Merge branch 'galaxyproject:main' into PaulineSGN-patch-1

.github/workflows/ci-main.yml

@@ -15,6 +15,11 @@ on:
       - 'learning-pathways/*'
       - 'faqs/**'
       - 'news/**'
+      - 'events/**'
+      - CONTRIBUTORS.yaml
+      - FUNDERS.yaml
+      - ORGANISATIONS.yaml
+
 
 jobs:
   lint:

.github/workflows/ci.yml

@@ -66,7 +66,7 @@ jobs:
         run: |
           bundle exec htmlproofer \
             --ignore-urls "/.*localhost.*/","/.*vimeo\.com.*/","/.*gitter\.im.*/","/.*drmaa\.org.*/","/.*slides.html#.*/,/#embedded_jbrowse/","/.*videos.*.mp4.png/","/krona_(all|multisample).html/" \
-            --ignore-files "/.*krona.*\.html/","/.*\/files\/.*/","/.*\/node_modules\/.*/","/\/tutorials\/.*\/docker\//","/.*content.html/" \
+            --ignore-files "/.*krona.*\.html/","/.*\/files\/.*/","/.*\/node_modules\/.*/","/\/tutorials\/.*\/docker\//","/.*content.html/","/.*recentrifuge.*\.html/" \
             --swap-urls "github.com/galaxyproject/training-material/tree/main:github.com/${GITHUB_REPOSITORY}/tree/${GITHUB_HEAD_REF}" \
             --disable-external=true \
             --enforce-https=false \
@@ -76,7 +76,11 @@ jobs:
         run: |
           ! fgrep -R 'lt;blockquote' _site
 
-      - name: Ensure no unexpected jekyll in output
+      - name: Ensure no poorly indented code blocks
+        run: |
+          bundle exec ruby bin/check-indent.rb
+
+      - name: Ensure no unexpected jekyll in output. If this fails, generally it means you should add a page.description to the front matter.
         run: |
           ! fgrep -R 'site.pages' _site
 
@@ -101,3 +105,7 @@ jobs:
       - name: Validate notebooks (If this fails, ask @hexylena to look at your notebook)
         run: |
           find _site | grep ipynb | xargs bundle exec ruby bin/check-valid-notebook.rb
+
+      - name: Check URL persistence
+        run: |
+          bash bin/check-url-persistence.sh

.github/workflows/cron-commit-cache.yml

@@ -0,0 +1,64 @@
+name: "[Cron] Update Commit Cache"
+on:
+  workflow_dispatch:
+  schedule:
+    - cron: '45 0 * * 1'
+jobs:
+  runner-job:
+    runs-on: ubuntu-latest
+    # Only run on main repo on and PRs that match the main repo.
+    if: |
+      github.repository == 'galaxyproject/training-material' &&
+      (github.event_name != 'pull_request' ||
+       github.event.pull_request.head.repo.full_name == github.repository)
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          fetch-depth: 1000
+
+      # BEGIN Dependencies
+      - uses: ruby/setup-ruby@v1
+        with:
+          ruby-version: "3.0"
+      - uses: actions/cache@v2
+        with:
+          path: |
+            vendor/bundle
+          key: ${{ runner.os }}-gems-${{ hashFiles('**/Gemfile.lock') }}
+          restore-keys: |
+            ${{ runner.os }}-gems-
+      - name: Install dependencies
+        run: |
+          gem install bundler
+          bundle config path vendor/bundle
+          bundle install --jobs 4 --retry 3
+          bundle pristine ffi
+      # END Dependencies
+
+      - name: Update commit cache
+        id: generate
+        run: |
+          # Check if the oldest commit of the commit cache is known in this history
+          last_cached_commit=$(ls metadata/git-mod-*.txt | cut -d- -f 3 | cut -d. -f 1)
+          git show $last_cached_commit
+          ec=$?
+          if (( ec != 0 )); then
+            # Worst case, we need to fetch more. just fetch everything to be safe.
+            git fetch --unshallow
+          fi
+
+          bundle exec ruby bin/commit-cache-update.rb
+
+      - name: Update geocoding of events
+        id: generate
+        run: |
+          bundle exec ruby bin/geocode.rb
+
+      - name: Create Pull Request
+        # If it's not a Pull Request then commit any changes as a new PR.
+        uses: peter-evans/create-pull-request@v3
+        with:
+          title: Update Cached Commit Data
+          branch-suffix: timestamp
+          commit-message: Update Cached Commit Data
+          add-paths: metadata/,events/

.github/workflows/deploy.yml

@@ -16,7 +16,14 @@ jobs:
     steps:
       - uses: actions/checkout@v2
         with:
-          fetch-depth: 0
+          # Avg commits between successive monday:
+          #  Min.   :  2.0
+          #  1st Qu.: 25.0
+          #  Median : 54.5
+          #  Mean   : 65.2
+          #  3rd Qu.: 94.0
+          #  Max.   :282.0
+          fetch-depth: 400
 
       # BEGIN Dependencies
       - uses: actions/setup-python@v2
@@ -48,7 +55,7 @@ jobs:
           bundle pristine ffi
       # END Dependencies
 
-      - name: Build Site
+      - name: Prepare Site Metadata
         run: |
           gem install bundler
           python -m pip install --upgrade pip
@@ -62,8 +69,12 @@ jobs:
           curl --retry 5 https://gallantries.github.io/video-library/api/videos.json > metadata/video-library.json
           curl --retry 5 https://gallantries.github.io/video-library/api/sessions.json > metadata/session-library.json
           rdoc bin _plugins/ --output gtn_rdoc
+
+      - name: Build Site
+        run: |
           JEKYLL_ENV=production bundle exec jekyll build --strict_front_matter -d _site/training-material
           cp metadata/feedback.csv _site/training-material/api/feedback.csv
+          cp metadata/feedback2.yaml _site/training-material/api/feedback2.yaml
         env:
           GTN_FORK: ${{ github.repository_owner }}
 

.github/workflows/google-form.rb → .github/workflows/google-form.yml

@@ -35,10 +35,10 @@
           bundle pristine ffi
       # END Dependencies
 
-      - name: Update Shortlinks
+      - name: Update google news
         id: generate
         run: |
-          ruby bin/google-form-news.rb >> $GITHUB_OUTPUT
+          bundle exec ruby bin/google-form-news.rb
 
       - name: Create Pull Request
         # If it's not a Pull Request then commit any changes as a new PR.

.github/workflows/matrix.yml

@@ -15,7 +15,7 @@ jobs:
     steps:
       - uses: actions/checkout@v2
         with:
-          fetch-depth: 0
+          fetch-depth: 200
 
       # BEGIN Dependencies
       - uses: ruby/setup-ruby@v1

.github/workflows/monthly-release.yml

@@ -32,7 +32,8 @@ jobs:
 
       - uses: actions/checkout@v2
         with:
-          fetch-depth: 0
+          # Based on logic in deploy.yml
+          fetch-depth: 1200
 
       # BEGIN Dependencies
       - uses: actions/setup-python@v2
@@ -66,13 +67,6 @@ jobs:
           bundle pristine ffi
       # END Dependencies
 
-      - name: Configure AWS credentials from GTN account
-        uses: aws-actions/configure-aws-credentials@v1
-        with:
-          aws-access-key-id: ${{ secrets.AWS_ACCESS_KEY_ID }}
-          aws-secret-access-key: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
-          aws-region: us-east-1
-
       - name: Build Site
         run: |
           git tag -l
@@ -92,6 +86,13 @@ jobs:
           SOURCE_TAG: ${{ env.release_tag }}
           GTN_FORK: ${{ github.repository_owner }}
 
+      - name: Configure AWS credentials from GTN account
+        uses: aws-actions/configure-aws-credentials@v4
+        with:
+          aws-access-key-id: ${{ secrets.AWS_ACCESS_KEY_ID }}
+          aws-secret-access-key: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+          aws-region: us-east-1
+
       - name: Deploy 🚀
         run: |
           pip install awscli

.github/workflows/update-libraries.yaml

@@ -35,10 +35,10 @@ jobs:
           bundle pristine ffi
       # END Dependencies
 
-      - name: Update Shortlinks
+      - name: Update data libraries
         id: generate
         run: |
-          grep zenodo_link: -R topics -l | grep '.md$' | xargs -r -n 1 ruby bin/update-data-library update --fragile
+          grep zenodo_link: -R topics -l | grep '.md$' | xargs -r -n 1 bundle exec ruby bin/update-data-library update --fragile
 
       - name: Create Pull Request
         # If it's not a Pull Request then commit any changes as a new PR.
@@ -49,4 +49,4 @@ jobs:
           title: Add missing data-library.yaml files
           branch-suffix: timestamp
           commit-message: Adds data-library.yaml for tutorials
-
+          add-paths: **/data-library.yaml

.github/workflows/video-dry.yml

@@ -12,15 +12,15 @@ jobs:
     runs-on: ubuntu-latest
     services:
       # Label used to access the service container
-      mozillatts:
-        image: synesthesiam/mozillatts
-        ports:
-          - 5002:5002
+      # mozillatts:
+      #   image: synesthesiam/mozillatts
+      #   ports:
+      #     - 5002:5002
     steps:
       # Shallow should be fine for video
       - uses: actions/checkout@v2
         with:
-          fetch-depth: 0
+          fetch-depth: 1
 
       # BEGIN Dependencies
       - uses: actions/setup-python@v2

.rubocop.yml

@@ -64,3 +64,7 @@ Lint/DuplicateBranch:
 # We keep having bugs, so, disable this for now.
 Style/FrozenStringLiteralComment:
   Enabled: false
+
+# Unnecessary
+Style/IfUnlessModifier:
+  Enabled: false

404.md

@@ -9,3 +9,5 @@ title: "404 Page Not Found"
 Perhaps you are here due to a mis-typed URL
 
 [Return to the homepage]({{ site.baseurl }}){:.btn.btn-primary}, or [Search]({% link search.md %}){:.btn.btn-secondary} for your page.
+
+<script>document.addEventListener('DOMContentLoaded', function () { plausible('404', { props: { path: document.location.pathname } }); });</script>