Merge remote-tracking branch 'origin/elixir-toolkit-theme' into elixi…

…r-toolkit-theme

.github/workflows/jekyll.yml → .github/workflows/deploy_jekyll.yml

@@ -1,41 +1,45 @@
-name: Jekyll site CI
+name: Deploy Jekyll site to Pages
 
 on:
+  # Runs on pushes targeting the default branch
   push:
-    branches: [ main, master ]
-  pull_request:
-    branches: [ main, master ]
+    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:
-    runs-on: ubuntu-24.04
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        working-directory: docs
     steps:
       - name: Checkout
         uses: actions/checkout@v3
-        with:
-          ref: ${{ github.event.inputs.branch }}
-
       - name: Setup Ruby
         uses: ruby/[email protected]
         with:
           ruby-version: '3.3'
           bundler-cache: true
           cache-version: 0
-
       - name: Setup Pages
         id: pages
-        uses: actions/configure-pages@v2
-
+        uses: actions/configure-pages@v3
       - name: Install dependencies
         run: |
           bundle install
-
       - name: Build with Jekyll
         # Outputs to the './_site' directory by default
         run: |
@@ -46,26 +50,20 @@ jobs:
           JEKYLL_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           JEKYLL_BUILD_BRANCH: ${{ github.ref_name }}
           JEKYLL_BASE_PATH: ${{ steps.pages.outputs.base_path }}
-
       - name: Upload artifact
-        uses: actions/upload-pages-artifact@v1
+        # Automatically uploads an artifact from the './_site' directory by default
+        uses: actions/upload-pages-artifact@v2
 
   deploy:
-    runs-on: ubuntu-latest
-    needs: build
-
-    if: |
-      github.event_name == 'workflow_dispatch' ||
-      (github.event_name == 'push' && github.event.repository.default_branch == github.ref_name)
-    concurrency:
-      group: "pages"
-      cancel-in-progress: true
-
     environment:
       name: github-pages
       url: ${{ steps.deployment.outputs.page_url }}
-
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        working-directory: docs
+    needs: build
     steps:
       - name: Deploy to GitHub Pages
         id: deployment
-        uses: actions/deploy-pages@v1
+        uses: actions/deploy-pages@v2

.github/workflows/lint_jekyll.yaml

@@ -0,0 +1,44 @@
+name: Lint Jekyll site
+
+on: [push, pull_request]
+
+jobs:
+  check-internal-links:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        working-directory: docs
+    steps:
+      - uses: actions/checkout@v3
+      - uses: ruby/[email protected]
+        with:
+          ruby-version: '3.3'
+          bundler-cache: true
+          cache-version: 0
+      - name: Setup Pages
+        id: pages
+        uses: actions/configure-pages@v3
+      - name: Install dependencies
+        run: |
+          bundle install
+      - name: Build with Jekyll
+        # Outputs to the './_site' directory by default
+        run: |
+          bundle exec jekyll build --baseurl "${{ steps.pages.outputs.base_path }}" --strict_front_matter 
+        env:
+          PAGES_REPO_NWO: ${{ github.repository }}
+          JEKYLL_ENV: production
+          JEKYLL_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          JEKYLL_BUILD_BRANCH: ${{ github.ref_name }}
+          JEKYLL_BASE_PATH: ${{ steps.pages.outputs.base_path }}
+      #- name: Validate HTML and check links
+      #  run: |
+      #    bundle exec htmlproofer \
+      #      --allow_missing_href=true \
+      #      --ignore-urls "/.*localhost.*/","/.*gitter\.im.*/" \
+      #      --enforce-https=false  \
+      #      --disable-external=true \
+      #      --ignore_empty_alt=true \
+      #      --ignore_missing_alt=true \
+      #      --check-internal-hash=false \
+      #      ./_site

docs/Gemfile

@@ -4,4 +4,5 @@ source "https://rubygems.org"
 gem 'github-pages', group: :jekyll_plugins
 
 # Webrick needed for Ruby v3.0+ compatibility
-gem "webrick"
+gem "webrick"
+gem "html-proofer"

docs/_config.yml

@@ -7,7 +7,7 @@ topnav_title: CoDex
 description: "Galaxy Communities Dock (Galaxy Codex) is a catalog of Galaxy resources (i.e. tools, training, workflows) that can be filtered for any community."
 # Metadata description of the website
 
-remote_theme: ELIXIR-Belgium/elixir-toolkit-theme@datatable-query
+remote_theme: ELIXIR-Belgium/elixir-toolkit-theme
 
 theme_variables:
   # biocommons blue