Merge branch 'main' into archive_akhistories

.github/workflows/ci.yml

@@ -48,8 +48,8 @@ jobs:
       - name: Validate all links, enforce alt text
         run: |
           bundle exec htmlproofer \
-            --ignore-urls "/.*localhost.*/","/.*vimeo\.com.*/","/.*gitter\.im.*/","/.*drmaa\.org.*/","/.*slides.html#.*/,/#embedded_jbrowse/","/.*videos.*.mp4.png/","/krona_(all|multisample).html/","/workflows\/trs_import/" \
-            --ignore-files "/.*krona.*\.html/","/.*\/files\/.*/","/.*\/node_modules\/.*/","/\/tutorials\/.*\/docker\//","/.*content.html/","/.*recentrifuge.*\.html/" \
+            --ignore-urls "/.*localhost.*/","/.*vimeo\.com.*/","/.*gitter\.im.*/","/.*drmaa\.org.*/","/.*slides.html#.*/,/#embedded_jbrowse/","/.*videos.*.mp4.png/","/krona_(all|multisample).html/","/workflows\/trs_import/","/api/","/by-tool/" \
+            --ignore-files "/.*krona.*\.html/","/.*\/files\/.*/","/.*\/node_modules\/.*/","/\/tutorials\/.*\/docker\//","/.*content.html/","/.*recentrifuge.*\.html/","/short/" \
             --swap-urls "github.com/galaxyproject/training-material/tree/main:github.com/${GITHUB_REPOSITORY}/tree/${GITHUB_HEAD_REF}" \
             --disable-external=true \
             --enforce-https=false \

.github/workflows/deploy.yml

@@ -70,15 +70,13 @@ 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
+          curl -L https://edamontology.org/EDAM.csv > metadata/EDAM.csv
           make rebuild-search-index ACTIVATE_ENV=pwd
-          cat metadata/swagger.yaml | python bin/yaml2json.py > api/swagger.json
-          rdoc bin _plugins/ --output gtn_rdoc
+          bundle exec rdoc bin _plugins/ --output gtn_rdoc --template rorvswild
 
       - 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 }}
 
@@ -96,6 +94,10 @@ jobs:
           jupyter lite build --contents /tmp/notebook
           mv _output _site/training-material/jupyter/
 
+      - name: Mandatory pre-deploy checks
+        run: |
+          bundle exec ruby bin/lint-deploy.rb
+
       - name: Deploy 🚀
         uses: peaceiris/actions-gh-pages@v3
         with:

.github/workflows/monthly-release-backfill.yml

@@ -71,7 +71,6 @@ jobs:
           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
           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
         env:
           SOURCE_TAG: ${{ github.event.inputs.selected_tag }}

.github/workflows/monthly-release.yml

@@ -76,7 +76,6 @@ jobs:
           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
           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
         env:
           SOURCE_TAG: ${{ env.release_tag }}

CONTRIBUTORS.yaml

@@ -707,6 +707,12 @@ dyusuf:
     affiliations:
       - uni-freiburg
 
+dometto:
+    name: Dawa Ometto
+    joined: 2024-12
+    affiliations:
+      - surf
+
 eancelet:
     name: Estelle Ancelet
     email: [email protected]
@@ -1694,6 +1700,12 @@ miRlyKayleigh:
     email: [email protected]
     joined: 2022-12
 
+mirelaminkova:
+    name: Mirela Minkova
+    joined: 2024-12
+    affiliations:
+      - surf
+
 moffmade:
     name: Cory Maughmer
     joined: 2018-06
@@ -1765,6 +1777,11 @@ nagoue:
     email: [email protected]
     orcid: 0000-0003-2750-1473
     joined: 2019-07
+
+Najatamk:
+    name: Najat Amoukou
+    email: [email protected]
+    joined: 2024-07
 
 nakucher:
     name: Natalie Kucher
@@ -2691,6 +2708,10 @@ yvesvdb:
     affiliations:
       - ifb
 
+yuliiaorlova:
+    name: Yuliia Orlova
+    joined: 2024-12
+
 zargham-ahmad:
     name: Zargham Ahmad
     email: [email protected]

GRANTS.yaml

@@ -204,6 +204,27 @@ h2020-defend:
       This work has received funding from the DEFEND project (www.defend2020.eu) with funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No 773701.
     url: https://www.defend2020.eu
 
+nfdi4bioimage:
+    name:  NFDI4Bioimage
+    short_name: "NFDI4Bioimage"
+    github: false
+    joined: 2024-12
+    funding_id: "501864659"
+    funding_database: dfg
+    funder_name: DFG
+    url: https://nfdi4bioimage.de
+    avatar: "/training-material/shared/images/nfdi4bioimage.jpeg"
+
+nfdi4plants:
+    short_name: DataPLANT
+    name: DataPLANT (NFDI4Plants)
+    joined: 2024-07
+    funding_id: "442077441"
+    funding_database: dfg
+    funder_name: DFG
+    url:  https://nfdi4plants.org
+    avatar: "/training-material/shared/images/logo-dataplant.svg"
+
 nhgri-anvil:
     name: National Human Genome Research Institute Genomic Data Science Analysis, Visualization, and Informatics Lab-Space
     short_name: "NHGRI ANVIL"
@@ -235,3 +256,6 @@ skills4eosc:
 
 
 
+
+
+

Gemfile

@@ -27,3 +27,7 @@ gem 'commander'
 
 # RO-Crates
 gem 'rubyzip', '~> 2.3.0'
+
+# Documentation
+gem 'rdoc', '~> 6.7'
+gem 'rorvswild_theme_rdoc'

Gemfile.lock

@@ -21,6 +21,7 @@ GEM
       rexml
     csl-styles (2.0.1)
       csl (~> 2.0)
+    date (3.4.1)
     em-websocket (0.5.3)
       eventmachine (>= 0.12.9)
       http_parser.rb (~> 0)
@@ -89,20 +90,27 @@ GEM
     pathutil (0.16.2)
       forwardable-extended (~> 2.6)
     pkg-config (1.5.5)
+    psych (5.2.1)
+      date
+      stringio
     public_suffix (5.0.3)
     racc (1.8.0)
     rainbow (3.1.1)
     rb-fsevent (0.11.2)
     rb-inotify (0.10.1)
       ffi (~> 1.0)
+    rdoc (6.9.1)
+      psych (>= 4.0.0)
     rexml (3.3.9)
+    rorvswild_theme_rdoc (0.2)
     rouge (4.1.3)
     rubyzip (2.3.2)
     safe_yaml (1.0.5)
     sass-embedded (1.69.5-x86_64-darwin)
       google-protobuf (~> 3.23)
     sass-embedded (1.69.5-x86_64-linux-gnu)
       google-protobuf (~> 3.23)
+    stringio (3.1.2)
     terminal-table (3.0.2)
       unicode-display_width (>= 1.1.1, < 3)
     typhoeus (1.4.0)
@@ -131,6 +139,8 @@ DEPENDENCIES
   kwalify
   nokogiri (>= 1.10.4)
   pkg-config
+  rdoc (~> 6.7)
+  rorvswild_theme_rdoc
   rubyzip (~> 2.3.0)
   webrick
 

Makefile

@@ -69,7 +69,7 @@ bundle-update: bundle-install  ## install gems if Ruby is already present (e.g.
 	bundle update
 .PHONE: bundle-update
 
-serve: api/swagger.json ## run a local server (You can specify PORT=, HOST=, and FLAGS= to set the port, host or to pass additional flags)
+serve: ## run a local server (You can specify PORT=, HOST=, and FLAGS= to set the port, host or to pass additional flags)
 	@echo "Tip: Want faster builds? Use 'serve-quick' in place of 'serve'."
 	@echo "Tip: to serve in incremental mode (faster rebuilds), use the command: make serve FLAGS=--incremental" && echo "" && \
 	$(ACTIVATE_ENV) && \
@@ -78,7 +78,7 @@ serve: api/swagger.json ## run a local server (You can specify PORT=, HOST=, and
 		${JEKYLL} serve --trace --strict_front_matter -d _site/training-material -P ${PORT} -H ${HOST} ${FLAGS}
 .PHONY: serve
 
-serve-quick: api/swagger.json ## run a local server (faster, some plugins disabled for speed)
+serve-quick: ## run a local server (faster, some plugins disabled for speed)
 	@echo "This will build the website with citations and other content disabled, and incremental on by default. To run the full preview (slower), use make serve" && echo "" && \
 	$(ACTIVATE_ENV) && \
 		mv Gemfile Gemfile.backup || true && \
@@ -110,7 +110,7 @@ build-gitpod: bundle-install  ## run a build on a gitpod.io environment
 	bundle exec jekyll build --config _config.yml
 .PHONY: build-gitpod
 
-build: clean api/swagger.json ## build files but do not run a server (You can specify FLAGS= to pass additional flags to Jekyll)
+build: clean ## build files but do not run a server (You can specify FLAGS= to pass additional flags to Jekyll)
 	$(ACTIVATE_ENV) && \
 		mv Gemfile Gemfile.backup || true && \
 		mv Gemfile.lock Gemfile.lock.backup || true && \
@@ -267,10 +267,6 @@ annotate: ## annotate the tutorials with usable Galaxy instances
 rebuild-search-index: ## Rebuild search index
 	node bin/lunr-index.js > search.json
 
-api/swagger.json: metadata/swagger.yaml
-	$(ACTIVATE_ENV) && \
-	cat metadata/swagger.yaml | python bin/yaml2json.py > api/swagger.json
-
 clean: ## clean up junk files
 	@rm -rf _site
 	@rm -rf .sass-cache

ORGANISATIONS.yaml

@@ -39,6 +39,14 @@ deNBI:
     name: de.NBI
     url: https://www.denbi.de/
 
+dfg:
+    name:  Deutsche Forschungsgemeinschaft
+    short_name: "DFG"
+    github: false
+    joined: 2024-12
+    url: https://www.dfg.de/de
+    avatar: "/training-material/shared/images/DFG_grant.png"
+
 earlham:
     name: Earlham Institute
     joined: 2017-09
@@ -208,13 +216,6 @@ ncbi:
     avatar: "/training-material/shared/images/ncbi.png"
     ror: "02meqm098"
 
-nfdi4plants:
-    short_name: DataPLANT
-    name: DataPLANT (NFDI4Plants)
-    joined: 2024-07
-    url:  https://nfdi4plants.org
-    avatar: "/training-material/shared/images/logo-dataplant.svg"
-
 NIH:
     name: National Institutes of Health
     short_name: "NIH"
@@ -317,6 +318,14 @@ swiss-tph:
     github: false
     ror: "03adhka07"
 
+surf:
+    short_name: SURF
+    name: SURF
+    url: https://www.surf.nl/
+    avatar: "/training-material/shared/images/surf.png"
+    github: false
+    ror: "009vhk114"
+
 tb-capt:
     short_name: TB-CAPT
     name: TB-CAPT
@@ -363,9 +372,3 @@ vib:
     github: false
     ror: "03xrhmk39"
 
-nfdi4bioimage:
-    short_name: NFDI4BIOIMAGE
-    name: NFDI4BIOIMAGE
-    joined: 2024-11
-    url:  https://nfdi4bioimage.de
-    avatar: "/training-material/shared/images/nfdi4bioimage.jpeg"

_includes/contributor-badge.html

@@ -3,11 +3,11 @@
 {%- else -%}
   {%- assign contributor_badge_entity = site | fetch_contributor: include.id -%}
   {%- assign name = contributor_badge_entity.short_name | default: contributor_badge_entity.name | default: include.id -%}
-  {% if include.small %}
-  <a href="{{ site.baseurl }}/hall-of-fame/{{ include.id }}/" class="contributor-badge contributor-{{ include.id }}">
-    {{ contributor_badge_entity | fetch_entity_avatar:include.id, 36 }}
+  {%- if include.small -%}
+  <a href="{{ site.baseurl }}/hall-of-fame/{{ include.id }}/" class="contributor-badge contributor-badge-small contributor-{{ include.id }}">
+    {{- contributor_badge_entity | fetch_entity_avatar:include.id, 36 -}}
   </a>
-  {% else %}
+  {%- else -%}
   <a href="{{ site.baseurl }}/hall-of-fame/{{ include.id }}/" class="contributor-badge contributor-{{ include.id }}">
     {%- if contributor_badge_entity.orcid -%}<img src="{% link assets/images/orcid.png %}" alt="orcid logo" width="36" height="36"/>{%- endif -%}
     {{ contributor_badge_entity | fetch_entity_avatar:include.id, 36 }}
@@ -16,5 +16,5 @@
   {%- include _includes/contributor-human-icons.html activity=include.activity -%}
   {%- endif -%}
   </a>
-  {% endif %}
+  {%- endif -%}
 {%- endif -%}

_includes/cyoa-choices.html

@@ -1,6 +1,8 @@
 <blockquote class="notranslate hands_on gtn-cyoa" id="gtn-cyoa{{ include.disambiguation }}">
-	<div class="box-title" aria-label="hands-on box: choose your own tutorial"><i class="fas fa-pencil-alt" aria-hidden="true"></i><span class="visually-hidden"></span> Hands-on: Choose Your Own Tutorial</div>
+	<div class="box-title" aria-label="hands-on box: choose your own tutorial"><i class="fas fa-pencil-alt" aria-hidden="true"></i><span class="visually-hidden"></span> {{ include.title | default: "Hands-on: Choose Your Own Tutorial" }}</div>
+	{% unless include.brief %}
 	<p>This is a "Choose Your Own Tutorial" section, where you can select between multiple paths. Click one of the buttons below to select how you want to follow the tutorial</p>
+	{% endunless %}
 	{% if include.text %}
 	<p>
 		{{ include.text }}

_includes/news-card.html

@@ -1,4 +1,3 @@
-<article>
 {% assign n = include.news %}
 
 {% if n.cover %}
@@ -18,38 +17,46 @@
  {% assign coverimagealt = "GTN logo with a multi-coloured star and the words Galaxy Training Network" %}
 {% endif %}
 
-<div class="card newsitem">
- <div class="card-header">
-     <a href="{% if n.external %}{{ n.link }}{% else %}{{site.baseurl}}{{n.url}}{% endif %}"><h3 class="card-title">{{n.title}}</h3></a>
-  </div>
- <div class="row no-gutters">
-  <div class="col-sm-5">
-   <img class="card-img newscover" src="{% unless coverimage contains 'http' %}{{site.baseurl}}/{% endunless %}{{coverimage}}" alt="{{ coverimagealt }}" loading="lazy">
-  </div>
-  <div class="col-sm-7">
-   <div class="card-body">
-        <!--<a href="{{site.baseurl}}{{n.url}}"><h4 class="card-title">{{n.title}}</h4></a>-->
-        <div class="text-muted">
-        {{ n.date | date: "%-d %B %Y" }}
+
+<div class="pathwayitem col-md-4">
+    <div class="card d-flex">
+       <a href="{% if n.external %}{{ n.link }}{% else %}{{site.baseurl}}{{n.url}}{% endif %}">
+      <div class="d-flex align-items-center" style="height:200px;">
+      <img class="card-img-top pathwaycover" src="{% unless coverimage contains 'http' %}{{site.baseurl}}/{% endunless %}{{coverimage}}" alt="{{ coverimagealt }}" loading="lazy">
+      </div>
+      </a>
+      <div class="card-body d-flex flex-column">
+        <h5 class="card-title">{{n.title}}</h5>
+        <div class="card-text">
+          {% for id in n.contributions.authorship %}
+            {% include _includes/contributor-badge.html id=id small=true %}
+          {% endfor %}
+          <div class="text-muted">
+            {{ n.date | date: "%-d %B %Y" }}
+          </div>
+
+          <a href="{% if n.external %}{{ n.link }}{% else %}{{site.baseurl}}{{n.url}}{% endif %}">
+
+          {% if n.external %}
+            This is an external post, please follow the link to read it.
+          {% else %}
+            {{ n.excerpt | strip_html }}
+          {% endif %}
+          </a>
+
         </div>
-        {% include _includes/contributors-line.html page=n %}
 
+      </div>
+
+      <div class="card-footer">
         {% for tag in n.tags %}
         {% unless tag == 'already-on-hub' %}
 <span class="label label-default tutorial_tag" style="{{ tag | colour_tag }}">{{ tag  }}</span>
         {% endunless %}
         {% endfor %}
-    <hr/>
-    <p class="card-text">
-      {% if n.external %}
-        This is an external post, please follow the link to read it.
-      {% else %}
-        {{ n.excerpt | strip_html }}
-      {% endif %}
-    </p>
-    <a href="{% if n.external %}{{ n.link }}{% else %}{{site.baseurl}}{{n.url}}{% endif %}" class="btn btn-primary">Full Story</a>
-   </div>
-  </div>
- </div>
+      </div>
+
+    </div>
 </div>
-</article>
+
+