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mkdocs.yml
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mkdocs.yml
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site_name: OpenScPCA Documentation
exclude_docs: | # syntax: https://www.mkdocs.org/user-guide/configuration/#exclude_docs
/contributing.md # docs contribution guidelines
/requirements.txt # docs requirements file
/general-style-guide.md # docs style guide
/style-guide-images # images used in the style guide
theme:
name: material
favicon: img/favicon.svg
logo: img/ccdlxalsf.svg
features:
- content.code.copy # code copy button in code blocks
- search.suggest # displays in light gray how you might complete the word
- navigation.tabs # persistent navbar on the top
- navigation.tabs.sticky # sticky navbar
- navigation.indexes # allow index pages to serve as overview pages for sections
- navigation.sections # bold headers for directories
- navigation.footer # allow users to jump to previous and next doc at the bottom of the page
plugins:
- search # search bar
markdown_extensions:
- admonition # https://squidfunk.github.io/mkdocs-material/setup/extensions/python-markdown/#admonition
- attr_list # https://github.com/squidfunk/mkdocs-material/blob/master/docs/setup/extensions/python-markdown.md#attribute-lists
- md_in_html # https://squidfunk.github.io/mkdocs-material/setup/extensions/python-markdown/#markdown-in-html
- pymdownx.highlight: # https://squidfunk.github.io/mkdocs-material/reference/code-blocks/#configuration
anchor_linenums: true
line_spans: __span
pygments_lang_class: true
- pymdownx.inlinehilite
- pymdownx.snippets
- pymdownx.superfences
- pymdownx.details # https://squidfunk.github.io/mkdocs-material/setup/extensions/python-markdown-extensions/#details
- pymdownx.emoji: # https://squidfunk.github.io/mkdocs-material/reference/icons-emojis/
emoji_index: !!python/name:material.extensions.emoji.twemoji
emoji_generator: !!python/name:material.extensions.emoji.to_svg
extra_css:
- stylesheets/extra.css
extra:
social:
- icon: fontawesome/brands/github
link: https://github.com/AlexsLemonade/OpenScPCA-analysis
name: OpenScPCA on Github
- icon: fontawesome/brands/slack
link: https://ccdatalab.org/slack
name: Cancer Data Science Slack
- icon: fontawesome/brands/x-twitter
link: https://twitter.com/CancerDataLab
name: Follow us on X
- icon: fontawesome/brands/linkedin
link: https://www.linkedin.com/showcase/childhood-cancer-data-lab/
name: Follow us on LinkedIn
copyright: Copyright © 2024 OpenScPCA Project Maintainers & Contributors | CC-BY 4.0 License
# Here is the basic structure of our navigation setup.
#nav:
# - Navbar section: <!-- Contents for this navbar section are stored in the directory called `section-path` -->
# - section-path/index.md
# - section-path/markdown-1.md <!-- left sidebar will display H1 title from the markdown file itself -->
# - section-path/markdown-2.md
# - Subsection name: <!-- This title appears as bold item in left sidebar -->
# - section-path/subsection-path/index.md <!-- summary page for this subsection -->
# - section-path/subsection-path/markdown-3.md
# Currently, we have templated out the follow navbar items
# Note that the overall website landing page is in `docs/index.md`.
# When you locally serve, mkdocs will complain that it isn't in the nav below - this is expected. It should not be in the nav below.
nav:
- Getting started: # welcome, familiarizing yourself with the project
- getting-started/making-your-first-analysis-contribution.md
- getting-started/explore-analysis.md
- Getting access to resources:
- getting-started/accessing-resources/index.md
- getting-started/accessing-resources/getting-access-to-data.md
- getting-started/accessing-resources/getting-access-to-compute.md
- Project tools:
- getting-started/project-tools/index.md
- getting-started/project-tools/writing-in-markdown.md
- getting-started/project-tools/using-the-terminal.md
- Technical setup: # Fork/clone, local environment setup
- technical-setup/index.md
- technical-setup/install-wsl-2.md
- technical-setup/install-a-git-client.md
- technical-setup/fork-the-repo.md
- technical-setup/clone-the-repo.md
- Environment setup:
- technical-setup/environment-setup/setup-conda.md
- technical-setup/environment-setup/setup-precommit.md
- technical-setup/environment-setup/configure-aws-cli.md
- technical-setup/environment-setup/install-r-rstudio.md
- Tools for communication: # Slack, issues, discussions
- communications-tools/index.md
- GitHub issues:
- communications-tools/github-issues/index.md
- communications-tools/github-issues/writing-issues.md
- communications-tools/github-issues/what-makes-a-good-issue.md
- communications-tools/github-issues/issue-templates.md
- Contributing to analyses: # Setting up an analysis, all the git stuff
- contributing-to-analyses/index.md
- Analysis modules:
- contributing-to-analyses/analysis-modules/index.md
- contributing-to-analyses/analysis-modules/creating-a-module.md
- contributing-to-analyses/analysis-modules/module-dependencies.md
- contributing-to-analyses/analysis-modules/compute-requirements.md
- contributing-to-analyses/analysis-modules/running-a-module.md
- contributing-to-analyses/analysis-modules/documenting-analysis.md
- contributing-to-analyses/analysis-modules/modifying-a-module.md
- contributing-to-analyses/analysis-modules/notebook-structure.md
- contributing-to-analyses/analysis-modules/script-structure.md
- Working with Git: # Creating branches, adding commits, all git interactions
- contributing-to-analyses/working-with-git/index.md
- contributing-to-analyses/working-with-git/working-with-branches.md
- contributing-to-analyses/working-with-git/staying-in-sync-with-upstream.md
- contributing-to-analyses/working-with-git/making-commits.md
- contributing-to-analyses/working-with-git/troubleshooting-commits.md
- contributing-to-analyses/working-with-git/push-to-origin.md
- Creating pull requests:
- contributing-to-analyses/creating-pull-requests/index.md
- contributing-to-analyses/creating-pull-requests/scoping-pull-requests.md
- contributing-to-analyses/creating-pull-requests/pull-request-template.md
- contributing-to-analyses/creating-pull-requests/before-file-pr.md
- contributing-to-analyses/creating-pull-requests/resolve-merge-conflicts.md
- contributing-to-analyses/creating-pull-requests/file-pull-request.md
- Code review and merging your pull request:
- contributing-to-analyses/pr-review-and-merge/index.md
- contributing-to-analyses/pr-review-and-merge/respond-to-review.md
- Ensuring reproducibility:
- ensuring-repro/index.md
- Managing software environments:
- ensuring-repro/managing-software/index.md
- ensuring-repro/managing-software/using-renv.md
- ensuring-repro/managing-software/using-conda.md
- ensuring-repro/managing-software/reporting-dependencies.md
- Automated OpenScPCA workflows:
- ensuring-repro/workflows/index.md
- ensuring-repro/workflows/run-module-gha.md
- ensuring-repro/workflows/build-docker-gha.md
- Working with Docker:
- ensuring-repro/docker/index.md
- ensuring-repro/docker/docker-images.md
- ensuring-repro/docker/using-images.md
- ensuring-repro/docker/updating-images.md
- The OpenScPCA Nextflow workflow:
- ensuring-repro/openscpca-nf/index.md
- Cloud storage and compute: # AWS
- aws/index.md
- aws/joining-aws.md
- aws/working-with-s3-buckets.md
- Virtual compute with Lightsail for Research:
- aws/lsfr/creating-vcs.md
- aws/lsfr/accessing-vcs.md
- aws/lsfr/working-with-volumes.md
- aws/lsfr/starting-development-on-lsfr.md
- aws/lsfr/working-with-snapshots.md
- Getting Help: # troubleshooting and FAQ
- troubleshooting-faq/index.md
- troubleshooting-faq/faq.md
- Policies: # CoC, Authorship, other policies
- policies/index.md
- policies/terms-of-use.md
- policies/privacy-policy.md
- policies/code-of-conduct.md
- policies/authorship.md
- policies/SECURITY.md
- Grant Opportunities:
- grant-opportunities/index.md