Merge branch 'main' into lint-iedb_api

Author: bernt-matthias

.github/dependabot.yml

@@ -0,0 +1,12 @@
+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://docs.github.com/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
+
+version: 2
+updates:
+  # Enable version updates for GitHub Actions
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"

.github/workflows/ci.yaml

@@ -7,7 +7,7 @@ on:
     types: [run-all-tool-tests-command]
 env:
   GALAXY_FORK: galaxyproject
-  GALAXY_BRANCH: release_24.1
+  GALAXY_BRANCH: release_25.1
   MAX_CHUNKS: 40
 jobs:
   setup:
@@ -27,7 +27,7 @@ jobs:
     steps:
     - name: Add reaction
       if: ${{ github.event.client_payload.slash_command.command == 'run-all-tool-tests' }}
-      uses: peter-evans/create-or-update-comment@v4
+      uses: peter-evans/create-or-update-comment@v5
       with:
         token: ${{ secrets.PAT }}
         repository: ${{ github.event.client_payload.github.payload.repository.full_name }}
@@ -43,7 +43,7 @@ jobs:
     - name: Determine latest commit in the Galaxy repo
       id: get-galaxy-sha
       run: echo "galaxy-head-sha=$(git ls-remote https://github.com/${{ steps.get-fork-branch.outputs.fork }}/galaxy refs/heads/${{ steps.get-fork-branch.outputs.branch }} | cut -f1)" >> $GITHUB_OUTPUT
-    - uses: actions/setup-python@v5
+    - uses: actions/setup-python@v6
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
@@ -56,9 +56,9 @@ jobs:
     # are not available as wheels, pip will build a wheel for them, which can be cached.
     - name: Install wheel
       run: pip install wheel
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
       with:
-        fetch-depth: 1
+        persist-credentials: false
     - name: Fake a Planemo run to update cache and determine commit range, repositories, and chunks
       uses: galaxyproject/planemo-ci-action@v1
       id: discover
@@ -84,10 +84,10 @@ jobs:
       matrix:
         python-version: ['3.11']
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
       with:
-        fetch-depth: 1
-    - uses: actions/setup-python@v5
+        persist-credentials: false
+    - uses: actions/setup-python@v6
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
@@ -104,8 +104,8 @@ jobs:
         fail-level: warn
         repository-list: ${{ needs.setup.outputs.repository-list }}
         tool-list: ${{ needs.setup.outputs.tool-list }}
-        additional-planemo-options: --biocontainers
-    - uses: actions/upload-artifact@v4
+        additional-planemo-options: --biocontainers --skip version_bumped
+    - uses: actions/upload-artifact@v5
       if: ${{ failure() }}
       with:
         name: 'Tool linting output'
@@ -132,12 +132,10 @@ jobs:
         ports:
           - 5432:5432
     steps:
-    # checkout the repository
-    # and use it as the current working directory
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
       with:
-        fetch-depth: 1
-    - uses: actions/setup-python@v5
+        persist-credentials: false
+    - uses: actions/setup-python@v6
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
@@ -164,7 +162,7 @@ jobs:
         galaxy-slots: ${{ steps.cpu-cores.outputs.count }}
         # Limit each test to 15 minutes
         test_timeout: 900
-    - uses: actions/upload-artifact@v4
+    - uses: actions/upload-artifact@v5
       with:
         name: 'Tool test output ${{ matrix.chunk }}'
         path: upload
@@ -183,10 +181,10 @@ jobs:
     # This job runs on Linux
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/download-artifact@v4
+    - uses: actions/download-artifact@v6
       with:
         path: artifacts
-    - uses: actions/setup-python@v5
+    - uses: actions/setup-python@v6
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
@@ -201,7 +199,8 @@ jobs:
       with:
         mode: combine
         html-report: true
-    - uses: actions/upload-artifact@v4
+        markdown-report: true
+    - uses: actions/upload-artifact@v5
       with:
         name: 'All tool test results'
         path: upload
@@ -213,7 +212,7 @@ jobs:
 
     - name: Create comment
       if: ${{ github.event.client_payload.slash_command.command == 'run-all-tool-tests' }}
-      uses: peter-evans/create-or-update-comment@v4
+      uses: peter-evans/create-or-update-comment@v5
       with:
         token: ${{ secrets.PAT }}
         repository: ${{ github.event.client_payload.github.payload.repository.full_name }}

.github/workflows/pr.yaml

@@ -15,7 +15,7 @@ on:
       - '*'
 env:
   GALAXY_FORK: galaxyproject
-  GALAXY_BRANCH: release_24.1
+  GALAXY_BRANCH: release_25.1
   MAX_CHUNKS: 4
   MAX_FILE_SIZE: 1M
 concurrency:
@@ -57,7 +57,7 @@ jobs:
     - name: Determine latest commit in the Galaxy repo
       id: get-galaxy-sha
       run: echo "galaxy-head-sha=$(git ls-remote https://github.com/${{ env.GALAXY_FORK }}/galaxy refs/heads/${{ env.GALAXY_BRANCH }} | cut -f1)" >> $GITHUB_OUTPUT
-    - uses: actions/setup-python@v5
+    - uses: actions/setup-python@v6
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
@@ -78,9 +78,10 @@ jobs:
       run: pip install wheel
     - name: Install flake8
       run: pip install flake8 flake8-import-order
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
       with:
         fetch-depth: 0
+        persist-credentials: false
     - name: Fake a Planemo run to update cache and determine commit range, repositories, and chunks
       uses: galaxyproject/planemo-ci-action@v1
       id: discover
@@ -111,10 +112,10 @@ jobs:
       matrix:
         python-version: ['3.11']
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
       with:
-        fetch-depth: 1
-    - uses: actions/setup-python@v5
+        persist-credentials: false
+    - uses: actions/setup-python@v6
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
@@ -123,6 +124,15 @@ jobs:
       with:
         path: ~/.cache/pip
         key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }}
+
+    - name: Set skip version check for push event (i.e. merge to main)
+      if: ${{ github.event_name != 'pull_request' }}
+      run:
+        echo "EXTRA_SKIP=--skip version_bumped" >> "$GITHUB_ENV"
+    - name: Set no skip vor pull_request events
+      if: ${{ github.event_name == 'pull_request' }}
+      run:
+        echo "EXTRA_SKIP=" >> "$GITHUB_ENV"
     - name: Planemo lint
       uses: galaxyproject/planemo-ci-action@v1
       id: lint
@@ -131,7 +141,8 @@ jobs:
         fail-level: warn
         repository-list: ${{ needs.setup.outputs.repository-list }}
         tool-list: ${{ needs.setup.outputs.tool-list }}
-    - uses: actions/upload-artifact@v4
+        additional-planemo-options: ${{ env.EXTRA_SKIP }}
+    - uses: actions/upload-artifact@v5
       if: ${{ failure() }}
       with:
         name: 'Tool linting output'
@@ -148,10 +159,10 @@ jobs:
       matrix:
         python-version: ['3.11']
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
       with:
-        fetch-depth: 1
-    - uses: actions/setup-python@v5
+        persist-credentials: false
+    - uses: actions/setup-python@v6
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
@@ -164,7 +175,7 @@ jobs:
       run: pip install flake8 flake8-import-order
     - name: Flake8
       run: echo '${{ needs.setup.outputs.repository-list }}' | xargs -d '\n' flake8 --output-file pylint_report.txt --tee
-    - uses: actions/upload-artifact@v4
+    - uses: actions/upload-artifact@v5
       if: ${{ failure() }}
       with:
         name: 'Python linting output'
@@ -177,12 +188,12 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-20.04]
+        os: [ubuntu-24.04]
         r-version: ['release']
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
       with:
-        fetch-depth: 1
+        persist-credentials: false
     - uses: r-lib/actions/setup-r@v2
       with:
         r-version: ${{ matrix.r-version }}
@@ -203,7 +214,7 @@ jobs:
         echo '${{ needs.setup.outputs.repository-list }}' | xargs -d '\n' -n 1 ./.github/styler.R --dry off
         git status
         git diff --exit-code | tee rlint_report.txt
-    - uses: actions/upload-artifact@v4
+    - uses: actions/upload-artifact@v5
       if: ${{ failure() }}
       with:
         name: 'R linting output'
@@ -215,9 +226,10 @@ jobs:
     if: ${{ github.event_name == 'pull_request' && needs.setup.outputs.repository-list != '' }}
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
       with:
         fetch-depth: 0
+        persist-credentials: false
     - name: Check file sizes
       run: |
         touch file_size_report.txt
@@ -230,7 +242,7 @@ jobs:
           cat file_size_report.txt
           exit 1
         fi
-    - uses: actions/upload-artifact@v4
+    - uses: actions/upload-artifact@v5
       if: ${{ failure() }}
       with:
         name: 'File size report'
@@ -258,10 +270,10 @@ jobs:
         ports:
           - 5432:5432
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
       with:
-        fetch-depth: 1
-    - uses: actions/setup-python@v5
+        persist-credentials: false
+    - uses: actions/setup-python@v6
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
@@ -293,8 +305,8 @@ jobs:
         chunk-count: ${{ needs.setup.outputs.chunk-count }}
         galaxy-slots: ${{ steps.cpu-cores.outputs.count }}
         # Limit each test to 15 minutes
-        test_timeout: 1800
-    - uses: actions/upload-artifact@v4
+        test_timeout: 900
+    - uses: actions/upload-artifact@v5
       with:
         name: 'Tool test output ${{ matrix.chunk }}'
         path: upload
@@ -313,10 +325,10 @@ jobs:
       matrix:
         python-version: ['3.11']
     steps:
-    - uses: actions/download-artifact@v4
+    - uses: actions/download-artifact@v6
       with:
         path: artifacts
-    - uses: actions/setup-python@v5
+    - uses: actions/setup-python@v6
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
@@ -332,7 +344,7 @@ jobs:
         mode: combine
         html-report: true
         markdown-report: true
-    - uses: actions/upload-artifact@v4
+    - uses: actions/upload-artifact@v5
       with:
         name: 'All tool test results'
         path: upload
@@ -344,7 +356,8 @@ jobs:
         mode: check
     - name: Check if all test chunks succeeded
       run: |
-        NFILES=$(ls artifacts/ | grep "Tool test output" | wc -l)
+        ls artifacts/
+        NFILES=$(find artifacts/ -name "tool_test_output.json" | wc -l)
         if [[ "${{ needs.setup.outputs.chunk-count }}" != "$NFILES" ]]; then
           exit 1
         fi
@@ -359,10 +372,10 @@ jobs:
       matrix:
         python-version: ['3.11']
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
       with:
-        fetch-depth: 1
-    - uses: actions/setup-python@v5
+        persist-credentials: false
+    - uses: actions/setup-python@v6
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
@@ -390,22 +403,22 @@ jobs:
   deploy-report:
     name: Report deploy status
     needs: [deploy]
-    if: ${{ always() && needs.deploy.result != 'success' && (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main' ) && github.repository_owner == 'galaxyproject' }}
+    if: ${{ always() && (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main' ) && github.repository_owner == 'galaxyproject' }}
     runs-on: ubuntu-latest
     steps:
     # report to the PR if deployment failed
     - name: Get PR object
-      uses: 8BitJonny/gh-get-current-pr@2.2.0
+      uses: 8BitJonny/gh-get-current-pr@4.0.0
       id: getpr
       with:
         sha: ${{ github.event.after }}
     - name: Create comment
-      uses: peter-evans/create-or-update-comment@v4
+      uses: peter-evans/create-or-update-comment@v5
       with:
         token: ${{ secrets.PAT }}
         issue-number: ${{ steps.getpr.outputs.number }}
         body: |
-          Attention: deployment ${{ needs.deploy.result }}!
+          Deployment status: **${{ needs.deploy.result }}**
 
           https://github.com/${{ github.repository }}/actions/runs/${{ github.run_id }}
 

.github/workflows/slash.yaml

@@ -8,7 +8,7 @@ jobs:
     steps:
       - name: Slash Command Dispatch
         if: github.repository_owner == 'galaxyproject'
-        uses: peter-evans/slash-command-dispatch@v4
+        uses: peter-evans/slash-command-dispatch@v5
         with:
           token: ${{ secrets.PAT }}
           commands: |

README.md

@@ -13,7 +13,8 @@ These repositories are maintained and developed by the [Intergalactic Utilities
 
 Pull Requests with dependencies specified as conda-package will be automatically tested and verified using [planemo](https://github.com/galaxyproject/planemo). If the tests pass and the pull request is merged, the tool will be automatically uploaded to the [Test](http://testtoolshed.g2.bx.psu.edu/)- and [Main Tool Shed](http://toolshed.g2.bx.psu.edu/).
 
-Other repositories with Galaxy tools:
+## Other repositories with Galaxy tools
+
  * [Björn Grüning repo](https://github.com/bgruening/galaxytools)
  * [Galaxy devteam repo](https://github.com/galaxyproject/tools-devteam)
  * Peter Cock's repos: