Merge branch 'galaxyproject:main' into main

Author: yguitton

.github/workflows/ci-main.yml

@@ -66,13 +66,20 @@ jobs:
           python bin/mergeyaml.py --nondocker > /dev/null
 
       - name: Check Tutorial Formatting
+        if: always()
         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
+          mkdir -p ./pr
+          find topics/ -name tutorial.md | xargs -n 1 python bin/check-broken-boxes.py | reviewdog -efm="%f:%l: %m" -filter-mode=file -reporter=local  -fail-level=error -diff='git diff main' > ./pr/reviewdog.txt
           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 }}
+          bundle exec ruby bin/lint.rb --format rdjson | reviewdog -filter-mode=file -f=rdjsonl -reporter=local -fail-level=error -diff='git diff main' > ./pr/reviewdog.json
+
+      - uses: actions/upload-artifact@v4
+        if: always()
+        with:
+          name: reviewdog
+          path: pr/
+
 
       # - name: rubocop
       #   uses: reviewdog/action-rubocop@v2

.github/workflows/reviewdog-comment.yml

@@ -0,0 +1,57 @@
+name: "Review comments"
+
+on:
+  workflow_run:
+    workflows: ["[CI] GTN Tutorial Linting"]
+    types: [completed]
+
+jobs:
+  comment:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 1
+          persist-credentials: false
+
+      - uses: reviewdog/action-setup@v1
+        with:
+          reviewdog_version: latest
+
+      - name: 'Download artifact'
+        uses: actions/github-script@v7
+        with:
+          script: |
+            let allArtifacts = await github.rest.actions.listWorkflowRunArtifacts({
+               owner: context.repo.owner,
+               repo: context.repo.repo,
+               run_id: context.payload.workflow_run.id,
+            });
+            let matchArtifact = allArtifacts.data.artifacts.filter((artifact) => {
+              return artifact.name == "reviewdog"
+            })[0];
+            let download = await github.rest.actions.downloadArtifact({
+               owner: context.repo.owner,
+               repo: context.repo.repo,
+               artifact_id: matchArtifact.id,
+               archive_format: 'zip',
+            });
+            const fs = require('fs');
+            const path = require('path');
+            const temp = '${{ runner.temp }}/artifacts';
+            if (!fs.existsSync(temp)){
+              fs.mkdirSync(temp);
+            }
+            fs.writeFileSync(path.join(temp, 'reviewdog.zip'), Buffer.from(download.data));
+
+      - name: 'Unzip artifact'
+        run: unzip reviewdog.zip -d "${{ runner.temp }}/artifacts"
+
+      - name: Add review comments
+        run: |
+          cat "${{ runner.temp }}/artifacts/reviewdog.txt" | reviewdog -efm="%f:%l: %m" -reporter=github-pr-review
+
+          cat "${{ runner.temp }}/artifacts/reviewdog.json" | reviewdog -reporter=github-pr-review -f=rdjsonl
+        env:
+            REVIEWDOG_GITHUB_API_TOKEN: ${{ secrets.REVIEW_BOT_TOKEN }}
+

.gitignore

@@ -1,5 +1,6 @@
 .DS_Store
 .bundle
+.env
 _site
 _pdf
 .directory

CODEOWNERS

@@ -14,7 +14,7 @@ _plugins/   @bebatut @hexylena
 
 # Topic Editorial Board members
 topics/introduction/               @jennaj  @delphine-l @teresa-m
-topics/admin/                      @hexylena  @natefoo  @bgruening  @martenson
+topics/admin/                      @hexylena  @natefoo  @bgruening  @martenson @mira-miracoli
 topics/ai4life/                    @beatrizserrano
 topics/assembly/                   @nekrut  @delphine-l
 topics/climate/                    @annefou

CONTRIBUTORS.yaml

@@ -1085,6 +1085,9 @@ guillaume-gricourt:
 hvelab:
     name: Helena Vela
     joined: 2024-09
+    contact_for_training: true
+    affiliations:
+      - biont
 
 hannahkimincompbio:
     name: Hannah Kim
@@ -1340,6 +1343,7 @@ jkreplak:
 
 jochenblom:
     name: Jochen Blom
+    elixir_node: de
     joined: 2025-04
 
 joelvdavies:
@@ -1593,15 +1597,17 @@ lgallegovillar:
 
 lldelisle:
     name: Lucille Delisle
-    email: lucille.delisle@epfl.ch
+    email: lucille.delisle@unige.ch
     orcid: 0000-0002-1964-4960
     joined: 2019-08
     elixir_node: ch
+    matrix: 'lldelisle:matrix.org'
     contact_for_training: true
+    maintainer_contact: matrix
     location:
       country: CH
-      lat: 46.52
-      lon: 6.56
+      lat: 46.19
+      lon: 6.15
     affiliations:
       - elixir-europe
 
@@ -1610,6 +1616,8 @@ lisanna:
     joined: 2023-09
     email: lisanna.paladin@gmail.com
     orcid: 0000-0003-0011-9397
+    elixir_node: de
+    contact_for_training: true
     affiliations:
       - elixir-europe
       - embl-ebi
@@ -1945,6 +1953,12 @@ mirelaminkova:
     affiliations:
       - surf
 
+mittler-works:
+    name: Nils Mittler
+    joined: 2025-06
+    affiliations:
+      - deKCD
+
 moffmade:
     name: Cory Maughmer
     joined: 2018-06
@@ -1955,6 +1969,10 @@ moheydarian:
     orcid: 0000-0001-9449-9364
     joined: 2017-09
 
+Morphy427: 
+    name: Elouan Le Mestric
+    joined: 2025-05
+
 mritchie:
     name: Matt Ritchie
     joined: 2018-09
@@ -2159,6 +2177,11 @@ odoppelt:
     affiliations:
       - elixir-europe
 
+ogerdfx:
+    name: Christine Oger
+    joined: 2025-06
+    elixir_node: fr
+
 olanag1:
     name: Olha Nahorna
     joined: 2019-07
@@ -2517,6 +2540,12 @@ sanjaysrikakulam:
       - elixir-europe
       - eurosciencegateway
 
+santamccloud:
+    name: Santino Faack
+    joined: 2025-07
+    affiliations:
+      - uni-freiburg
+
 saramorsy:
     name: Sara Morsy
     joined: 2021-10
@@ -2609,6 +2638,9 @@ shiltemann:
 silviadg87:
     name: Silvia Di Giorgio
     joined: 2025-05
+    contact_for_training: true
+    affiliations:
+      - biont
 
 Shorla:
     name: Olushola Ogunkelu
@@ -2765,6 +2797,11 @@ sunyi000:
     email: yi.sun@embl.de
     joined: 2021-03
 
+maulakhan:
+    name: Arif UI Maula Khan
+    email: arif.khan@embl.de
+    joined: 2025-07
+
 Swathi266:
     name: Swathi Nataraj
     joined: 2024-12
@@ -2918,6 +2955,12 @@ tsenapathi:
 tflowers15:
     name: Tristan Reynolds
     joined: 2025-03
+    email: treynolds@unimelb.edu.au
+    orcid: 0000-0002-6606-5953
+    affiliations:
+      - AustralianBioCommons
+      - unimelb
+      - melbournebioinformatics
 
 trungN:
     name: Nguyen Vo Minh Trung

GRANTS.yaml

@@ -242,6 +242,19 @@ nhgri-gdscn:
     funding_id: 75N92022P00232
     funding_database: highergov
 
+oscars:
+    name: "Open Science Clusters' Action for Research & Society"
+    short_name: "OSCARS"
+    joined: 2025-07
+    funding_id: "101129751"
+    funding_database: cordis
+    funder_name: Horizon Europe
+    funding_statement: |
+      The OSCARS project has received funding from the European Commission’s Horizon Europe Research and Innovation programme under grant agreement No. 101129751
+    url: https://oscars-project.eu/
+    github: false
+    avatar: "/training-material/shared/images/logos/OSCARS-logo-EUflag.png"
+    
 skills4eosc:
     name: Skills for European Open Science Cloud
     short_name: "Skills4SEOSC"

ORGANISATIONS.yaml

@@ -144,6 +144,12 @@ FAIR2Adapt:
     url: https://eosc.eu/eu-project/fair2adapt/
     avatar: "/training-material/shared/images/logos/FAIR2Adapt.png"
 
+fiesta:
+    short_name: OSCARS-FIESTA
+    name: FAIR Image Analysis across Sciences
+    url: https://oscars-project.eu/projects/fair-image-analysis-across-sciences
+    avatar: "/training-material/shared/images/logos/logo-FIESTA.png"
+    
 find:
     short_name: FIND
     name: The Foundation for Innovative New Diagnostics
@@ -229,6 +235,11 @@ madland:
     url: https://madland.science
     avatar: "/training-material/shared/images/logo-madland.jpg"
 
+melbournebioinformatics:
+    name: Melbourne Bioinformatics
+    url: https://mdhs.unimelb.edu.au/melbournebioinformatics
+    avatar: "/training-material/shared/images/Melbourne-Bioinformatics-logo.png"
+    
 moffitt:
     name: Moffitt Cancer Center
     url: https://www.moffitt.org/
@@ -421,6 +432,11 @@ uni-freiburg:
     github: false
     ror: "0245cg223"
 
+unimelb:
+    name: The University of Melbourne
+    url: https://www.unimelb.edu.au
+    avatar: "/training-material/shared/images/unimelb_Logo_RGB.png"    
+
 UTas:
     short_name: UTas
     name: University of Tasmania

_config.yml

@@ -92,8 +92,8 @@ abbreviate:
 # update invite link gxy.io link here when needed: https://github.com/galaxyproject/gxy.io/blob/main/group_vars/all.yaml
 slack:
   invite_link: http://gxy.io/gtn-slack  # this points to the invite link
-  general_channel: https://gtnsmrgsbord.slack.com/archives/C01MNM98X9V
-  social_channel: https://gtnsmrgsbord.slack.com/archives/C01EDBVMHBQ
+  general_channel: https://gtnsmrgsbord.slack.com/channels/general
+  social_channel: https://gtnsmrgsbord.slack.com/channels/social
   single_cell_channel: https://gtnsmrgsbord.slack.com/archives/C06PBRR40D7
 
 

_layouts/event.html

@@ -257,7 +257,12 @@ <h5 class="card-title">Join {{support.platform | default: "Slack" }}!</h5>
 
             <ol>
               <li>Join {{support.platform}} via this <a href="{{support.join_link | default: site.slack.invite_link }}">Invite Link</a></li>
-              <li>Join the event channel: <a href="{{support.link | default: site.slack.general_channel}}">#{{event.infrastructure.support.channel | default: "general"}}</a></li>
+{% if support.platform == "Slack" and support.channel %}
+  {% assign channel_link = "https://gtnsmrgsbord.slack.com/channels/" | append: support.channel %}
+{% else %}
+  {% assign channel_link = support.link | default: site.slack.general_channel %}
+{% endif %}
+              <li>Join the event channel: <a href="{{channel_link}}">#{{event.infrastructure.support.channel | default: "general"}}</a></li>
               <li>Introduce yourself here!</li>
             </ol>
 

_layouts/topic-maintainer.html

@@ -58,6 +58,22 @@ <h2>Action Items</h2>
 			<td>{% if topic.learning_path_cta or topic.learning_path_ctas %} Done ✅ {% else %} Pending ❌ {% endif %}</td>
 			<td>By providing a Learning Pathway CTA, we can help guide learners to the best resources for learning about this topic.</td>
 		</tr>
+		<tr>
+			<td>Review Feedback Received</td>
+			<td> Ongoing 🔁 </td>
+			<td> Review all <a href="https://training.galaxyproject.org/feedback#topic-{{topic.title | slugify }}" >feedback received for the {{topic.title}} topic</a> and create GitHub issues or PRs where needed. </td>
+		</tr>
+		<tr>
+			<td>Review open Pull Requests</td>
+			<td> Ongoing 🔁 </td>
+			<td> View all <a href="https://github.com/galaxyproject/training-material/pulls?q=is%3Apr+is%3Aopen+label%3A{{topic.name}}" >open PRs in the {{topic.title}} topic</a> and review, comment and merge!</td>
+		</tr>
+		<tr>
+			<td>Review open GitHub Issues</td>
+			<td> Ongoing 🔁 </td>
+			<td> View all <a href="https://github.com/galaxyproject/training-material/issues?q=is%3Aissue%20state%3Aopen%20label%3A{{topic.name}}" >open issues related to the {{topic.title}} topic</a> and comment, fix, or ask others for help!</td>
+		</tr>
+
 	</tbody>
 </table>