which can be interconverted by rotations about formally single bonds . It allows for the prediction of the physical and chemical properties and interactions of molecules based on their possible 3D conformations, as well as their biological activity. In drug discovery, it is integral to obtain all the possible conformations of molecules for various tasks, such as three-dimensional quantitative structure-activity relationships (3D-QSAR), pharmacophore searching, molecular docking and thermodynamic calculations. Deep generative modelling, which aims to learn complex data distributions, is a recent promising approach to tackle the conformation generation problem . When studying molecules it is important to understand them as three-dimensional structures formed by atoms bonded to each other. To encode the chemical properties, molecules could be represented as graphs where atoms (nodes) are connected by bonds (edges). Representing molecules as 3D molecular graphs captures the spatial arrangement of a molecule, which in turn determines its chemical property. A molecule could take up any conformation based on all possible permutations and combinations of spatial arrangements of atoms. However, some conformations may not occur physically, due to e.g steric hindrance, which arises when the spatial arrangement of atoms leads to unfavourable interactions/repulsive forces, leading to a higher energy state and less stable conformation.

      Therefore, we are only interested in conformations that fall in stable low-energy minima, as these low-energy conformations are the ones that the molecule will most likely adopt under natural conditions and play a crucial role in determining the molecule’s behaviour and properties. By identifying and characterizing the low-energy conformations, researchers gain insights into their stability, reactivity and interactions with other molecules.

      Formulating the conformation generation problem

      A formulation of the conformation generation problem, adapted from

      We can formulate the problem of conformation generation as a conditional generative problem where we aim to generate stable conformations \(C\) from a molecule’s graph \(G\). For each \(G\) given its conformations \(C\) as i.i.d samples from an underlying Boltzmann distribution , our goal is to learn a generative model $$p_\theta(C G)$$ to draw possible conformations from.

      Roto-translation equivariance

      A visualisation of roto-translation equivariance, adapted from

      To generate stable molecular conformations, we need an algorithm that preserves roto-translation equivariance of the conformations that previous work has not focused on. To explain this property, let us delve into what equivariance is. A representation \(φ\) is equivariant with a transformation \(g\) of the input if the transformation can be transferred to the representation output. Invariance is a special case of equivariance obtained when the transformation is the identity map .

      In the context of molecular conformations, we have to achieve the special case of equivariance in terms of rotation and translation, namely, roto-translation equivariance of the conformations which ensures that however the molecule is rotated or translated, the estimated (conditional) likelihood should be unaffected. GeoDiff considers the SE(3) Lie group which can be used to represent rotation and translation in 3D space .

      Decomposing GeoDiff

      The diffusion model of GeoDiff, adapted from

      Legend:

      • \(C^{0}\) denotes the ground truth conformations
      • \(C^{t}\), where \(t = 1,···, T\) is the index for diffusion steps and \(C^{t}\), is the sequence of latent variables with the same dimension
      • \(q(C^{t} \mid C^{t-1})\) is the fixed posterior distribution
      • \(p_\theta(C^{t-1} \mid G, C^{t})\) are the Markov kernels through which the conformations are refined

      A primer on Diffusion Models

      A diffusion probabilistic model can be described as a latent variable model with two processes: the forward and the reverse generative processes. Intuitively, the diffusion process progressively injects small noises into \(C^{0}\), while the generative process learns to revert the diffusion process by gradually eliminating the noise to recover the ground truth. Diffusion models are trained by adding noise to the input, which the model then learns how to remove.

      In this blog post, we use the GeoDiff implementation of diffusion models to explain how the diffusion model works and how it is being used for the geometric representation of molecules. The implementation of the diffusion model in GeoDiff is inspired by the DDPM paper . To give a quick overview, the forward process \(q\) transforms the original input into complete noise over a certain number of timesteps and follows a normal distribution; the \(p_0\) involves denoising complete noise to the actual input using a neural network.

      Forward process

      Let \(q(\mathbf{C}^0)\) be the real data distribution of molecular conformation. We can sample from this distribution to get a conformation, \(\mathbf{C}^0 \sim q(\mathbf{C}^0)\). We define the forward diffusion process which adds Gaussian noise at each time step \(t\), according to a known variance schedule \beta_t which can be linear, quadratic, cosine, etc. as follows:

      \[\begin{align}\tag{1} q\left(\mathcal{C}^{1: T} \mid \mathcal{C}^0\right)=\prod_{t=1}^T q\left(\mathcal{C}^t \mid \mathcal{C}^{t-1}\right) \end{align}\]

      where \(\quad q\left(\mathcal{C}^t \mid \mathcal{C}^{t-1}\right)=\mathcal{N}\left(\mathcal{C}^t ; \sqrt{1-\beta_t} \mathcal{C}^{t-1}, \beta_t I\right)\)

      Instead of having to compute \(q\left(\mathcal{C}^t \mid \mathcal{C}^{t-1}\right)\) at every timestep \(t\), we could compute at an arbitrary timestep in closed form:

      \[\begin{equation}\tag{2} q\left(\mathcal{C}^t \mid \mathcal{C}^0\right)=\mathcal{N}\left(\mathcal{C}^t ; \sqrt{\bar{\alpha}_t} \mathcal{C}^0,\left(1-\bar{\alpha}_t\right) I\right) \end{equation}\]

      where \(\alpha_t=1-\beta_t\) and \(\bar{\alpha}_t=\prod_{s=1}^t \alpha_s\)

      Thus with a sufficiently large number of timesteps, the forward process could convert \(\mathcal{C}^0\) to whitened isotropic Gaussian and so we could set \(p\left(\mathcal{C}^T\right)\) as a standard Gaussian distribution.

      Reverse Process

      The reverse process involved recovering the original conformation \(\mathcal{C}^0\) from the white noise \(\mathcal{C}^T\) . We need the conditional distribution \(p_\theta\left(\mathcal{C}^{t-1} \mid \mathcal{G}, \mathcal{C}^t\right)\) to sample some random Gaussian noise \(\mathcal{C}^t\), and “denoise” gradually to end up with a sample from the real distribution \(\mathcal{C}^0\).

      However, the conditional distribution of \(p_\theta\left(\mathcal{C}^{t-1} \mid \mathcal{G}, \mathcal{C}^t\right)\) is intractable as it requires knowing the distribution of all possible conformations in order to calculate this conditional probability. Hence, a neural network could be used to learn this conditional probability distribution, let’s call it \(p_\theta\), with \(\theta\) being the parameters of the neural network, updated by gradient descent. Thus, we formulate the reverse process as a conditional Markov chain with learnable transitions:

      \[\begin{align*}\tag{3} p_\theta\left(\mathcal{C}^{0: T-1} \mid \mathcal{G}, \mathcal{C}^T\right)=\prod_{t=1}^T p_\theta\left(\mathcal{C}^{t-1} \mid \mathcal{G}, \mathcal{C}^t\right) \end{align*}\]

      where \(\quad p_\theta\left(\mathcal{C}^{t-1} \mid \mathcal{G}, \mathcal{C}^t\right)=\mathcal{N}\left(\mathcal{C}^{t-1} ; \mu_\theta\left(\mathcal{G}, \mathcal{C}^t, t\right), \sigma_t^2 I\right)\)

      Hence, the neural network in the reverse process needs to learn/represent the mean and variance. However, just like the DDPM paper, GeoDiff also lets the variance be user-defined and fixed, and \(\mu_\theta\) is the neural network that estimates means.

      GeoDiff uses a parametrisation trick inspired by the diffusion model implementation from the DDPM paper such that this parametrisation resembles Langevin dynamics and simplifies the diffusion model’s variational bound to an objective that resembles denoising score matching. Moreover, in the context of molecular conformation generation, this parametrisation trick is analogous to the physical force fields , which also gradually push particles towards convergence around the equilibrium states, and is defined by the following equation:

      \[\begin{align*}\tag{4} \mu_\theta\left(\mathcal{C}^t, t\right)=\frac{1}{\sqrt{\alpha_t}}\left(\mathcal{C}^t-\frac{\beta_t}{\sqrt{1-\bar{\alpha}_t}} \epsilon_\theta\left(\mathcal{G}, \mathcal{C}^t, t\right)\right) \end{align*}\]

      where \(\epsilon_\theta\) are neural networks with trainable parameters \(\theta\).

      Now, we need to make \(\epsilon_\theta\) roto-translational equivariant which we elaborate on in the next section.

      Making the reverse process roto-translation equivariant

      Firstly, we need to assume the prior distribution of the conformations and the intermediary conformations generated during the forward process are systems with zero centre of mass (CoM) or CoM-free systems . By considering CoM-free systems, moving the particles to zero CoM can always ensure translational invariance in the Markov kernels.

      GeoDiff employs the use of an equivariant convolutional layer, named graph field network (GFN) inspired by . In the \(l\)-th layer, GFN takes node embeddings \(h_l \in \mathbb{R}^{n \times b}\) (\(b\) denotes the feature dimension) and corresponding coordinate embeddings \(x_l \in \mathbb{R}^{n \times 3}\) as inputs, and outputs \(h_{l+1}\) and \(x_{l+1}\) as follows:

      \[\begin{align} \tag{5} & \mathbf{m}_{i j}=\Phi_m\left(\mathbf{h}_i^l, \mathbf{h}_j^l,\left\|\mathbf{x}_i^l-\mathbf{x}_j^l\right\|^2, e_{i j} ; \theta_m\right) \\ \tag{6} & \mathbf{h}_i^{l+1}=\Phi_h\left(\mathbf{h}_i^l, \sum_{j \in \mathcal{N}(i)} \mathbf{m}_{i j} ; \theta_h\right) \\ & \mathbf{x}_i^{l+1}=\sum_{j \in \mathcal{N}(i)} \frac{1}{d_{i j}}\left(\mathbf{c}_i-\mathbf{c}_j\right) \Phi_x\left(\mathbf{m}_{i j} ; \theta_x\right) \tag{7} \end{align}\]

      where

      • \(\Phi\) are feed-forward networks
      • \(d_{ij}\) are interatomic distances
      • \(\mathcal{N}(i)\) is the neighbourhood of the \(i\)-th node, which consists of both connected atoms and other ones within a radius threshold \(\tau\).

      By introducing the neighbourhood function, we enable the model to accurately represent distant interactions between atoms, as well as the ability to handle partially disconnected molecular graphs. Initial embeddings \(h_0\) are combinations of atom and timestep embeddings, and \(x_0\) are atomic coordinates. A key change in GFN compared to a vanilla GNN is \(x\) being updated as a combination of radial directions weighted by \(\Phi_x\): \(\mathbb{R}^b \rightarrow \mathbb{R}\) as seen in equation \((7)\). This allows the roto-translation equivariance property to be induced in the reverse process.

      Improved Training Objective

      Now, we need to set the training objective having considered the reverse process dynamics. We cannot compute the exact log-likelihood of the generative process, as it involves computing the likelihood of the observed molecular conformation given the parameters of the model. However, this likelihood is difficult to compute, as it would require integrating over all possible intermediate conformations, giving us a high-dimensional integral that cannot be solved analytically. Therefore, the authors have opted to maximize the variational lower bound (ELBO), as defined below:

      \[\begin{aligned} \mathbb{E}\left[\log p_\theta\left(\mathcal{C}^0 \mid \mathcal{G}\right)\right] & =\mathbb{E}\left[\log \mathbb{E}_{q\left(\mathcal{C}^{1: T} \mid \mathcal{C}^0\right)} \frac{p_\theta\left(\mathcal{C}^{0: T} \mid \mathcal{G}\right)}{q\left(\mathcal{C}^{1: T} \mid \mathcal{C}^0\right)}\right] \\ & \geq-\mathbb{E}_q\left[\sum_{t=1}^T D_{\mathrm{KL}}\left(q\left(\mathcal{C}^{t-1} \mid \mathcal{C}^t, \mathcal{C}^0\right) \| p_\theta\left(\mathcal{C}^{t-1} \mid \mathcal{C}^t, \mathcal{G}\right)\right)\right]:=-\mathcal{L}_{\mathrm{ELBO}}\end{aligned}\]

      where \(q\left(\mathcal{C}^{t-1} \mid \mathcal{C}^t, \mathcal{C}^0\right)\) is analytically tractable as \(\mathcal{N}\left(\frac{\sqrt{\bar{\alpha}_{t-1}} \beta_t}{1-\bar{\alpha}_t} \mathcal{C}^0+\frac{\sqrt{\alpha_t}\left(1-\bar{\alpha}_{t-1}\right)}{1-\bar{\alpha}_t} \mathcal{C}^t, \frac{1-\bar{\alpha}_{t-1}}{1-\bar{\alpha}_t} \beta_t\right)\).

      Using the parametrisation trick in the reverse process as seen in equation \((4)\), the ELBO could be simplified by taking the KL divergences between Gaussians as weighted \(\mathcal{L}_2\) distances between the means \(\epsilon_\theta\) and \(\epsilon^3\) as follows: \(\mathcal{L}_{\mathrm{ELBO}}=\sum_{t=1}^T \gamma_t \mathbb{E}_{\left\{\mathcal{C}^0, \mathcal{G}\right\} \sim q\left(\mathcal{C}^0, \mathcal{G}\right), \epsilon \sim \mathcal{N}(0, I)}\left[\left\|\epsilon-\epsilon_\theta\left(\mathcal{G}, \mathcal{C}^t, t\right)\right\|_2^2\right]\) where \(\mathcal{C}^t=\sqrt{\bar{\alpha}_t} \mathcal{C}^0+\sqrt{1-\bar{\alpha}_t} \epsilon\).

      The idea behind this objective is to independently sample chaotic conformations of different timesteps from \(q\left(C^{t-1} \mid C^t, C^0\right)\), and use \(\epsilon_\theta\) to approximate the noise vector \(\epsilon\).

      Sampling

      Now, we can generate stable molecular conformations via sampling. Given a graph \(\mathcal{G}\), its geometry \(\mathcal{C}^0\) is generated by first sampling chaotic particles \(\mathcal{C}^T \sim p\left(\mathcal{C}^T\right)\). For each timestep in the reverse process \(t=T, T-\) \(1, \cdots, 1\), we first shift the CoM of the conformation to zero, compute the transition means, \(\mu_\theta\left(\mathcal{G}, \mathcal{C}^t, t\right)\), using equation \((4)\) and sample \(\mathcal{C}^{t-1} \sim\) \(p_\theta\left(\mathcal{C}^{t-1} \mid \mathcal{G}, \mathcal{C}^t\right)\). The sampling algorithm is given in pseudo-code below:

      Algorithm 1 Sampling Algorithm of GEODIFF
      Input: the molecular graph \(\mathcal{G}\), the learned reverse model \(\epsilon_\theta\).
      Output: the molecular conformation \(\mathcal{C}\).
      1: Sample \(\mathcal{C}^T \sim p\left(\mathcal{C}^T\right)=\mathcal{N}(0, I)\)
      2: for \(s=T, T-1, \cdots, 1\) do
      3: \(\quad\) Shift \(\mathcal{C}^s\) to zero CoM
      4: \(\quad\) Compute \(\mu_\theta\left(\mathcal{C}^s, \mathcal{G}, s\right)\) from \(\epsilon_\theta\left(\mathcal{C}^s, \mathcal{G}, s\right)\) using equation 4
      5: \(\quad\) Sample \(\mathcal{C}^{s-1} \sim \mathcal{N}\left(\mathcal{C}^{s-1} ; \mu_\theta\left(\mathcal{C}^{\mathcal{s}}, \mathcal{G}, s\right), \sigma_t^2 I\right)\)
      6: end for
      7: return \(\mathcal{C}^0\) as $\mathcal{C}$$

      But why generative models?

      The purpose of prediciting molecular conformations is to enable human experts to analyse the properties of the molecules and understand how these properties affect the viability of a molecule as a drug candidate. Therefore, it is important that the molecular conformations generated are diverse to capture the different possible conformations that could occur in nature but the conformations generated should not deviate significantly such that the analysis is affected. To set a threshold for the different possible conformations, the standard metric used has been selecting conformations that are within a certain root-mean-square deviation (RMSD), say a few ångströms, of the true structure.

      However, the objective of maximizing the proportion of predictions with RMSD within some tolerance \(\epsilon\) is not differentiable and thus, cannot be used for training with stochastic gradient descent. Instead, maximizing the expected proportion of predictions with RMSD < \(\epsilon\) corresponds to maximizing the likelihood of the true structure under the model’s output distribution, in the limit as \(\epsilon\) goes to 0. This concept inspires the development of a generative model, whose objective is to minimize an upper bound on the negative log-likelihood of observed molecular structures under the distribution of the model. As a result, the problem of molecular docking is treated as a task of learning a distribution over possible positions of a ligand molecule conditioned on the protein structure and a diffusion generative model is developed to represent this space. Therefore, this observation has motivated several works on the use of generative models for molecular conformation generation, such as GeoDiff.

      Future work

      While diffusion models have shown promising results over the past months, there is still a need for further research and development to address some of the limitations and drawbacks of the use of diffusion models in conformer generation. As explained in our blog post, generative models are well-suited for molecular conformation generation. However, there are other kinds of established generative models, such as autoencoders that have been used for the same task . For instance, comparing diffusion models and autoencoders, diffusion models can handle all noise levels with a single set of parameters, without any bottlenecks, which an autoencoder would have . Thus, it is essential to study the advantages and disadvantages of different types and variants of generative models for conformation generation and understand what changes could be done to them to make them more suitable for molecular conformation.

      It must be noted that the experiments described in the study are done on benchmark geometric datasets, GEOM-QM9 and GEOM-Drugs , rather than industrial data, with a relatively small number of samples/drug/molecular compounds. Industry data may exhibit greater variability than standard geometric datasets, as they may be more diverse, complex and subject to greater fluctuations than these geometric datasets, which tend to be more standardized and more predictable.

      GeoDiff as a framework sets a precedent for future work that could marry the concepts of geometric deep learning and diffusion models across various domains. In the context of drug discovery, it would be interesting to extend this framework to more challenging structures, such as proteins, which may enable more accurate prediction of protein folding, protein-protein interactions and protein-ligand binding positions which would facilitate the design of new drugs and treatments. Additionally, this framework could potentially be applied to other complex systems beyond proteins, such as RNA molecules, to enable more efficient and accurate prediction of their behaviour and properties. Continued research in this area has the potential to revolutionize drug discovery and development, as well as advance our understanding of the fundamental principles governing the behaviour of complex biological systems.

      Research on the application of diffusion models in the life and natural sciences is still in its infancy, with great potential for improvement in terms of both theory as well as empirical testing. The GeoDiff model could be improved in terms of more efficient sampling and improved likelihood maximization methods. Traditionally, generating samples from diffusion models demand iterative approaches that involve a large number of evaluation steps. Recent work, such as the paper on Torsional Diffusion was able to speed up the sampling process, while also enhancing the quality of the resulting samples. Experimentally, Torsional Diffusion only takes 5 to 20 steps in comparison to GeoDiff which takes around 5000 steps .

      Looking ahead, GeoDiff has set a clear example for the use of diffusion models on geometric representations which could be extended to several problems, especially in the field of drug discovery. The novel contributions made by

      are motivated by the physical characteristics of the molecular conformation generation problem, which has resulted in a strong candidate method for conformation generation that could act as a springboard for even more effective and efficient methods that would eventually benefit the field of drug discovery as a whole.

      ]]>      Anonymous      Sample Blog Post2022-12-01T00:00:00+00:002022-12-01T00:00:00+00:00https://deep-learning-mit.github.io/staging/blog/2022/distill-exampleEquations

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      Images and Figures

      Its generally a better idea to avoid linking to images hosted elsewhere - links can break and you might face losing important information in your blog post. To include images in your submission in this way, you must do something like the following:

      {% include figure.html path="assets/img/2022-12-01-distill-example/iclr.png" class="img-fluid" %}
+

      which results in the following image:

      To ensure that there are no namespace conflicts, you must save your asset to your unique directory /assets/img/2023-05-01-[SUBMISSION NAME] within your submission.

      Please avoid using the direct markdown method of embedding images; they may not be properly resized. Some more complex ways to load images (note the different styles of the shapes/shadows):

      A simple, elegant caption looks good between image rows, after each row, or doesn't have to be there at all.

      Interactive Figures

      Here’s how you could embed interactive figures that have been exported as HTML files. Note that we will be using plotly for this demo, but anything built off of HTML should work (no extra javascript is allowed!). All that’s required is for you to export your figure into HTML format, and make sure that the file exists in the assets/html/[SUBMISSION NAME]/ directory in this repository’s root directory. To embed it into any page, simply insert the following code anywhere into your page.

      {% include [FIGURE_NAME].html %} 
+

      For example, the following code can be used to generate the figure underneath it.

      import pandas as pd
+import plotly.express as px
+
+df = pd.read_csv('https://raw.githubusercontent.com/plotly/datasets/master/earthquakes-23k.csv')
+
+fig = px.density_mapbox(
+    df, lat='Latitude', lon='Longitude', z='Magnitude', radius=10,
+    center=dict(lat=0, lon=180), zoom=0, mapbox_style="stamen-terrain")
+fig.show()
+
+fig.write_html('./assets/html/2022-12-01-distill-example/plotly_demo_1.html')
+

      And then include it with the following:

      <div class="l-page">
+  <iframe src="{{ 'assets/html/2022-12-01-distill-example/plotly_demo_1.html' | relative_url }}" frameborder='0' scrolling='no' height="600px" width="100%"></iframe>
+</div>
+

      Voila!

      Citations

      Citations are then used in the article body with the <d-cite> tag. The key attribute is a reference to the id provided in the bibliography. The key attribute can take multiple ids, separated by commas.

      The citation is presented inline like this: (a number that displays more information on hover). If you have an appendix, a bibliography is automatically created and populated in it.

      Distill chose a numerical inline citation style to improve readability of citation dense articles and because many of the benefits of longer citations are obviated by displaying more information on hover. However, we consider it good style to mention author last names if you discuss something at length and it fits into the flow well — the authors are human and it’s nice for them to have the community associate them with their work.

      Footnotes

      Just wrap the text you would like to show up in a footnote in a <d-footnote> tag. The number of the footnote will be automatically generated.This will become a hoverable footnote.

      Code Blocks

      This theme implements a built-in Jekyll feature, the use of Rouge, for syntax highlighting. It supports more than 100 languages. This example is in C++. All you have to do is wrap your code in a liquid tag:

      {% highlight c++ linenos %}
      code code code
      {% endhighlight %}

      The keyword linenos triggers display of line numbers. You can try toggling it on or off yourself below:

      int main(int argc, char const \*argv[])
+{
+string myString;
+
+    cout << "input a string: ";
+    getline(cin, myString);
+    int length = myString.length();
+
+    char charArray = new char * [length];
+
+    charArray = myString;
+    for(int i = 0; i < length; ++i){
+        cout << charArray[i] << " ";
+    }
+
+    return 0;
+}

      Diagrams

      This theme supports generating various diagrams from a text description using jekyll-diagrams plugin. Below, we generate a few examples of such diagrams using languages such as mermaid, plantuml, vega-lite, etc.

      Note: different diagram-generation packages require external dependencies to be installed on your machine. Also, be mindful of that because of diagram generation the fist time you build your Jekyll website after adding new diagrams will be SLOW. For any other details, please refer to jekyll-diagrams README.

      Note: This is not supported for local rendering!

      The diagram below was generated by the following code:

      {% mermaid %}
+sequenceDiagram
+    participant John
+    participant Alice
+    Alice->>John: Hello John, how are you?
+    John-->>Alice: Great!
+{% endmermaid %}
+
      JohnAliceHello John, how are you?Great!JohnAlice

      Blockquotes

      We do not grow absolutely, chronologically. We grow sometimes in one dimension, and not in another, unevenly. We grow partially. We are relative. We are mature in one realm, childish in another. —Anais Nin

      Layouts

      The main text column is referred to as the body. It is the assumed layout of any direct descendants of the d-article element.

      .l-body

      For images you want to display a little larger, try .l-page:

      .l-page

      All of these have an outset variant if you want to poke out from the body text a little bit. For instance:

      .l-body-outset

      .l-page-outset

      Occasionally you’ll want to use the full browser width. For this, use .l-screen. You can also inset the element a little from the edge of the browser by using the inset variant.

      .l-screen

      .l-screen-inset

      The final layout is for marginalia, asides, and footnotes. It does not interrupt the normal flow of .l-body sized text except on mobile screen sizes.

      .l-gutter

      Other Typography?

      Emphasis, aka italics, with asterisks (*asterisks*) or underscores (_underscores_).

      Strong emphasis, aka bold, with asterisks or underscores.

      Combined emphasis with asterisks and underscores.

      Strikethrough uses two tildes. Scratch this.

      1. First ordered list item
      2. Another item ⋅⋅* Unordered sub-list.
      3. Actual numbers don’t matter, just that it’s a number ⋅⋅1. Ordered sub-list
      4. And another item.

      ⋅⋅⋅You can have properly indented paragraphs within list items. Notice the blank line above, and the leading spaces (at least one, but we’ll use three here to also align the raw Markdown).

      ⋅⋅⋅To have a line break without a paragraph, you will need to use two trailing spaces.⋅⋅ ⋅⋅⋅Note that this line is separate, but within the same paragraph.⋅⋅ ⋅⋅⋅(This is contrary to the typical GFM line break behaviour, where trailing spaces are not required.)

      • Unordered list can use asterisks
      • Or minuses
      • Or pluses

      I’m an inline-style link

      I’m an inline-style link with title

      I’m a reference-style link

      I’m a relative reference to a repository file

      You can use numbers for reference-style link definitions

      Or leave it empty and use the link text itself.

      URLs and URLs in angle brackets will automatically get turned into links. http://www.example.com or http://www.example.com and sometimes example.com (but not on Github, for example).

      Some text to show that the reference links can follow later.

      Here’s our logo (hover to see the title text):

      Inline-style: alt text

      Reference-style: alt text

      Inline code has back-ticks around it.

      var s = "JavaScript syntax highlighting";
+alert(s);
+
      s = "Python syntax highlighting"
+print s
+
      No language indicated, so no syntax highlighting. 
+But let's throw in a <b>tag</b>.
+

      Colons can be used to align columns.

      Tables Are Cool
      col 3 is right-aligned $1600
      col 2 is centered $12
      zebra stripes are neat $1

      There must be at least 3 dashes separating each header cell. The outer pipes (|) are optional, and you don’t need to make the raw Markdown line up prettily. You can also use inline Markdown.

      Markdown Less Pretty
      Still renders nicely
      1 2 3

      Blockquotes are very handy in email to emulate reply text. This line is part of the same quote.

      Quote break.

      This is a very long line that will still be quoted properly when it wraps. Oh boy let’s keep writing to make sure this is long enough to actually wrap for everyone. Oh, you can put Markdown into a blockquote.

      Here’s a line for us to start with.

      This line is separated from the one above by two newlines, so it will be a separate paragraph.

      This line is also a separate paragraph, but… This line is only separated by a single newline, so it’s a separate line in the same paragraph.

      ]]>      Albert Einstein       \ No newline at end of file diff --git a/home.md b/home.md deleted file mode 100644 index f5344476..00000000 --- a/home.md +++ /dev/null @@ -1,192 +0,0 @@ ---- -layout: page -title: ICLR 2022 Blog Track -tags: [proposal, call] -authors: Bubeck, Sebastien (Microsoft); Dobre, David (Mila); Gauthier, Charlie (Mila); Gidel, Gauthier (Mila); Vernade, Claire (DeepMind) ---- - -
      -

      - ICLR Logo -

      - -## Important Information - -- The track has concluded and accepted blogposts are viewable [here]({{ site.url }}/blog)! -- We've released a video talking about this track in more detail - -We would like to thank everyone who took part in this experiment and for making it a success! - -

      - -## Contents - -- [Accepted Posts](#accepted-posts) -- [Motivation](#motivation) -- [Submissions](#submissions) -- [Organizers](#organizers) - - -## Motivation - -The Machine Learning community is currently experiencing a -[reproducibility crisis](https://neuripsconf.medium.com/designing-the-reproducibility-program-for-neurips-2020-7fcccaa5c6ad) -and a reviewing crisis [[Littman, 2021]](#Litt). Because of the highly competitive and noisy -reviewing process of ML conferences [[Tran et al., 2020]](#Tran), researchers have an incentive to -oversell their results, slowing down the progress and diminishing the -integrity of the scientific community. Moreover with the growing number -of papers published and submitted at the main ML conferences [[Lin et al., 2020]](#Lin), it has -become more challenging to keep track of the latest advances in the -field. - -Blog posts are becoming an increasingly popular and useful way to talk -about science [[Brown and Woolston, 2018]](#Brow). -They offer substantial value to the scientific community -by providing a flexible platform to foster open, human, and transparent -discussions about new insights or limitations of a scientific -publication. However, because they are not as recognized as standard -scientific publications, only a minority of researchers manage to -maintain an active blog and get visibility for their efforts. Many are -well-established researchers ([Francis Bach](https://francisbach.com/), -[Ben Recht](https://www.argmin.net/), [Ferenc -Huszár](https://www.inference.vc/), [Lilian -Weng](https://lilianweng.github.io/lil-log/)) or big corporations that -leverage entire teams of graphic designers designer and writers to -polish their blogs ([Facebook AI](https://ai.facebook.com/blog/?page=1), -[Google AI](https://ai.googleblog.com/), -[DeepMind](https://deepmind.com/blog), -[OpenAI](https://openai.com/blog/)). As a result, the incentives for -writing scientific blog posts are largely personal; it is unreasonable -to expect a significant portion of the machine learning community to -contribute to such an initiative when everyone is trying to establish -themselves through publications. - - -### A Blog Post Conference Track - -Our goal is to create a formal call for blog posts at ICLR to -incentivize and reward researchers to review past work and summarize the -outcomes, develop new intuitions, or highlight some shortcomings. A very -influential initiative of this kind happened after the second world war -in France. Because of the lack of up-to-date textbooks, a collective of -mathematicians under the pseudonym Nicolas Bourbaki [[Halmos 1957]](#Halm), decided to start a -series of textbooks about the foundations of mathematics [[Bourbaki, 1939]](#Bour). -In the same vein, we aim at providing a new way to summarize scientific knowledge in -the ML community. - -Due to the large diversity of topics that can be discussed in a blog -post, we decided to restrict the range of topics for this call for blog -posts. We identified that the blog posts that would bring to most value -to the community and the conference would be posts that distill and -discuss *previously published papers*. - -### A call for blog posts discussing work previously published at ICLR - -The format and process for this blog post track is as follows: - -- Write a post about a paper previously published at ICLR, with the - constraint that one cannot write a blog post on work that they have - a conflict of interest with. This implies that one cannot review - their own work, or work originating from their institution or - company. We want to foster productive discussion about *ideas*, and - prevent posts that intentionally aim to help or hurt individuals or - institutions. - -- Blogs will be peer-reviewed (double-blind, see - Section 2.5) - for quality and novelty of the content: clarity and pedagogy of the - exposition, new theoretical or practical insights, - reproduction/extension of experiments, etc. - -- The posts will be published under a unified template (see - Section 2.4 - and - Section 2.5) - and hosted on the conference website or our own Github page. - - -## Submissions - -**Note: The track has concluded and we are not accepting any more submissions!** - -Our goal is to avoid heavily engineered, professionally-made -blog-posts---Such as the “100+ hours” mentioned as a standard by the [Distill - guidelines](https://distill.pub/journal/)---to entice ideas and clear writing rather than dynamic -visualizations or embedded javascript engines. - -As a result, we restrict submissions to the Markdown format. We believe -this is a good trade-off between complexity and flexibility. Markdown -enables users to easily embed media such as images, gifs, audio, and -video as well as write mathematical equations using MathJax, without -requiring users to know how to create HTML web pages. This (mostly) -static format is also fairly portable; users can download the blog post -without much effort for offline reading or archival purposes. More -importantly, this format can be easily hosted and maintained through -GitHub. - -> Please checkout the submitting section for a detailed overview on the -> process of creating and submitting a blog post. - - -## Organizers - -  - -
        -
      • - -
        -

        Gauthier Gidel

        -

        gidelgau [ at ] mila.quebec

        -
        -
        • -
      • - -
        -

        Charlier Gauthier

        -

        charlie.gauthier [ at ] umontreal.ca

        -
        -
        • -
      • - -
        -

        David Dobre

        -

        david-a.dobre [ at ] mila.quebec

        -
        -
        • -
      • - -
        -

        Sébastien Bubeck

        -

        sebubeck [ at ] microsoft.com

        -
        -
        • -
      • - -
        -

        Claire Vernade

        -

        vernade [ at ] deepmind.com

        -
        -
        • -
      - ---- - -## References - -Michael L Littman. Collusion rings threaten the integrity of computer science research. Communications of the ACM, 2021. - -David Tran, Alex Valtchanov, Keshav Ganapathy, Raymond Feng, Eric Slud, Micah Goldblum, and Tom Goldstein. An open review of openreview: A critical analysis of the machine learning conference review process. arXiv, 2020. - -Hsuan-Tien Lin, Maria-Florina Balcan, Raia Hadsell, and Marc’Aurelio Ranzato. What we learned from neurips2020 reviewing process. Medium https://medium.com/@NeurIPSConf/what-we-learned-from-neurips-2020-reviewing-process-e24549eea38f, 2020. - -Eryn Brown and Chris Woolston. Why science blogging still matters. Nature, 2018. - -Paul R Halmos. Nicolas bourbaki. Scientific American, 1957. - -Nicolas Bourbaki. Elements of mathematics. Éditions Hermann, 1939. - - - - - diff --git a/home/index.html b/home/index.html new file mode 100644 index 00000000..ffb1c30f --- /dev/null +++ b/home/index.html @@ -0,0 +1 @@ + ICLR 2022 Blog Track | 6.S898 Deep Learning Blogs 2023


      ICLR Logo

      Important Information

      • The track has concluded and accepted blogposts are viewable here!
      • We’ve released a video talking about this track in more detail

      We would like to thank everyone who took part in this experiment and for making it a success!

      Contents

      Motivation

      The Machine Learning community is currently experiencing a reproducibility crisis and a reviewing crisis [Littman, 2021]. Because of the highly competitive and noisy reviewing process of ML conferences [Tran et al., 2020], researchers have an incentive to oversell their results, slowing down the progress and diminishing the integrity of the scientific community. Moreover with the growing number of papers published and submitted at the main ML conferences [Lin et al., 2020], it has become more challenging to keep track of the latest advances in the field.

      Blog posts are becoming an increasingly popular and useful way to talk about science [Brown and Woolston, 2018]. They offer substantial value to the scientific community by providing a flexible platform to foster open, human, and transparent discussions about new insights or limitations of a scientific publication. However, because they are not as recognized as standard scientific publications, only a minority of researchers manage to maintain an active blog and get visibility for their efforts. Many are well-established researchers (Francis Bach, Ben Recht, Ferenc Huszár, Lilian Weng) or big corporations that leverage entire teams of graphic designers designer and writers to polish their blogs (Facebook AI, Google AI, DeepMind, OpenAI). As a result, the incentives for writing scientific blog posts are largely personal; it is unreasonable to expect a significant portion of the machine learning community to contribute to such an initiative when everyone is trying to establish themselves through publications.

      A Blog Post Conference Track

      Our goal is to create a formal call for blog posts at ICLR to incentivize and reward researchers to review past work and summarize the outcomes, develop new intuitions, or highlight some shortcomings. A very influential initiative of this kind happened after the second world war in France. Because of the lack of up-to-date textbooks, a collective of mathematicians under the pseudonym Nicolas Bourbaki [Halmos 1957], decided to start a series of textbooks about the foundations of mathematics [Bourbaki, 1939]. In the same vein, we aim at providing a new way to summarize scientific knowledge in the ML community.

      Due to the large diversity of topics that can be discussed in a blog post, we decided to restrict the range of topics for this call for blog posts. We identified that the blog posts that would bring to most value to the community and the conference would be posts that distill and discuss previously published papers.

      A call for blog posts discussing work previously published at ICLR

      The format and process for this blog post track is as follows:

      • Write a post about a paper previously published at ICLR, with the constraint that one cannot write a blog post on work that they have a conflict of interest with. This implies that one cannot review their own work, or work originating from their institution or company. We want to foster productive discussion about ideas, and prevent posts that intentionally aim to help or hurt individuals or institutions.

      • Blogs will be peer-reviewed (double-blind, see Section 2.5) for quality and novelty of the content: clarity and pedagogy of the exposition, new theoretical or practical insights, reproduction/extension of experiments, etc.

      • The posts will be published under a unified template (see Section 2.4 and Section 2.5) and hosted on the conference website or our own Github page.

      Submissions

      Note: The track has concluded and we are not accepting any more submissions!

      Our goal is to avoid heavily engineered, professionally-made blog-posts—Such as the “100+ hours” mentioned as a standard by the Distill guidelines—to entice ideas and clear writing rather than dynamic visualizations or embedded javascript engines.

      As a result, we restrict submissions to the Markdown format. We believe this is a good trade-off between complexity and flexibility. Markdown enables users to easily embed media such as images, gifs, audio, and video as well as write mathematical equations using MathJax, without requiring users to know how to create HTML web pages. This (mostly) static format is also fairly portable; users can download the blog post without much effort for offline reading or archival purposes. More importantly, this format can be easily hosted and maintained through GitHub.

      Please checkout the submitting section for a detailed overview on the process of creating and submitting a blog post.

      Organizers

       

      • Gauthier Gidel

        gidelgau [ at ] mila.quebec

      • Charlier Gauthier

        charlie.gauthier [ at ] umontreal.ca

      • David Dobre

        david-a.dobre [ at ] mila.quebec

      • Sébastien Bubeck

        sebubeck [ at ] microsoft.com

      • Claire Vernade

        vernade [ at ] deepmind.com

      References

      Michael L Littman. Collusion rings threaten the integrity of computer science research. Communications of the ACM, 2021.

      David Tran, Alex Valtchanov, Keshav Ganapathy, Raymond Feng, Eric Slud, Micah Goldblum, and Tom Goldstein. An open review of openreview: A critical analysis of the machine learning conference review process. arXiv, 2020.

      Hsuan-Tien Lin, Maria-Florina Balcan, Raia Hadsell, and Marc’Aurelio Ranzato. What we learned from neurips2020 reviewing process. Medium https://medium.com/@NeurIPSConf/what-we-learned-from-neurips-2020-reviewing-process-e24549eea38f, 2020.

      Eryn Brown and Chris Woolston. Why science blogging still matters. Nature, 2018.

      Paul R Halmos. Nicolas bourbaki. Scientific American, 1957.

      Nicolas Bourbaki. Elements of mathematics. Éditions Hermann, 1939.

      \ No newline at end of file diff --git a/index.html b/index.html index 6a60cbf0..2f62364f 100644 --- a/index.html +++ b/index.html @@ -1,65 +1 @@ ---- -layout: default -title: Home ---- - -
      - {% for post in paginator.posts %} - {% if post.hide == null or post.hide == false %} -
      -

      - - {{ post.title }} - -

      - - {{ post.date | date_to_string }} | {% for tag in post.tags %} - {{ tag }} - {% endfor %} - - {{ post.authors }} - - -
      - {{ post.excerpt }} -
      -
      -
      - {% endif %} - {% endfor %} -
      - - - - + Redirecting…

      Redirecting…

      Click here if you are not redirected. \ No newline at end of file diff --git a/index.markdown b/index.markdown deleted file mode 100644 index 06715078..00000000 --- a/index.markdown +++ /dev/null @@ -1,6 +0,0 @@ ---- -# Feel free to add content and custom Front Matter to this file. -# To modify the layout, see https://jekyllrb.com/docs/themes/#overriding-theme-defaults - -layout: home ---- diff --git a/index.md b/index.md deleted file mode 100644 index 9b432d22..00000000 --- a/index.md +++ /dev/null @@ -1,4 +0,0 @@ ---- -title: home -redirect_to: /blog ---- diff --git a/news/announcement_1/index.html b/news/announcement_1/index.html index 3333a286..82c3a6b5 100644 --- a/news/announcement_1/index.html +++ b/news/announcement_1/index.html @@ -1 +1 @@ - Announcement_1 | You R. Name

      Announcement_1

      October 22, 2015

      2015

      A simple inline announcement.

      \ No newline at end of file + Announcement_1 | 6.S898 Deep Learning Blogs 2023

      Announcement_1

      October 22, 2015

      2015

      A simple inline announcement.

      \ No newline at end of file diff --git a/news/announcement_2/index.html b/news/announcement_2/index.html index 5410b4c6..d4046cdf 100644 --- a/news/announcement_2/index.html +++ b/news/announcement_2/index.html @@ -1 +1 @@ - A long announcement with details | You R. Name

      A long announcement with details

      November 7, 2015

      2015

      Announcements and news can be much longer than just quick inline posts. In fact, they can have all the features available for the standard blog posts. See below.

      Jean shorts raw denim Vice normcore, art party High Life PBR skateboard stumptown vinyl kitsch. Four loko meh 8-bit, tousled banh mi tilde forage Schlitz dreamcatcher twee 3 wolf moon. Chambray asymmetrical paleo salvia, sartorial umami four loko master cleanse drinking vinegar brunch. Pinterest DIY authentic Schlitz, hoodie Intelligentsia butcher trust fund brunch shabby chic Kickstarter forage flexitarian. Direct trade cold-pressed meggings stumptown plaid, pop-up taxidermy. Hoodie XOXO fingerstache scenester Echo Park. Plaid ugh Wes Anderson, freegan pug selvage fanny pack leggings pickled food truck DIY irony Banksy.

      Hipster list

      • brunch
      • fixie
      • raybans
      • messenger bag

      Hoodie Thundercats retro, tote bag 8-bit Godard craft beer gastropub. Truffaut Tumblr taxidermy, raw denim Kickstarter sartorial dreamcatcher. Quinoa chambray slow-carb salvia readymade, bicycle rights 90’s yr typewriter selfies letterpress cardigan vegan.

      Pug heirloom High Life vinyl swag, single-origin coffee four dollar toast taxidermy reprehenderit fap distillery master cleanse locavore. Est anim sapiente leggings Brooklyn ea. Thundercats locavore excepteur veniam eiusmod. Raw denim Truffaut Schlitz, migas sapiente Portland VHS twee Bushwick Marfa typewriter retro id keytar.

      We do not grow absolutely, chronologically. We grow sometimes in one dimension, and not in another, unevenly. We grow partially. We are relative. We are mature in one realm, childish in another. —Anais Nin

      Fap aliqua qui, scenester pug Echo Park polaroid irony shabby chic ex cardigan church-key Odd Future accusamus. Blog stumptown sartorial squid, gastropub duis aesthetic Truffaut vero. Pinterest tilde twee, odio mumblecore jean shorts lumbersexual.

      \ No newline at end of file + A long announcement with details | 6.S898 Deep Learning Blogs 2023

      A long announcement with details

      November 7, 2015

      2015

      Announcements and news can be much longer than just quick inline posts. In fact, they can have all the features available for the standard blog posts. See below.

      Jean shorts raw denim Vice normcore, art party High Life PBR skateboard stumptown vinyl kitsch. Four loko meh 8-bit, tousled banh mi tilde forage Schlitz dreamcatcher twee 3 wolf moon. Chambray asymmetrical paleo salvia, sartorial umami four loko master cleanse drinking vinegar brunch. Pinterest DIY authentic Schlitz, hoodie Intelligentsia butcher trust fund brunch shabby chic Kickstarter forage flexitarian. Direct trade cold-pressed meggings stumptown plaid, pop-up taxidermy. Hoodie XOXO fingerstache scenester Echo Park. Plaid ugh Wes Anderson, freegan pug selvage fanny pack leggings pickled food truck DIY irony Banksy.

      Hipster list

      • brunch
      • fixie
      • raybans
      • messenger bag

      Hoodie Thundercats retro, tote bag 8-bit Godard craft beer gastropub. Truffaut Tumblr taxidermy, raw denim Kickstarter sartorial dreamcatcher. Quinoa chambray slow-carb salvia readymade, bicycle rights 90’s yr typewriter selfies letterpress cardigan vegan.

      Pug heirloom High Life vinyl swag, single-origin coffee four dollar toast taxidermy reprehenderit fap distillery master cleanse locavore. Est anim sapiente leggings Brooklyn ea. Thundercats locavore excepteur veniam eiusmod. Raw denim Truffaut Schlitz, migas sapiente Portland VHS twee Bushwick Marfa typewriter retro id keytar.

      We do not grow absolutely, chronologically. We grow sometimes in one dimension, and not in another, unevenly. We grow partially. We are relative. We are mature in one realm, childish in another. —Anais Nin

      Fap aliqua qui, scenester pug Echo Park polaroid irony shabby chic ex cardigan church-key Odd Future accusamus. Blog stumptown sartorial squid, gastropub duis aesthetic Truffaut vero. Pinterest tilde twee, odio mumblecore jean shorts lumbersexual.

      \ No newline at end of file diff --git a/news/announcement_3/index.html b/news/announcement_3/index.html index 2e9b4295..940e1f24 100644 --- a/news/announcement_3/index.html +++ b/news/announcement_3/index.html @@ -1 +1 @@ - Announcement_3 | You R. Name

      Announcement_3

      January 15, 2016

      2016

      A simple inline announcement with Markdown emoji! :sparkles: :smile:

      \ No newline at end of file + Announcement_3 | 6.S898 Deep Learning Blogs 2023

      Announcement_3

      January 15, 2016

      2016

      A simple inline announcement with Markdown emoji! :sparkles: :smile:

      \ No newline at end of file diff --git a/public/css/custom.css b/public/css/custom.css index d01bbdd1..31f7e5b5 100644 --- a/public/css/custom.css +++ b/public/css/custom.css @@ -1,18 +1 @@ -.content-tag { - text-decoration: underline; - display: inline; -} - -.content-tag:before { - content: "#"; - text-decoration: none; -} - -.content-tag:after { - content: " "; - text-decoration: none; -} - -.content-tag:hover { - text-decoration: none; -} +.content-tag{text-decoration:underline;display:inline}.content-tag:before{content:"#";text-decoration:none}.content-tag:after{content:" ";text-decoration:none}.content-tag:hover{text-decoration:none} \ No newline at end of file diff --git a/public/css/lanyon.css b/public/css/lanyon.css index 70d452be..cf30b744 100644 --- a/public/css/lanyon.css +++ b/public/css/lanyon.css @@ -1,558 +1,2 @@ -/* - * ___ - * /\_ \ - * \//\ \ __ ___ __ __ ___ ___ - * \ \ \ /'__`\ /' _ `\/\ \/\ \ / __`\ /' _ `\ - * \_\ \_/\ \_\.\_/\ \/\ \ \ \_\ \/\ \_\ \/\ \/\ \ - * /\____\ \__/.\_\ \_\ \_\/`____ \ \____/\ \_\ \_\ - * \/____/\/__/\/_/\/_/\/_/`/___/> \/___/ \/_/\/_/ - * /\___/ - * \/__/ - * - * Designed, built, and released under MIT license by @mdo. Learn more at - * https://github.com/poole/lanyon. - */ - - -/* - * Contents - * - * Global resets - * Masthead - * Sidebar - * Slide effect - * Posts and pages - * Pagination - * Reverse layout - * Themes - */ - - -/* - * Global resets - * - * Update the foundational and global aspects of the page. - */ - -/* Prevent scroll on narrow devices */ -html, -body { - overflow-x: hidden; -} - -html { - font-family: "PT Serif", Georgia, "Times New Roman", serif; -} - -h1, h2, h3, h4, h5, h6 { - font-family: "PT Sans", Helvetica, Arial, sans-serif; - font-weight: 400; - color: #313131; - letter-spacing: -.025rem; -} - - -/* - * Wrapper - * - * The wrapper is used to position site content when the sidebar is toggled. We - * use an outter wrap to position the sidebar without interferring with the - * regular page content. - */ - -.wrap { - position: relative; - width: 100%; -} - - -/* - * Container - * - * Center the page content. - */ - -.container { - max-width: 28rem; -} -@media (min-width: 38em) { - .container { - max-width: 32rem; - } -} -@media (min-width: 56em) { - .container { - max-width: 56rem; - } -} - - -/* - * Masthead - * - * Super small header above the content for site name and short description. - */ - -.masthead { - padding-top: 1rem; - padding-bottom: 1rem; - margin-bottom: 3rem; - border-bottom: 1px solid #eee; -} -.masthead-title { - margin-top: 0; - margin-bottom: 0; - color: #505050; -} -.masthead-title a { - color: #505050; -} -.masthead-title small { - font-size: 75%; - font-weight: 400; - color: #c0c0c0; - letter-spacing: 0; -} - -@media (max-width: 48em) { - .masthead-title { - text-align: center; - } - .masthead-title small { - display: none; - } -} - - -/* - * Sidebar - * - * The sidebar is the drawer, the item we are toggling with our handy hamburger - * button in the corner of the page. - * - * This particular sidebar implementation was inspired by Chris Coyier's - * "Offcanvas Menu with CSS Target" article, and the checkbox variation from the - * comments by a reader. It modifies both implementations to continue using the - * checkbox (no change in URL means no polluted browser history), but this uses - * `position` for the menu to avoid some potential content reflow issues. - * - * Source: http://css-tricks.com/off-canvas-menu-with-css-target/#comment-207504 - */ - -/* Style and "hide" the sidebar */ -.sidebar { - position: fixed; - top: 0; - bottom: 0; - left: -14rem; - width: 14rem; - visibility: hidden; - overflow-y: auto; - font-family: "PT Sans", Helvetica, Arial, sans-serif; - font-size: .875rem; /* 15px */ - color: rgba(255,255,255,.6); - background-color: #202020; - -webkit-transition: all .3s ease-in-out; - transition: all .3s ease-in-out; -} -@media (min-width: 30em) { - .sidebar { - font-size: .75rem; /* 14px */ - } -} - -/* Sidebar content */ -.sidebar a { - font-weight: normal; - color: #fff; -} -.sidebar-item { - padding: 1rem; -} -.sidebar-item p:last-child { - margin-bottom: 0; -} - -/* Sidebar nav */ -.sidebar-nav { - border-bottom: 1px solid rgba(255,255,255,.1); -} -.sidebar-nav-item { - display: block; - padding: .5rem 1rem; - border-top: 1px solid rgba(255,255,255,.1); -} -.sidebar-nav-item.active, -a.sidebar-nav-item:hover, -a.sidebar-nav-item:focus { - text-decoration: none; - background-color: rgba(255,255,255,.1); - border-color: transparent; -} - -@media (min-width: 48em) { - .sidebar-item { - padding: 1.5rem; - } - .sidebar-nav-item { - padding-left: 1.5rem; - padding-right: 1.5rem; - } -} - -/* Hide the sidebar checkbox that we toggle with `.sidebar-toggle` */ -.sidebar-checkbox { - position: absolute; - opacity: 0; - -webkit-user-select: none; - -moz-user-select: none; - user-select: none; -} - -/* Style the `label` that we use to target the `.sidebar-checkbox` */ -.sidebar-toggle { - position: absolute; - top: .8rem; - left: 1rem; - display: flex; - align-items: center; - padding: .25rem .75rem; - color: #505050; - background-color: #fff; - border-radius: .25rem; - cursor: pointer; -} - -.sidebar-toggle::before { - display: inline-block; - width: 32px; - height: 32px; - content: ""; - background: url("data:image/svg+xml,%3Csvg viewBox='0 0 16 16' fill='%23555' xmlns='http://www.w3.org/2000/svg'%3E%3Cpath fill-rule='evenodd' d='M2.5 11.5A.5.5 0 013 11h10a.5.5 0 010 1H3a.5.5 0 01-.5-.5zm0-4A.5.5 0 013 7h10a.5.5 0 010 1H3a.5.5 0 01-.5-.5zm0-4A.5.5 0 013 3h10a.5.5 0 010 1H3a.5.5 0 01-.5-.5z' clip-rule='evenodd'/%3E%3C/svg%3E") no-repeat; -} - -.sidebar-toggle:active, -#sidebar-checkbox:focus ~ .sidebar-toggle, -#sidebar-checkbox:checked ~ .sidebar-toggle { - color: #fff; - background-color: #555; -} - -.sidebar-toggle:active:before, -#sidebar-checkbox:focus ~ .sidebar-toggle::before, -#sidebar-checkbox:checked ~ .sidebar-toggle::before { - background: url("data:image/svg+xml,%3Csvg viewBox='0 0 16 16' fill='%23fff' xmlns='http://www.w3.org/2000/svg'%3E%3Cpath fill-rule='evenodd' d='M2.5 11.5A.5.5 0 013 11h10a.5.5 0 010 1H3a.5.5 0 01-.5-.5zm0-4A.5.5 0 013 7h10a.5.5 0 010 1H3a.5.5 0 01-.5-.5zm0-4A.5.5 0 013 3h10a.5.5 0 010 1H3a.5.5 0 01-.5-.5z' clip-rule='evenodd'/%3E%3C/svg%3E") no-repeat; -} - -@media (min-width: 30.1em) { - .sidebar-toggle { - position: fixed; - } -} - -@media print { - .sidebar-toggle { - display: none; - } -} - -/* Slide effect - * - * Handle the sliding effects of the sidebar and content in one spot, seperate - * from the default styles. - * - * As an a heads up, we don't use `transform: translate3d()` here because when - * mixed with `position: fixed;` for the sidebar toggle, it creates a new - * containing block. Put simply, the fixed sidebar toggle behaves like - * `position: absolute;` when transformed. - * - * Read more about it at http://meyerweb.com/eric/thoughts/2011/09/12/. - */ - -.wrap, -.sidebar, -.sidebar-toggle { - -webkit-backface-visibility: hidden; - -ms-backface-visibility: hidden; - backface-visibility: hidden; -} -.wrap, -.sidebar-toggle { - -webkit-transition: -webkit-transform .3s ease-in-out; - transition: transform .3s ease-in-out; -} - -#sidebar-checkbox:checked + .sidebar { - z-index: 10; - visibility: visible; -} -#sidebar-checkbox:checked ~ .sidebar, -#sidebar-checkbox:checked ~ .wrap, -#sidebar-checkbox:checked ~ .sidebar-toggle { - -webkit-transform: translateX(14rem); - -ms-transform: translateX(14rem); - transform: translateX(14rem); -} - - -/* - * Posts and pages - * - * Each post is wrapped in `.post` and is used on default and post layouts. Each - * page is wrapped in `.page` and is only used on the page layout. - */ - -.page, -.post { - margin-bottom: 4em; -} - -/* Blog post or page title */ -.page-title, -.post-title, -.post-title a { - color: #303030; -} -.page-title, -.post-title { - margin-top: 0; -} - -/* Meta data line below post title */ -.post-date { - display: block; - margin-top: -.5rem; - margin-bottom: 1rem; - color: #9a9a9a; -} - -/* Related blog */ -.related { - padding-top: 2rem; - padding-bottom: 2rem; - border-top: 1px solid #eee; -} -.related-posts { - padding-left: 0; - list-style: none; -} -.related-posts h3 { - margin-top: 0; -} -.related-posts li small { - font-size: 75%; - color: #999; -} -.related-posts li a:hover { - color: #268bd2; - text-decoration: none; -} -.related-posts li a:hover small { - color: inherit; -} - - -/* - * Pagination - * - * Super lightweight (HTML-wise) blog pagination. `span`s are provide for when - * there are no more previous or next blog to show. - */ - -.pagination { - overflow: hidden; /* clearfix */ - margin-left: -1rem; - margin-right: -1rem; - font-family: "PT Sans", Helvetica, Arial, sans-serif; - color: #ccc; - text-align: center; -} - -/* Pagination items can be `span`s or `a`s */ -.pagination-item { - display: block; - padding: 1rem; - border: 1px solid #eee; -} -.pagination-item:first-child { - margin-bottom: -1px; -} - -/* Only provide a hover state for linked pagination items */ -a.pagination-item:hover { - background-color: #f5f5f5; -} - -@media (min-width: 30em) { - .pagination { - margin: 3rem 0; - } - .pagination-item { - float: left; - width: 50%; - } - .pagination-item:first-child { - margin-bottom: 0; - border-top-left-radius: 4px; - border-bottom-left-radius: 4px; - } - .pagination-item:last-child { - margin-left: -1px; - border-top-right-radius: 4px; - border-bottom-right-radius: 4px; - } -} - - -/* - * Reverse layout - * - * Flip the orientation of the page by placing the `.sidebar` and sidebar toggle - * on the right side. - */ - -.layout-reverse .sidebar { - left: auto; - right: -14rem; -} -.layout-reverse .sidebar-toggle { - left: auto; - right: 1rem; -} - -.layout-reverse #sidebar-checkbox:checked ~ .sidebar, -.layout-reverse #sidebar-checkbox:checked ~ .wrap, -.layout-reverse #sidebar-checkbox:checked ~ .sidebar-toggle { - -webkit-transform: translateX(-14rem); - -ms-transform: translateX(-14rem); - transform: translateX(-14rem); -} - - -/* - * Themes - * - * Apply custom color schemes by adding the appropriate class to the `body`. - * Based on colors from Base16: http://chriskempson.github.io/base16/#default. - */ - -/* Red */ -.theme-base-08 .sidebar, -.theme-base-08 .sidebar-toggle:active, -.theme-base-08 #sidebar-checkbox:checked ~ .sidebar-toggle { - background-color: #ac4142; -} -.theme-base-08 .container a, -.theme-base-08 .sidebar-toggle, -.theme-base-08 .related-posts li a:hover { - color: #ac4142; -} - -/* Orange */ -.theme-base-09 .sidebar, -.theme-base-09 .sidebar-toggle:active, -.theme-base-09 #sidebar-checkbox:checked ~ .sidebar-toggle { - background-color: #d28445; -} -.theme-base-09 .container a, -.theme-base-09 .sidebar-toggle, -.theme-base-09 .related-posts li a:hover { - color: #d28445; -} - -/* Yellow */ -.theme-base-0a .sidebar, -.theme-base-0a .sidebar-toggle:active, -.theme-base-0a #sidebar-checkbox:checked ~ .sidebar-toggle { - background-color: #f4bf75; -} -.theme-base-0a .container a, -.theme-base-0a .sidebar-toggle, -.theme-base-0a .related-posts li a:hover { - color: #f4bf75; -} - -/* Green */ -.theme-base-0b .sidebar, -.theme-base-0b .sidebar-toggle:active, -.theme-base-0b #sidebar-checkbox:checked ~ .sidebar-toggle { - background-color: #90a959; -} -.theme-base-0b .container a, -.theme-base-0b .sidebar-toggle, -.theme-base-0b .related-posts li a:hover { - color: #90a959; -} - -/* Cyan */ -.theme-base-0c .sidebar, -.theme-base-0c .sidebar-toggle:active, -.theme-base-0c #sidebar-checkbox:checked ~ .sidebar-toggle { - background-color: #75b5aa; -} -.theme-base-0c .container a, -.theme-base-0c .sidebar-toggle, -.theme-base-0c .related-posts li a:hover { - color: #75b5aa; -} - -/* Blue */ -.theme-base-0d .sidebar, -.theme-base-0d .sidebar-toggle:active, -.theme-base-0d #sidebar-checkbox:checked ~ .sidebar-toggle { - background-color: #6a9fb5; -} -.theme-base-0d .container a, -.theme-base-0d .sidebar-toggle, -.theme-base-0d .related-posts li a:hover { - color: #6a9fb5; -} - -/* Magenta */ -.theme-base-0e .sidebar, -.theme-base-0e .sidebar-toggle:active, -.theme-base-0e #sidebar-checkbox:checked ~ .sidebar-toggle { - background-color: #aa759f; -} -.theme-base-0e .container a, -.theme-base-0e .sidebar-toggle, -.theme-base-0e .related-posts li a:hover { - color: #aa759f; -} - -/* Brown */ -.theme-base-0f .sidebar, -.theme-base-0f .sidebar-toggle:active, -.theme-base-0f #sidebar-checkbox:checked ~ .sidebar-toggle { - background-color: #8f5536; -} -.theme-base-0f .container a, -.theme-base-0f .sidebar-toggle, -.theme-base-0f .related-posts li a:hover { - color: #8f5536; -} - - -/* - * Overlay sidebar - * - * Make the sidebar content overlay the viewport content instead of pushing it - * aside when toggled. - */ - -.sidebar-overlay #sidebar-checkbox:checked ~ .wrap { - -webkit-transform: translateX(0); - -ms-transform: translateX(0); - transform: translateX(0); -} -.sidebar-overlay #sidebar-checkbox:checked ~ .sidebar-toggle { - box-shadow: 0 0 0 .25rem #fff; -} -.sidebar-overlay #sidebar-checkbox:checked ~ .sidebar { - box-shadow: .25rem 0 .5rem rgba(0,0,0,.1); -} - -/* Only one tweak for a reverse layout */ -.layout-reverse.sidebar-overlay #sidebar-checkbox:checked ~ .sidebar { - box-shadow: -.25rem 0 .5rem rgba(0,0,0,.1); -} +html,body{overflow-x:hidden}html{font-family:"PT Serif",Georgia,"Times New Roman",serif}h1,h2,h3,h4,h5,h6{font-family:"PT Sans",Helvetica,Arial,sans-serif;font-weight:400;color:#313131;letter-spacing:-.025rem}.wrap{position:relative;width:100%}.container{max-width:28rem}@media(min-width:38em){.container{max-width:32rem}}@media(min-width:56em){.container{max-width:56rem}}.masthead{padding-top:1rem;padding-bottom:1rem;margin-bottom:3rem;border-bottom:1px solid #eee}.masthead-title{margin-top:0;margin-bottom:0;color:#505050}.masthead-title a{color:#505050}.masthead-title small{font-size:75%;font-weight:400;color:#c0c0c0;letter-spacing:0}@media(max-width:48em){.masthead-title{text-align:center}.masthead-title small{display:none}}.sidebar{position:fixed;top:0;bottom:0;left:-14rem;width:14rem;visibility:hidden;overflow-y:auto;font-family:"PT Sans",Helvetica,Arial,sans-serif;font-size:.875rem;color:rgba(255,255,255,.6);background-color:#202020;-webkit-transition:all .3s ease-in-out;transition:all .3s ease-in-out}@media(min-width:30em){.sidebar{font-size:.75rem}}.sidebar a{font-weight:normal;color:#fff}.sidebar-item{padding:1rem}.sidebar-item p:last-child{margin-bottom:0}.sidebar-nav{border-bottom:1px solid rgba(255,255,255,.1)}.sidebar-nav-item{display:block;padding:.5rem 1rem;border-top:1px solid rgba(255,255,255,.1)}.sidebar-nav-item.active,a.sidebar-nav-item:hover,a.sidebar-nav-item:focus{text-decoration:none;background-color:rgba(255,255,255,.1);border-color:transparent}@media(min-width:48em){.sidebar-item{padding:1.5rem}.sidebar-nav-item{padding-left:1.5rem;padding-right:1.5rem}}.sidebar-checkbox{position:absolute;opacity:0;-webkit-user-select:none;-moz-user-select:none;user-select:none}.sidebar-toggle{position:absolute;top:.8rem;left:1rem;display:flex;align-items:center;padding:.25rem .75rem;color:#505050;background-color:#fff;border-radius:.25rem;cursor:pointer}.sidebar-toggle::before{display:inline-block;width:32px;height:32px;content:"";background:url("data:image/svg+xml,%3CsvgviewBox='001616'fill='%23555'xmlns='http://www.w3.org/2000/svg'%3E%3Cpathfill-rule='evenodd'd='M2.511.5A.5.5001311h10a.5.500101H3a.5.5001-.5-.5zm0-4A.5.500137h10a.5.500101H3a.5.5001-.5-.5zm0-4A.5.500133h10a.5.500101H3a.5.5001-.5-.5z'clip-rule='evenodd'/%3E%3C/svg%3E") no-repeat}.sidebar-toggle:active,#sidebar-checkbox:focus ~ .sidebar-toggle,#sidebar-checkbox:checked ~ .sidebar-toggle{color:#fff;background-color:#555}.sidebar-toggle:active:before,#sidebar-checkbox:focus ~ .sidebar-toggle::before,#sidebar-checkbox:checked ~ .sidebar-toggle::before{background:url("data:image/svg+xml,%3CsvgviewBox='001616'fill='%23fff'xmlns='http://www.w3.org/2000/svg'%3E%3Cpathfill-rule='evenodd'd='M2.511.5A.5.5001311h10a.5.500101H3a.5.5001-.5-.5zm0-4A.5.500137h10a.5.500101H3a.5.5001-.5-.5zm0-4A.5.500133h10a.5.500101H3a.5.5001-.5-.5z'clip-rule='evenodd'/%3E%3C/svg%3E") no-repeat}@media(min-width:30.1em){.sidebar-toggle{position:fixed}}@media print{.sidebar-toggle{display:none}}.wrap,.sidebar,.sidebar-toggle{-webkit-backface-visibility:hidden;-ms-backface-visibility:hidden;backface-visibility:hidden}.wrap,.sidebar-toggle{-webkit-transition:-webkit-transform .3s ease-in-out;transition:transform .3s ease-in-out}#sidebar-checkbox:checked+.sidebar{z-index:10;visibility:visible}#sidebar-checkbox:checked ~ .sidebar,#sidebar-checkbox:checked ~ .wrap,#sidebar-checkbox:checked ~ .sidebar-toggle{-webkit-transform:translateX(14rem);-ms-transform:translateX(14rem);transform:translateX(14rem)}.page,.post{margin-bottom:4em}.page-title,.post-title,.post-title a{color:#303030}.page-title,.post-title{margin-top:0}.post-date{display:block;margin-top:-.5rem;margin-bottom:1rem;color:#9a9a9a}.related{padding-top:2rem;padding-bottom:2rem;border-top:1px solid #eee}.related-posts{padding-left:0;list-style:none}.related-posts h3{margin-top:0}.related-posts li small{font-size:75%;color:#999}.related-posts li a:hover{color:#268bd2;text-decoration:none}.related-posts li a:hover small{color:inherit}.pagination{overflow:hidden;margin-left:-1rem;margin-right:-1rem;font-family:"PT Sans",Helvetica,Arial,sans-serif;color:#ccc;text-align:center}.pagination-item{display:block;padding:1rem;border:1px solid #eee}.pagination-item:first-child{margin-bottom:-1px}a.pagination-item:hover{background-color:#f5f5f5}@media(min-width:30em){.pagination{margin:3rem 0}.pagination-item{float:left;width:50%}.pagination-item:first-child{margin-bottom:0;border-top-left-radius:4px;border-bottom-left-radius:4px}.pagination-item:last-child{margin-left:-1px;border-top-right-radius:4px;border-bottom-right-radius:4px}}.layout-reverse .sidebar{left:auto;right:-14rem}.layout-reverse .sidebar-toggle{left:auto;right:1rem}.layout-reverse #sidebar-checkbox:checked ~ .sidebar,.layout-reverse #sidebar-checkbox:checked ~ .wrap,.layout-reverse #sidebar-checkbox:checked ~ .sidebar-toggle{-webkit-transform:translateX(-14rem);-ms-transform:translateX(-14rem);transform:translateX(-14rem)}.theme-base-08 .sidebar,.theme-base-08 .sidebar-toggle:active,.theme-base-08 #sidebar-checkbox:checked ~ .sidebar-toggle{background-color:#ac4142}.theme-base-08 .container a,.theme-base-08 .sidebar-toggle,.theme-base-08 .related-posts li a:hover{color:#ac4142}.theme-base-09 .sidebar,.theme-base-09 .sidebar-toggle:active,.theme-base-09 #sidebar-checkbox:checked ~ .sidebar-toggle{background-color:#d28445} +.theme-base-09 .container a,.theme-base-09 .sidebar-toggle,.theme-base-09 .related-posts li a:hover{color:#d28445}.theme-base-0a .sidebar,.theme-base-0a .sidebar-toggle:active,.theme-base-0a #sidebar-checkbox:checked ~ .sidebar-toggle{background-color:#f4bf75}.theme-base-0a .container a,.theme-base-0a .sidebar-toggle,.theme-base-0a .related-posts li a:hover{color:#f4bf75}.theme-base-0b .sidebar,.theme-base-0b .sidebar-toggle:active,.theme-base-0b #sidebar-checkbox:checked ~ .sidebar-toggle{background-color:#90a959}.theme-base-0b .container a,.theme-base-0b .sidebar-toggle,.theme-base-0b .related-posts li a:hover{color:#90a959}.theme-base-0c .sidebar,.theme-base-0c .sidebar-toggle:active,.theme-base-0c #sidebar-checkbox:checked ~ .sidebar-toggle{background-color:#75b5aa}.theme-base-0c .container a,.theme-base-0c .sidebar-toggle,.theme-base-0c .related-posts li a:hover{color:#75b5aa}.theme-base-0d .sidebar,.theme-base-0d 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#sidebar-checkbox:checked ~ .sidebar{box-shadow:.25rem 0 .5rem rgba(0,0,0,.1)}.layout-reverse.sidebar-overlay #sidebar-checkbox:checked ~ .sidebar{box-shadow:-.25rem 0 .5rem rgba(0,0,0,.1)} \ No newline at end of file diff --git a/public/css/poole.css b/public/css/poole.css index 39396548..f15d7bb2 100644 --- a/public/css/poole.css +++ b/public/css/poole.css @@ -1,430 +1 @@ -/* - * ___ - * /\_ \ - * _____ ___ ___\//\ \ __ - * /\ '__`\ / __`\ / __`\\ \ \ /'__`\ - * \ \ \_\ \/\ \_\ \/\ \_\ \\_\ \_/\ __/ - * \ \ ,__/\ \____/\ \____//\____\ \____\ - * \ \ \/ \/___/ \/___/ \/____/\/____/ - * \ \_\ - * \/_/ - * - * Designed, built, and released under MIT license by @mdo. 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b/robots.txt @@ -1,7 +1,4 @@ ---- -permalink: /robots.txt ---- User-agent: * Disallow: -Sitemap: {{ site.baseurl | prepend: site.url }}/sitemap.xml +Sitemap: https://deep-learning-mit.github.io/staging/sitemap.xml diff --git a/sitemap.xml b/sitemap.xml new file mode 100644 index 00000000..c63e62e7 --- /dev/null +++ b/sitemap.xml @@ -0,0 +1 @@ + https://deep-learning-mit.github.io/staging/news/announcement_1/ 2015-10-22T19:59:00+00:00 https://deep-learning-mit.github.io/staging/news/announcement_2/ 2015-11-07T20:11:00+00:00 https://deep-learning-mit.github.io/staging/news/announcement_3/ 2016-01-15T11:59:00+00:00 https://deep-learning-mit.github.io/staging/blog/2022/distill-example/ 2022-12-01T00:00:00+00:00 https://deep-learning-mit.github.io/staging/blog/2023/diffusion-is-all-you-need/ 2023-02-17T00:00:00+00:00 https://deep-learning-mit.github.io/staging/blog/2023/test/ 2023-02-17T00:00:00+00:00 https://deep-learning-mit.github.io/staging/_pages/dropdown/ https://deep-learning-mit.github.io/staging/home/ https://deep-learning-mit.github.io/staging/ https://deep-learning-mit.github.io/staging/ https://deep-learning-mit.github.io/staging/tags/ https://deep-learning-mit.github.io/staging/blog/2022/ https://deep-learning-mit.github.io/staging/blog/2023/ https://deep-learning-mit.github.io/staging/blog/ https://deep-learning-mit.github.io/staging/news/announcement_1/ 2023-10-19T16:53:13+00:00 https://deep-learning-mit.github.io/staging/news/announcement_2/ 2023-10-19T16:53:13+00:00 https://deep-learning-mit.github.io/staging/news/announcement_3/ 2023-10-19T16:53:13+00:00 https://deep-learning-mit.github.io/staging/publications/ 2023-10-19T16:53:14+00:00 https://deep-learning-mit.github.io/staging/source.html 2023-10-19T16:53:14+00:00 \ No newline at end of file diff --git a/tags.md b/tags.md deleted file mode 100644 index 5d4a958f..00000000 --- a/tags.md +++ /dev/null @@ -1,60 +0,0 @@ ---- -layout: page -title: Tags ---- - -{% comment %} -======================= -The following part extracts all the tags from your posts and sort tags, so that you do not need to manually collect your tags to a place. -======================= -{% endcomment %} -{% assign rawtags = "" %} -{% for post in site.posts %} - {% assign ttags = post.tags | join:'|' | append:'|' %} - {% assign rawtags = rawtags | append:ttags %} -{% endfor %} -{% assign rawtags = rawtags | split:'|' | sort %} - -{% comment %} -======================= -The following part removes dulpicated tags and invalid tags like blank tag. -======================= -{% endcomment %} -{% assign tags = "" %} -{% for tag in rawtags %} - {% if tag != "" %} - {% if tags == "" %} - {% assign tags = tag | split:'|' %} - {% endif %} - {% unless tags contains tag %} - {% assign tags = tags | join:'|' | append:'|' | append:tag | split:'|' %} - {% endunless %} - {% endif %} -{% endfor %} - -

      -{% comment %} -======================= -The purpose of this snippet is to list all your posts posted with a certain tag. -======================= -{% endcomment %} -{% for tag in tags %} -

      {{ tag }}

      - -{% endfor %} -
      diff --git a/tags/index.html b/tags/index.html new file mode 100644 index 00000000..4409bf18 --- /dev/null +++ b/tags/index.html @@ -0,0 +1 @@ + Tags | 6.S898 Deep Learning Blogs 2023
      \ No newline at end of file