Merge branch 'main' into nomadscientist-patch-1

.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

.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

.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

.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/s3-sync-action@v0.5.1
+        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/'

.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:

CONTRIBUTORS.yaml

@@ -705,7 +705,7 @@ angiolini:
     joined: 2024-05
     elixir_node: uk
     orcid: 0000-0002-0814-8830
-    
+
 emmaleith:
     name: Emma Leith
     email: leith023@umn.edu
@@ -840,7 +840,7 @@ GabrielaLopez:
     orcid: 0000-0002-0814-8830
     joined: 2023-01
     elixir_node: uk
-    
+
 gallardoalba:
     name: Cristóbal Gallardo
     joined: 2020-11
@@ -950,6 +950,13 @@ hexylena:
       lat: 51.91
       lon: 4.46
 
+hfraser:
+  name: Heather Fraser
+  joined: 2024-09
+  email: heather.fraser@open.ac.uk
+  elixir_node: uk
+  github: false
+
 hmenager:
     name: Hervé Ménager
     joined: 2017-09
@@ -998,7 +1005,7 @@ hujambo-dunia:
 igcbioinformatics:
     name: IGC Bioinformatics Unit
     joined: 2018-12
-    
+
 igormakunin:
     name: Igor Makunin
     joined: 2024-09
@@ -1361,7 +1368,7 @@ LonsBio:
 loraine-gueguen:
     name: Loraine Guéguen
     joined: 2017-09
-    
+
 lybCNU:
     name: Yongbin Li
     joined: 2024-08
@@ -1551,7 +1558,7 @@ Melkeb:
 melpetera:
     name: Mélanie Petera
     joined: 2019-06
-    
+
 meltemktn:
     name: Meltem Kutnu
     joined: 2024-09
@@ -1562,6 +1569,12 @@ mgramm1:
     orcid: 0000-0002-4217-5277
     joined: 2021-03
 
+mhintze:
+    name: Mark Hintze
+    email: mark.hintze@open.ac.uk
+    joined: 2024-09
+    github: false
+
 miaomiaozhou88:
     name: Miaomiao Zhou
     email: m.zhou1@avans.nl
@@ -1674,7 +1687,7 @@ nakucher:
     name: Natalie Kucher
     email: nkucher3@jhu.edu
     joined: 2023-06
-    
+
 natalie-wa:
     name: Natalie Whitaker-Allen
     email: nwhitak5@jh.edu
@@ -1884,7 +1897,7 @@ paulzierep:
 
 pavanvidem:
     name: Pavankumar Videm
-    orcid: 0000-0002-5192-126X  
+    orcid: 0000-0002-5192-126X
     joined: 2017-09
     affiliations:
       - uni-freiburg
@@ -2150,7 +2163,7 @@ shwdey:
     name: Shweta Pandey
     email: shwphd@gmail.com
     joined: 2024-06
-    
+
 simonbray:
     name: Simon Bray
     joined: 2019-05
@@ -2344,7 +2357,7 @@ timonschlegel:
     name: Timon Schlegel
     orcid: 0009-0001-3228-105X
     joined: 2024-05
-    
+
 timothygriffin:
     name: Timothy J. Griffin
     email: tgriffin@umn.edu
@@ -2399,7 +2412,7 @@ tsenapathi:
 
 trungN:
     name: Nguyen Vo Minh Trung
-    joined: 2024-09    
+    joined: 2024-09
 
 TKlingstrom:
     name: Tomas Klingström

_layouts/base.html

@@ -46,7 +46,13 @@
         {%- elsif page.tags contains "gat" %}{% assign coverimage = "assets/images/gat.png" %}
         {%- else %}{% assign coverimage = "assets/images/GTNLogo1000.png" %}{% endif %}
         {% assign og_image = page.og_image | default: page['cover-image'] | default: topic.og_image | default: coverimage | default: "assets/images/GTNLogo1000.png" %}
+	{%- if page.layout == "tutorial_hands_on" or page.layout == "tutorial_slides" or page.layout == "event" or page.layout == "workflow" or page.layout == "faq" or page.layout == "introduction_slides" or page.layout == "learning-pathway"  -%}
+	<meta property="og:image" content="https://galaxy-training.s3.amazonaws.com/social{{ page.url | replace: ".html", ".png" }}">
+	{% elsif page.layout == "topic" or page.layout == "recordings" %}
+	<meta property="og:image" content="https://galaxy-training.s3.amazonaws.com/social{{ page.url }}index.png">
+	{%- else -%}
 	<meta property="og:image" content="{% if og_image contains 'https://' %}{{ og_image }}{% else %}{{ site.url }}{{ site.baseurl }}/{{ og_image }}{% endif %}">
+	{%- endif -%}
 
         {%- if page.layout == "tutorial_hands_on" -%}
         <script type="application/ld+json">

_layouts/base_slides.html

@@ -41,7 +41,11 @@
         {%- elsif page.tags contains "gat" %}{% assign coverimage = "/assets/images/gat.png" %}
         {%- else %}{% assign coverimage = "/assets/images/GTNLogo1000.png" %}{% endif %}
         {% assign og_image = page.og_image | default: page['cover-image'] | default: topic.og_image | default: coverimage | default: "assets/images/GTNLogo1000.png" %}
+	{%- if page.layout == "tutorial_slides" or page.layout == "introduction_slides" -%}
+	<meta property="og:image" content="https://galaxy-training.s3.amazonaws.com/social{{ page.url | replace: ".html", ".png" }}">
+	{%- else -%}
 	<meta property="og:image" content="{% if og_image contains 'https://' %}{{ og_image }}{% else %}{{ site.url }}{{ site.baseurl }}/{{ og_image }}{% endif %}">
+	{% endif %}
 
         <script type="application/ld+json">
             {% include _includes/material.jsonld material=page topic=topic site=site %}

_layouts/contributor_index.html

@@ -23,9 +23,9 @@
 					<h1>
 						{{ entity.name | default: page.contributor }}
 					</h1>
-				{% if entity.funder_name %}
-					<p>Funded by {{ entity.funder_name }}</p>
-				{% endif %}
+					{% if entity.funder%}
+					<p>The activities listed below were partially funded by this project.</p>
+					{% endif %}
 				</hgroup>
 
 				{% if entity.bio %}
@@ -34,9 +34,6 @@ <h1>
 				</p>
 				{% endif %}
 
-				{% if entity.funder %}
-				<div class="label label-default label-large" style="{{ 'GTN Funder' | colour_tag }}">GTN Funder</div>
-				{% endif %}
 				{% if entity.in_memoriam %}
 				<div class="alert alert-dark" role="alert">
 					<h2 class="alert-heading">In Memoriam</h2>

_layouts/event.html

@@ -38,9 +38,11 @@ <h1>{{ event.title }}</h1>
   <li class="nav-item" role="presentation">
     <button class="nav-link active" id="home-tab" data-toggle="tab" data-target="#overview" type="button" role="tab" aria-controls="overview" aria-selected="true">Course Overview</button>
   </li>
+  {% if event.program %}
   <li class="nav-item" role="presentation">
     <button class="nav-link" id="program-tab" data-toggle="tab" data-target="#program" type="button" role="tab" aria-controls="program" aria-selected="false">Program</button>
   </li>
+  {% endif %}
   {% if event.infrastructure %}
   <li class="nav-item" role="presentation">
      <button class="nav-link" id="setup-tab" data-toggle="tab" data-target="#setup" type="button" role="tab" aria-controls="setup" aria-selected="false" >Setup</button>
@@ -61,8 +63,10 @@ <h1>{{ event.title }}</h1>
     <p>{{ event.description | markdownify }}</p>
     <p>{{ content | markdownify }}</p>
 
+    {% if event.audience %}
     <h3>Who is this course for?</h3>
     {{ event.audience }}
+    {% endif %}
 
     {% if event.requirements %}
     <h3 id="requirements">Requirements</h3>
@@ -424,10 +428,12 @@ <h3>Promote the Event</h3>
           {% elsif event.registration.open == false %}
           <a href="#" class="btn btn-primary btn-lg btn-block">Registration opens soon!</a>
           {% else %}
-		  <a href="{{ event.registration.link }}" class="btn btn-primary btn-lg btn-block">Register Now!</a>
-            {% if event.registration.deadline %}
-            <p style="margin-top:1em"><b>Deadline:</b> {{event.registration.deadline | date: "%-d %B %Y" }}</p>
-            {% endif %}
+            {% if event.registration.link %}
+		    <a href="{{ event.registration.link }}" class="btn btn-primary btn-lg btn-block">Register Now!</a>
+              {% if event.registration.deadline %}
+              <p style="margin-top:1em"><b>Deadline:</b> {{event.registration.deadline | date: "%-d %B %Y" }}</p>
+              {% endif %}
+            {%endif %}
           {% endif %}
 		{% endif %}
         {% endunless %}
@@ -436,8 +442,10 @@ <h3>Promote the Event</h3>
 		<b> Event details </b>
 		<table>
 			<tr><td style="min-width: 2rem">{% icon event-date %}</td><td>{{ event | collapse_date_pretty }}</td></tr>
-			<tr><td>{% icon event-location %}</td><td>{% if event.location %}{{ event.location | format_location }}{% else %}Please set a location{% endif %}</td></tr>
+			<tr><td>{% icon event-location %}</td><td>{% if event.location %}{{ event.location | format_location }}{% elsif event.mode == "online" %}Online{% else %}Please set a location{% endif %}</td></tr>
+            {% if event.cost %}
 			<tr><td>{% icon event-cost %}</td><td>{{ event.cost }}</td></tr>
+            {% endif %}
 			{% if event.contact_email %}
 			<tr><td>{% icon email %}</td><td><a href="mailto:{{ event.contact_email }}?subject={{ event.title | uri_escape }}">{{event.contact_email}}</a></td></tr>
 			{% endif %}

_layouts/tutorial_hands_on.html

@@ -289,11 +289,14 @@ <h3>You've Finished the Tutorial</h3>
                         <p style="display: none" id="tutorial-finish-text">Please also consider filling out the <a href="#gtn-feedback">Feedback Form</a> as well!</p>
                         <script>
                         function tutorial_finish() {
-                          if(plausible !== undefined){
-                            plausible('TutorialComplete', {callback: tutorial_finish_finish, props: {path: document.location.pathname}})
-                          } else {
-                            tutorial_finish_finish();
+                          if(typeof plausible !== 'undefined'){
+                            // Plausible may be undefined (script blocked)
+                            // or it may be defined, but opted-out (select box/DNT), 
+                            // which means `plausible()` will work but not send data, *nor* execute the callback.
+                            plausible('TutorialComplete', {props: {path: document.location.pathname}})
                           }
+                          // since the callback is completely cosmetic, we'll just issue it optimistically.
+                          tutorial_finish_finish();
                         }
                         function tutorial_finish_finish() {
                           document.getElementById("tutorial-finish-button").innerText = 'Congrats! Thanks for letting us know! 🎉'

_plugins/generator-recordings.rb

@@ -28,6 +28,7 @@ def generate(site)
         page2.data['topic_name'] = material['topic_name']
         page2.data['tutorial_name'] = material['tutorial_name']
         page2.data['material'] = material
+        page2.data['title'] = 'Recordings for ' + material['title']
         site.pages << page2
       end
     end