Merge pull request #2 from SuLab/main

Fork Sync

.github/workflows/update_website.yml

@@ -0,0 +1,34 @@
+name: Update Website
+
+on:
+  push
+
+jobs:
+  generate_pages:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+
+      - name: Set up Python enviornment
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.8
+
+      - name: Set up build enviornment
+        run: |
+          pip install matplotlib
+          pip install networkx
+          pip install numpy
+          pip install pandas
+          pip install git+https://github.com/mmayers12/path_plots
+          pip install -U PyYAML
+
+      - name: Generate new documentation
+        run: python3 parse.py
+
+      - name: Commit changes
+        uses: EndBug/add-and-commit@v7
+        with:
+          add: 'pages/\*.md images/\*.png'

.gitignore

@@ -100,5 +100,12 @@ venv.bak/
 # mkdocs documentation
 /site
 
+# Mac
+.DS_Store
+
+# Jekyll
+Gemfile.lock
+_site
+
 # mypy
 .mypy_cache/

Gemfile

@@ -0,0 +1,7 @@
+source "https://rubygems.org"
+
+# to publish on github page
+gem 'github-pages', group: :jekyll_plugins
+
+# to publich without github page
+#gem "jekyll"

_config.yml

@@ -0,0 +1,72 @@
+repository: SuLab/DrugMechDB
+output: web
+topnav_title: DrugMechDB
+site_title: DrugMechDB
+company_name: Su Lab
+host: 127.0.0.1
+port: 4000
+exclude:
+  - .idea/
+  - .gitignore
+  - vendor
+feedback_subject_line: DrugMechDB
+feedback_email: [email protected]
+feedback_disable: true
+highlighter: rouge
+
+markdown: kramdown
+kramdown:
+ input: GFM
+ auto_ids: true
+ hard_wrap: false
+ syntax_highlighter: rouge
+
+collections:
+  tooltips:
+    output: false
+
+defaults:
+  -
+    scope:
+      path: ""
+      type: "pages"
+    values:
+      layout: "page"
+      comments: false
+      search: true
+      sidebar: home_sidebar
+      topnav: topnav
+  -
+    scope:
+      path: ""
+      type: "tooltips"
+    values:
+      layout: "page"
+      search: true
+      tooltip: true
+
+  -
+    scope:
+      path: ""
+      type: "posts"
+    values:
+      layout: "post"
+      comments: false
+      search: true
+      sidebar: home_sidebar
+      topnav: topnav
+
+sidebars:
+- home_sidebar
+- mydoc_sidebar
+- product1_sidebar
+- product2_sidebar
+- other
+
+description: "A database of paths that represent the mechanism of action from a drug to a disease in an indication."
+
+# url: http://idratherbewriting.com
+# baseurl: /documentation-theme-jekyll
+
+
+github: [metadata]

_data/alerts.yml

@@ -0,0 +1,15 @@
+tip: '<div class="alert alert-success" role="alert"><i class="fa fa-check-square-o"></i> <b>Tip: </b>'
+note: '<div class="alert alert-info" role="alert"><i class="fa fa-info-circle"></i> <b>Note: </b>'
+important: '<div class="alert alert-warning" role="alert"><i class="fa fa-warning"></i> <b>Important: </b>'
+warning: '<div class="alert alert-danger" role="alert"><i class="fa fa-exclamation-circle"></i> <b>Warning: </b>'
+end: '</div>'
+
+callout_danger: '<div class="bs-callout bs-callout-danger">'
+callout_default: '<div class="bs-callout bs-callout-default">'
+callout_primary: '<div class="bs-callout bs-callout-primary">'
+callout_success: '<div class="bs-callout bs-callout-success">'
+callout_info: '<div class="bs-callout bs-callout-info">'
+callout_warning: '<div class="bs-callout bs-callout-warning">'
+
+hr_faded: '<hr class="faded"/>'
+hr_shaded: '<hr class="shaded"/>'

_data/definitions.yml

@@ -0,0 +1,9 @@
+elephant: "This is a sample definition."
+
+baseball: "Baseball is considered America's pasttime sport, though that may be more of a historical term than a current one. There's a lot more excitement about football than baseball. A baseball game is somewhat of a snooze to watch, for the most part."
+
+basketball: "Basketball is a sport involving two teams of five players each competing to put a ball through a small circular rim 10 feet above the ground. Basketball requires players to be in top physical condition, since they spend most of the game running back and forth along a 94-foot-long floor."
+
+football: "No doubt the most fun sport to watch, football also manages to accrue the most injuries with the players. From concussions to blown knees, football players have short sport lives."
+
+soccer: "If there's one sport that dominates the world landscape, it's soccer. However, US soccer fans are few and far between. Apart from the popularity of soccer during the World Cup, most people don't even know the name of the professional soccer organization in their area."

_data/glossary.yml

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+jekyll_platform: "Jekyll is a static site generator that builds sites using most modern web technologies."
+
+fractious: "Like a little mischevious child, full of annoying and constant trouble."
+
+gratuitous: "Something that is unwarranted and uncouth, like the social equivalent of a flagrant foul."
+
+haughty: "Proud and flaunting it. Holding your head high up like a snooty, too-good-for-everything rich person."
+
+impertinent: "Someone acting rude and insensitive to others."
+
+intrepid: "Brave and courageous especially in a difficult, dangerous situation."

_data/samplelist.yml

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+entries:
+- title: Sidebar
+  folders:
+  - title: Food
+
+    folderitems:
+    - title: Bananas
+      url: bananas.html
+
+      subfolders:
+      - title: Apples
+
+        subfolderitems:
+        - title:  Fuji apples
+          url: fuji_apples.html
+
+
+        - title: Gala apples
+          url: gala_apples.html
+
+name:
+  husband: Tom
+  wife: Shannon
+
+bikes:
+  - title: mountain bikes
+  - title: road bikes
+  - title: hybrid bikes
+
+
+salesteams:
+  - title: Regions
+    subfolderitems:
+      - location: US
+      - location: Spain
+      - location: France
+
+toc:
+  - title: Group 1
+    subfolderitems:
+      - page: Thing 1
+      - page: Thing 2
+      - page: Thing 3
+  - title: Group 2
+    subfolderitems:
+      - page: Piece 1
+      - page: Piece 2
+      - page: Piece 3
+  - title: Group 3
+    subfolderitems:
+      - page: Widget 1
+      - page: Widget 2
+      - page: Widget 3
+
+something: &hello Greetings earthling!
+myref: *hello
+
+about:
+ - zero
+ - one
+ - two
+ - three
+
+numbercolors:
+ - zero:
+   properties: red
+ - one:
+   properties: yellow
+ - two:
+   properties: green
+ - three:
+   properties: blue
+
+mypages:
+- section1: Section 1
+  audience: developers
+  product: acme
+  url: facebook.com
+- section2: Section 2
+  audience: writers
+  product: acme
+  url: google.com
+- section3: Section 3
+  audience: developers
+  product: acme
+  url: amazon.com
+- section4: Section 4
+  audience: writers
+  product: gizmo
+  url: apple.com
+- section5: Section 5
+  audience: writers
+  product: acme
+  url: microsoft.com
+
+feedback: >
+  This is my feedback to you.
+  Even if I include linebreaks here,
+  all of the linebreaks will be removed when the value is inserted.
+
+block: |
+    This pipe does something a little different.
+    It preserves the breaks.
+    This is really helpful for code samples,
+    since you can format the code samples with
+       the appropriate
+       white spacing.