MAINT: update workflows to most recent actions

.github/workflows/ci.yml

@@ -1,6 +1,6 @@
 # From https://github.com/galaxyproject/galaxy-tool-repository-template/blob/main/.github/workflows/ci.yaml
 # License (spdx): MIT
-# Last updated: 2022-07-14
+# Last updated: 2024-10-29
 # Search for "MODIFIED" to see modifications from original
 #
 name: Weekly global Tool Linting and Tests
@@ -15,7 +15,7 @@ on:
 # MODIFIED END
 env:
   GALAXY_FORK: galaxyproject
-  GALAXY_BRANCH: release_23.1  # MODIFIED
+  GALAXY_BRANCH: release_24.1
   MAX_CHUNKS: 40
 jobs:
   setup:
@@ -31,31 +31,31 @@ jobs:
       chunk-list: ${{ steps.discover.outputs.chunk-list }}
     strategy:
       matrix:
-        python-version: ['3.7']
+        python-version: ['3.11']
     steps:
     - name: Add reaction
       if: ${{ github.event.client_payload.slash_command.command == 'run-all-tool-tests' }}
-      uses: peter-evans/create-or-update-comment@v1
+      uses: peter-evans/create-or-update-comment@v4
       with:
         token: ${{ secrets.PAT }}
         repository: ${{ github.event.client_payload.github.payload.repository.full_name }}
         comment-id: ${{ github.event.client_payload.github.payload.comment.id }}
-        reaction-type: hooray
+        reactions: hooray
     - name: Set galaxy fork and branch
       id: get-fork-branch
       run: |
         TMP="${{ github.event.client_payload.slash_command.args.named.fork }}"
-        echo "::set-output name=fork::${TMP:-$GALAXY_FORK}"
+        echo "fork=${TMP:-$GALAXY_FORK}" >> $GITHUB_OUTPUT
         TMP="${{ github.event.client_payload.slash_command.args.named.branch }}"
-        echo "::set-output name=branch::${TMP:-$GALAXY_BRANCH}"
+        echo "branch=${TMP:-$GALAXY_BRANCH}" >> $GITHUB_OUTPUT
     - name: Determine latest commit in the Galaxy repo
       id: get-galaxy-sha
-      run: echo "::set-output name=galaxy-head-sha::$(git ls-remote https://github.com/${{ steps.get-fork-branch.outputs.fork }}/galaxy refs/heads/${{ steps.get-fork-branch.outputs.branch }} | cut -f1)"
-    - uses: actions/setup-python@v1
+      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
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
-      uses: actions/cache@v2
+      uses: actions/cache@v4
       id: cache-pip
       with:
         path: ~/.cache/pip
@@ -64,7 +64,7 @@ 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@v2
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 1
     - name: Fake a Planemo run to update cache and determine commit range, repositories, and chunks
@@ -82,6 +82,42 @@ jobs:
       run: |
         echo 'Using ${{ steps.discover.outputs.chunk-count }} chunks (${{ steps.discover.outputs.chunk-list }})'
 
+  lint:
+    name: Check for missing containers
+    needs: setup
+    if: ${{ needs.setup.outputs.repository-list != '' || needs.setup.outputs.tool-list != '' }}
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ['3.11']
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        fetch-depth: 1
+    - uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Cache .cache/pip
+      uses: actions/cache@v4
+      id: cache-pip
+      with:
+        path: ~/.cache/pip
+        key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }}
+    - name: Planemo lint
+      uses: galaxyproject/planemo-ci-action@v1
+      id: lint
+      with:
+        mode: lint
+        repository-list: ${{ needs.setup.outputs.repository-list }}
+        tool-list: ${{ needs.setup.outputs.tool-list }}
+        additional-planemo-options: --biocontainers -s stdio,tests,output,inputs,help,general,command,citations,tool_xsd,xml_order,tool_urls,shed_metadata,urls,readme,shed_yaml,repository_dependencies,tool_dependencies_actions,tool_dependencies_sha256sum,tool_dependencies_xsd,expansion
+    - uses: actions/upload-artifact@v4
+      if: ${{ failure() }}
+      with:
+        name: 'Tool linting output'
+        path: lint_report.txt
+
   test:
     name: Test tools
     # This job runs on Linux
@@ -92,7 +128,7 @@ jobs:
       fail-fast: false
       matrix:
         chunk: ${{ fromJson(needs.setup.outputs.chunk-list) }}
-        python-version: ['3.7']
+        python-version: ['3.11']
     services:
       postgres:
         image: postgres:11
@@ -105,18 +141,23 @@ jobs:
     steps:
     # checkout the repository
     # and use it as the current working directory
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 1
-    - uses: actions/setup-python@v1
+    - uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
-      uses: actions/cache@v2
+      uses: actions/cache@v4
       id: cache-pip
       with:
         path: ~/.cache/pip
         key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }}
+    - name: Get number of CPU cores
+      uses: SimenB/github-actions-cpu-cores@v2
+      id: cpu-cores
+    - name: Clean dotnet folder for space
+      run: rm -Rf /usr/share/dotnet
     - name: Planemo test
       uses: galaxyproject/planemo-ci-action@v1
       id: test
@@ -127,7 +168,10 @@ jobs:
         galaxy-branch: ${{ needs.setup.outputs.branch }}
         chunk: ${{ matrix.chunk }}
         chunk-count: ${{ needs.setup.outputs.chunk-count }}
-    - uses: actions/upload-artifact@v2
+        galaxy-slots: ${{ steps.cpu-cores.outputs.count }}
+        # Limit each test to 15 minutes
+        test_timeout: 900
+    - uses: actions/upload-artifact@v4
       with:
         name: 'Tool test output ${{ matrix.chunk }}'
         path: upload
@@ -142,18 +186,18 @@ jobs:
     needs: [setup, test]
     strategy:
       matrix:
-        python-version: ['3.7']
+        python-version: ['3.11']
     # This job runs on Linux
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/download-artifact@v2
+    - uses: actions/download-artifact@v4
       with:
         path: artifacts
-    - uses: actions/setup-python@v1
+    - uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
-      uses: actions/cache@v2
+      uses: actions/cache@v4
       id: cache-pip
       with:
         path: ~/.cache/pip
@@ -164,19 +208,20 @@ jobs:
       with:
         mode: combine
         html-report: true
-    - uses: actions/upload-artifact@v2
+    - uses: actions/upload-artifact@v4
       with:
         name: 'All tool test results'
         path: upload
+    - run: cat upload/tool_test_output.md >> $GITHUB_STEP_SUMMARY
     - name: Create URL to the run output
       if: ${{ github.event.client_payload.slash_command.command == 'run-all-tool-tests' }}
       id: vars
-      run: echo "::set-output name=run-url::https://github.com/$GITHUB_REPOSITORY/actions/runs/$GITHUB_RUN_ID"
+      run: echo "run-url=https://github.com/$GITHUB_REPOSITORY/actions/runs/$GITHUB_RUN_ID" >> $GITHUB_OUTPUT
 
 # MODIFIED START
 #    - name: Create comment
 #      if: ${{ github.event.client_payload.slash_command.command == 'run-all-tool-tests' }}
-#      uses: peter-evans/create-or-update-comment@v1
+#      uses: peter-evans/create-or-update-comment@v4
 #      with:
 #        token: ${{ secrets.PAT }}
 #        repository: ${{ github.event.client_payload.github.payload.repository.full_name }}
@@ -190,7 +235,6 @@ jobs:
 #
 #          [1]: ${{ steps.vars.outputs.run-url }}
 # MODIFIED END
-
     - name: Check outputs
       uses: galaxyproject/planemo-ci-action@v1
       id: check