Merge branch 'main' into edit_CUTnRUN

galaxyproject · Feb 6, 2025 · 840c13f · 840c13f
2 parents 3c41b9e + 2fcbcb0
commit 840c13f
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diff --git a/.github/workflows/ci-main.yml b/.github/workflows/ci-main.yml
@@ -68,6 +68,8 @@ jobs:
       - name: Check Tutorial Formatting
         run: |
           find topics/ -name tutorial.md | xargs -n 1 python bin/check-broken-boxes.py | reviewdog -efm="%f:%l: %m" -filter-mode=file -reporter=github-pr-review -fail-level=any
+          set -e
+          set -o pipefail
           bundle exec ruby bin/lint.rb --format rdjson | reviewdog -filter-mode=file -reporter=github-pr-review -f=rdjsonl -fail-level=any
         env:
             REVIEWDOG_GITHUB_API_TOKEN: ${{ secrets.GITHUB_TOKEN }}

diff --git a/.github/workflows/ci.yml b/.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 \

diff --git a/.github/workflows/deploy.yml b/.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:

diff --git a/.github/workflows/monthly-release-backfill.yml b/.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 }}

diff --git a/.github/workflows/monthly-release.yml b/.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 }}

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-22.04
+    runs-on: ubuntu-24.04
     services:
       # Label used to access the service container
       mozillatts:
@@ -34,7 +34,7 @@ jobs:
           ruby-version: "3.2"
       - uses: actions/setup-node@v4
         with:
-          node-version: '19'
+          node-version: '22'
       - uses: actions/cache@v4
         with:
           path: |
@@ -46,11 +46,14 @@ 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 update
+          sudo apt-get install -y build-essential libxi-dev libglu1-mesa-dev libglew-dev pkg-config libpixman-1-dev libcairo2-dev libpango1.0-dev mesa-utils xvfb # for node
+          rm Gemfile.lock
           gem install bundler
           bundle config path vendor/bundle
           bundle install --jobs 4 --retry 3
           npm install
+          npm install github:sailplan/editly #temporary fix, see https://github.com/mifi/editly/issues/286, once fixed, remove this and restore line to package.json:  "editly": "^0.14.0"
           bundle pristine ffi
       # END Dependencies
 

diff --git a/CONTRIBUTORS.yaml b/CONTRIBUTORS.yaml
@@ -6,7 +6,7 @@
 #
 #  EXAMPLE CONTRIBUTOR:
 #
-# userid:                  # madatory; your github username
+# userid:                  # mandatory; your github username
 #   name: Namey Name       # mandatory; your name
 #   joined: 2017-09        # mandatory; the month you added yourself to this file
 #   email: [email protected]                      # your email address
@@ -51,7 +51,7 @@ awspolly:
 
 # our real contributors <3 (please add yourself in alphabetical order)
 
-    
+
 a-asai:
     name: Atsushi Asai
     email: [email protected]
@@ -103,7 +103,7 @@ adairama:
     joined: 2024-12
     location:
       country: SG
-    
+
 
 ahmedhamidawan:
     name: Ahmed Hamid Awan
@@ -507,6 +507,10 @@ Camila-goclowski:
     email: [email protected]
     linkedin: camila-goclowski
 
+carloscheemendonca:
+    name: Carlos Chee Mendonça
+    joined: 2025-01
+
 charitylaw:
     name: Charity Law
     joined: 2018-09
@@ -582,6 +586,13 @@ combesf:
     affiliations:
       - elixir-europe
 
+CordulaHege:
+    name: Cordula Almut Selma Hege
+    joined: 2024-11
+    affiliations:
+        - nfdi4microbiota
+        - hzi-bifo
+
 coverbeck:
     name: Charles Overbeck
     email: [email protected]
@@ -615,10 +626,37 @@ danielabutano:
     name: Daniela Butano
     joined: 2019-09
 
+dawnmy:
+    name: Zhi-Luo Deng
+    joined: 2024-11
+    affiliations:
+      - hzi-bifo
+      - nfdi4microbiota
+
 Sch-Da:
     name: Daniela Schneider
     joined: 2024-10
 
+dadrasarmin:
+    name: Armin Dadras
+    joined: 2025-01
+    email: [email protected]
+    fediverse: https://mastodon.social/@dadrasarmin
+    fediverse_flavor: mastodon
+    bluesky: dadrasarmin.bsky.social
+    linkedin: armindadras
+    matrix: 'armin.dadras:matrix.org'
+    orcid: 0000-0001-7649-2388
+    maintainer_contact: matrix
+    contact_for_training: true
+    affiliations:
+        - uni-freiburg
+        - eurosciencegateway
+    location:
+        country: DE
+        lat: 47.997791
+        lon: 7.842609
+
 dannon:
     name: Dannon Baker
     joined: 2017-09
@@ -639,6 +677,10 @@ dbrites:
     name: Daniela Brites
     joined: 2022-03
 
+debroas:
+    name: Didier Debroas
+    joined: 2024-12
+
 dechendb:
     name: Dechen Bhuming
     joined: 2023-06
@@ -707,6 +749,12 @@ dyusuf:
     affiliations:
       - uni-freiburg
 
+dometto:
+    name: Dawa Ometto
+    joined: 2024-12
+    affiliations:
+      - surf
+
 eancelet:
     name: Estelle Ancelet
     email: [email protected]
@@ -838,8 +886,11 @@ foellmelanie:
     matrix: 'foellmelanie:matrix.org'
     orcid: 0000-0002-1887-7543
     joined: 2018-10
+    elixir_node: de
     affiliations:
       - uni-freiburg
+      - deNBI
+      - elixir-europe
 
 fpsom:
     name: Fotis E. Psomopoulos
@@ -917,6 +968,14 @@ garimavs:
     email: [email protected]
     joined: 2022-03
 
+GaryRobertson:
+    name: Gary Robertson
+    joined: 2024-11
+    affiliations:
+       - hzi-bifo
+       - nfdi4microbiota
+    github: false
+
 gatwirival:
     name: Valentine Gatwiri
     email: [email protected]
@@ -946,9 +1005,9 @@ GokceOGUZ:
     email: [email protected]
     orcid: 0000-0003-1044-7204
     linkedin: gokce-oguz
-    location: 
+    location:
       country: SG
-    
+
 guerler:
     name: Aysam Guerler
     joined: 2017-09
@@ -975,6 +1034,14 @@ hechth:
   orcid: 0000-0001-6744-996X
   elixir_node: cz
 
+HeshamAlmessady:
+  name: Hesham Almessady
+  joined: 2024-11
+  github: false
+  affiliations:
+    - hzi-bifo
+    - nfdi4microbiota
+
 heylf:
     name: Florian Heyl
     joined: 2018-08
@@ -1355,6 +1422,12 @@ Lain-inrae:
     affiliations:
       - elixir-europe
 
+laurarussell:
+    name: Laura Russell
+    joined: 2025-01
+    affiliations:
+      - gbif
+
 lcooper:
     name: Laura Cooper
     joined: 2024-03
@@ -1694,6 +1767,12 @@ miRlyKayleigh:
     email: [email protected]
     joined: 2022-12
 
+mirelaminkova:
+    name: Mirela Minkova
+    joined: 2024-12
+    affiliations:
+      - surf
+
 moffmade:
     name: Cory Maughmer
     joined: 2018-06
@@ -1766,6 +1845,11 @@ nagoue:
     orcid: 0000-0003-2750-1473
     joined: 2019-07
 
+Najatamk:
+    name: Najat Amoukou
+    email: [email protected]
+    joined: 2024-07
+
 nakucher:
     name: Natalie Kucher
     email: [email protected]
@@ -1982,8 +2066,8 @@ paulocilasjr:
     joined: 2024-09
     email: [email protected]
     orcid: 0000-0002-4403-6684
-    affiliations: 
-    - moffitt 
+    affiliations:
+    - moffitt
     twitter: paulocilasjr
 
 paulzierep:
@@ -2073,8 +2157,8 @@ qchiujunhao:
     name: Junhao Qiu
     joined: 2024-02
     orcid: 0009-0005-4322-3401
-    affiliations: 
-    - moffitt 
+    affiliations:
+    - moffitt
     email: [email protected]
 
 Quickbeasts51429:
@@ -2106,6 +2190,11 @@ r1corre:
     orcid: 0000-0001-6354-2278
     joined: 2019-04
 
+reid-wagner:
+    name: Reid Wagner
+    email: [email protected]
+    joined: 2024-11
+
 rikeshi:
     name: Erik Schill
     joined: 2021-05
@@ -2337,6 +2426,13 @@ sophia120199:
     name: Sophia Hampe
     joined: 2023-04
 
+sophiepamerlon:
+    name: Sophie Pamerlon
+    joined: 2025-01
+    affiliations:
+      - pndb
+      - gbif
+
 stain:
     name: Stian Soiland-Reyes
     email: [email protected]
@@ -2691,6 +2787,10 @@ yvesvdb:
     affiliations:
       - ifb
 
+yuliiaorlova:
+    name: Yuliia Orlova
+    joined: 2024-12
+
 zargham-ahmad:
     name: Zargham Ahmad
     email: [email protected]