Merge remote-tracking branch 'origin/main' into new_events

galaxyproject · Oct 15, 2024 · 311d362 · 311d362
2 parents 4cbcc6a + e4adb5a
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diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md
@@ -1,9 +1,13 @@
-!!! DELETE THIS BEFORE SUBMITTING!!! It's just a checklist to help you :)
+TODO: Describe your changes here..
 
-1. Give your pull request a **good title**
-    - e.g. "Fix typo in ansible-galaxy tutorial" or "Add new transcriptomics tutorial covering a new sequencing technology"
-2. Describe your changes in detail, list anything you still need some help with or things that are still TODO
-3. Check that your images are allowed to be re-hosted by the GTN!
-4. Not ready for review yet? Make it a **Draft** pull request
+<!-- Contributor Checklist
+
+1. Give your pull request a descriptive title
+2. Describe your changes in detail at the top of this text box
+3. List anything you still need some help with or things that are still TODO
+4. Check that your images are allowed to be re-hosted by the GTN!
+5. Not ready for review yet? Make it a **Draft** pull request
    - Once you are done making changes, choose **Ready for Review**
    - Then the automated tests will run and we will know to review and merge it
+
+-->
diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml
@@ -51,11 +51,12 @@ jobs:
             ${{ runner.os }}-gems-
       - name: Install dependencies
         run: |
-          sudo apt-get install -y build-essential libxi-dev libglu1-mesa-dev libglew-dev pkg-config # for node
+          sudo apt-get install -y build-essential libxi-dev libglu1-mesa-dev libglew-dev pkg-config graphviz # for node
           gem install bundler
           bundle config path vendor/bundle
           bundle install --jobs 4 --retry 3
-          npm install
+          rm -f package.json package-lock.json yarn.lock
+          npm install markdown-yaml-metadata-parser lunr
           bundle pristine ffi
       # END Dependencies
 
@@ -68,7 +69,6 @@ jobs:
           make annotate ACTIVATE_ENV=pwd
           curl -L https://docs.google.com/spreadsheets/d/1NfZhi5Jav7kl9zFCkeb7rIC2F8xW1isruv1TeO4WpNI/export\?format\=tsv | ruby bin/prepare_feedback.rb
           curl -L https://hexylena.github.io/toolshed-version-database/tool-meta.json > metadata/tool-meta.json
-          npm install
           make rebuild-search-index ACTIVATE_ENV=pwd
           cat metadata/swagger.yaml | python bin/yaml2json.py > api/swagger.json
           rdoc bin _plugins/ --output gtn_rdoc

diff --git a/.github/workflows/monthly-release-backfill.yml b/.github/workflows/monthly-release-backfill.yml
@@ -47,7 +47,8 @@ jobs:
           pip install pyyaml
           bundle config path vendor/bundle
           bundle install --jobs 4 --retry 3
-          npm install
+          rm -f package.json package-lock.json yarn.lock
+          npm install markdown-yaml-metadata-parser lunr
           bundle pristine ffi
       # END Dependencies
 
@@ -68,7 +69,6 @@ jobs:
           sed -i s"|^github_repository_branch: .*|github_repository_branch: '${SOURCE_TAG}'|g" _config.yml
           sed -i s"|^title: .*|title: 'GTN Archive ${SOURCE_TAG}'|g" _config.yml
           curl -L https://hexylena.github.io/toolshed-version-database/tool-meta.json > metadata/tool-meta.json
-          npm install
           make rebuild-search-index ACTIVATE_ENV=pwd
           cat metadata/swagger.yaml | python bin/yaml2json.py > api/swagger.json
           JEKYLL_ENV=production bundle exec jekyll build --strict_front_matter -d _site/training-material

diff --git a/.github/workflows/monthly-release.yml b/.github/workflows/monthly-release.yml
@@ -54,7 +54,8 @@ jobs:
           pip install pyyaml
           bundle config path vendor/bundle
           bundle install --jobs 4 --retry 3
-          npm install
+          rm -f package.json package-lock.json yarn.lock
+          npm install markdown-yaml-metadata-parser lunr
           bundle pristine ffi
       # END Dependencies
 
@@ -70,7 +71,6 @@ jobs:
           sed -i s"|^github_repository_branch: .*|github_repository_branch: '${SOURCE_TAG}'|g" _config.yml
           sed -i s"|^title: .*|title: 'GTN Archive ${SOURCE_TAG}'|g" _config.yml
           curl -L https://hexylena.github.io/toolshed-version-database/tool-meta.json > metadata/tool-meta.json
-          npm install
           make rebuild-search-index ACTIVATE_ENV=pwd
           cat metadata/swagger.yaml | ruby bin/yaml2json.rb > api/swagger.json
           JEKYLL_ENV=production bundle exec jekyll build --strict_front_matter -d _site/training-material

diff --git a/.github/workflows/social.yml b/.github/workflows/social.yml
@@ -0,0 +1,74 @@
+name: "[Social] Autogenerate missing social media cards"
+
+on:
+  schedule:
+    # * is a special character in YAML so you have to quote this string
+    # We'll run this daily at noon.
+    - cron:  '0 12 * * *'
+  workflow_dispatch:
+    inputs:
+      all_old:
+        type: string
+        description: If you want to re-generate ALL images set to a non-empty value
+
+jobs:
+  runner-job:
+    if: github.repository_owner == 'galaxyproject'
+    runs-on: ubuntu-latest
+    steps:
+      # Shallow should be fine for video
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 500
+
+      # BEGIN Dependencies
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+          architecture: 'x64'
+      - name: Install dependencies
+        run: |
+          sudo apt-get install -y imagemagick
+          mkdir -p ~/.fonts/
+          wget https://galaxy-training.s3.amazonaws.com/social/recursive.ttf -O ~/.fonts/recursive.ttf
+          fc-cache -rv
+      # END Dependencies
+
+
+      # We get the previous build ID to know how many videos were changed since
+      # then.
+      #
+      # We *could* fetch the diff in the past N days but if a build fails for
+      # any reason, we'd lose those changes permanently and things would never
+      # get built.
+      #
+      # So instead we just track the last successfully built timestamp
+      - name: Previous build ID
+        id: build_id
+        run: |
+          echo "timestamp=$(curl https://galaxy-training.s3.amazonaws.com/social/timestamp.txt -f 2>/dev/null || echo none)" >> $GITHUB_ENV
+
+          # Support regenerating all
+          if [[ "${{ github.event.inputs.selected_tag }}" != "" ]]; then
+            echo "timestamp=0" >> $GITHUB_ENV
+          fi
+
+      # The actual compilation process deposits everything in the ./social/ folder.
+      # And requires fetching metadata from the live website (api/social-meta.json)
+      - name: Build Social Media Cards
+        run: |
+          mkdir -p social/
+          python bin/social-cards.py $PREVIOUS_TIMESTAMP
+        env:
+          PREVIOUS_TIMESTAMP: ${{ env.timestamp }}
+
+      # Deploy step, scary.
+      - uses: jakejarvis/[email protected]
+        with:
+          args: --acl public-read --follow-symlinks
+        env:
+          AWS_S3_BUCKET: galaxy-training
+          AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
+          AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+          SOURCE_DIR: './social/'
+          DEST_DIR: 'social/'
diff --git a/.github/workflows/video.yml b/.github/workflows/video.yml
@@ -10,7 +10,7 @@ on:
 jobs:
   runner-job:
     if: github.repository_owner == 'galaxyproject'
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     services:
       # Label used to access the service container
       mozillatts:

diff --git a/CONTRIBUTORS.yaml b/CONTRIBUTORS.yaml
@@ -709,7 +709,7 @@ angiolini:
     joined: 2024-05
     elixir_node: uk
     orcid: 0000-0002-0814-8830
-    
+
 emmaleith:
     name: Emma Leith
     email: [email protected]
@@ -844,7 +844,7 @@ GabrielaLopez:
     orcid: 0000-0002-0814-8830
     joined: 2023-01
     elixir_node: uk
-    
+
 gallardoalba:
     name: Cristóbal Gallardo
     joined: 2020-11
@@ -914,6 +914,7 @@ hechth:
   joined: 2020-01
   email: [email protected]
   orcid: 0000-0001-6744-996X
+  elixir_node: cz
 
 heylf:
     name: Florian Heyl
@@ -953,6 +954,13 @@ hexylena:
       lat: 51.91
       lon: 4.46
 
+hfraser:
+  name: Heather Fraser
+  joined: 2024-09
+  email: [email protected]
+  elixir_node: uk
+  github: false
+
 hmenager:
     name: Hervé Ménager
     joined: 2017-09
@@ -1001,7 +1009,7 @@ hujambo-dunia:
 igcbioinformatics:
     name: IGC Bioinformatics Unit
     joined: 2018-12
-    
+
 igormakunin:
     name: Igor Makunin
     joined: 2024-09
@@ -1364,7 +1372,7 @@ LonsBio:
 loraine-gueguen:
     name: Loraine Guéguen
     joined: 2017-09
-    
+
 lybCNU:
     name: Yongbin Li
     joined: 2024-08
@@ -1554,7 +1562,7 @@ Melkeb:
 melpetera:
     name: Mélanie Petera
     joined: 2019-06
-    
+
 meltemktn:
     name: Meltem Kutnu
     joined: 2024-09
@@ -1565,6 +1573,12 @@ mgramm1:
     orcid: 0000-0002-4217-5277
     joined: 2021-03
 
+mhintze:
+    name: Mark Hintze
+    email: [email protected]
+    joined: 2024-09
+    github: false
+
 miaomiaozhou88:
     name: Miaomiao Zhou
     email: [email protected]
@@ -1677,7 +1691,7 @@ nakucher:
     name: Natalie Kucher
     email: [email protected]
     joined: 2023-06
-    
+
 natalie-wa:
     name: Natalie Whitaker-Allen
     email: [email protected]
@@ -1830,6 +1844,19 @@ RareSeas:
     name: Adelaide Rhodes
     joined: 2021-05
 
+paige-kulzer:
+  name: Paige Kulzer
+  joined: 2024-10
+  email: [email protected]
+  linkedin: paige-kulzer-210b97274
+  contact_for_training: true
+  bio:
+    "My current role involves bioinformatics, data management, and training for a genome browser called the Integrated Genome Browser (IGB)."
+  location:
+    country: US
+    lat: 35.227
+    lon: -80.843
+
 PatCapon39:
     name: Patrick Capon
     joined: 2024-02
@@ -1874,7 +1901,7 @@ paulzierep:
 
 pavanvidem:
     name: Pavankumar Videm
-    orcid: 0000-0002-5192-126X  
+    orcid: 0000-0002-5192-126X
     joined: 2017-09
     affiliations:
       - uni-freiburg
@@ -2140,7 +2167,7 @@ shwdey:
     name: Shweta Pandey
     email: [email protected]
     joined: 2024-06
-    
+
 simonbray:
     name: Simon Bray
     joined: 2019-05
@@ -2183,6 +2210,11 @@ slugger70:
 
         "Have I told you about my watch?"
 
+SNG888:
+    name: Sandra Ng
+    email: [email protected]
+    joined: 2023-07
+
 Sofokli5:
     name: Sofoklis Keisaris
     email: [email protected]
@@ -2263,6 +2295,12 @@ tb143:
     name: Tim Beck
     joined: 2023-09
 
+tbrown91:
+    name: Tom Brown
+    email: [email protected]
+    orcid: 0000-0001-8293-4816
+    joined: 2024-08
+
 tcollins2011:
     name: Tyler Collins
     joined: 2024-09
@@ -2293,6 +2331,16 @@ themudo:
     name: Gonçalo Themudo
     joined: 2021-10
 
+ThibaudGlinez:
+    name: Glinez Thibaud
+    email: [email protected]
+    orcid: 0009-0006-8655-7505
+    joined: 2024-02
+    elixir_node: fr
+    affiliations:
+      - pndb
+      - elixir-europe
+
 thobalose:
     name: Thoba Lose
     joined: 2019-11
@@ -2313,7 +2361,7 @@ timonschlegel:
     name: Timon Schlegel
     orcid: 0009-0001-3228-105X
     joined: 2024-05
-    
+
 timothygriffin:
     name: Timothy J. Griffin
     email: [email protected]
@@ -2368,7 +2416,7 @@ tsenapathi:
 
 trungN:
     name: Nguyen Vo Minh Trung
-    joined: 2024-09    
+    joined: 2024-09
 
 TKlingstrom:
     name: Tomas Klingström
@@ -2423,6 +2471,8 @@ wee-snufkin:
     name: Julia Jakiela
     email: [email protected]
     joined: 2022-06
+    elixir_node: uk
+    orcid: 0009-0001-2017-8805
 
 willdurand:
     name: William Durand
@@ -2452,6 +2502,12 @@ wm75:
       - uni-freiburg
       - elixir-europe
 
+wverastegui:
+    name: Wudmir Rojas
+    email: [email protected]
+    joined: 2024-10
+    elixir_node: cz
+
 xiliu:
     name: Xi Liu
     github: false
@@ -2505,6 +2561,11 @@ yvesvdb:
     affiliations:
       - ifb
 
+zargham-ahmad:
+    name: Zargham Ahmad
+    email: [email protected]
+    joined: 2024-10
+    elixir_node: cz
 
 SNG888:
     name: Sandra Ng

diff --git a/_includes/tutorial_list.html b/_includes/tutorial_list.html
@@ -44,7 +44,12 @@
           {% endif %}
 
           {% if material.layout == 'custom' %} <!-- e.g. for events -->
-            <td> {{material.title | markdownify }} </td>
+            <td>
+              {{material.title | markdownify }} 
+              <div class="duplicate" style="display: none;">
+                {{material.description | markdownify }}
+              </div>
+            </td>
             <td colspan="3"> {{material.description | markdownify }}</td>
           {% else %}
           <td class="tutorial_title">