update CI

.github/workflows/ci.yaml

@@ -7,7 +7,7 @@ on:
     types: [run-all-tool-tests-command]
 env:
   GALAXY_FORK: galaxyproject
-  GALAXY_BRANCH: release_23.0
+  GALAXY_BRANCH: release_23.2
   MAX_CHUNKS: 40
 jobs:
   setup:
@@ -23,7 +23,7 @@ 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' }}
@@ -74,6 +74,42 @@ 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@v3
+      with:
+        fetch-depth: 1
+    - uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Cache .cache/pip
+      uses: actions/cache@v3
+      id: cache-pip
+      with:
+        path: ~/.cache/pip
+        key: pip_cache_py_${{ 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 tests,output,inputs,help,general,command,citations,tool_xsd,xml_order,tool_urls,shed_metadata
+    - uses: actions/upload-artifact@v3
+      if: ${{ failure() }}
+      with:
+        name: 'Tool linting output'
+        path: lint_report.txt
+
   test:
     name: Test tools
     # This job runs on Linux
@@ -84,7 +120,7 @@ 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
@@ -142,7 +178,7 @@ jobs:
     needs: [setup, test]
     strategy:
       matrix:
-        python-version: ['3.7']
+        python-version: ['3.11']
     # This job runs on Linux
     runs-on: ubuntu-latest
     steps:

.github/workflows/pr.yaml

@@ -1,13 +1,23 @@
 name: Galaxy Tool Linting and Tests for push and PR
 on:
   pull_request:
+    paths-ignore:
+      - '.github/**'
+      - 'deprecated/**'
+      - 'docs/**'
+      - '*'
   push:
     branches:
       - main
       - master
+    paths-ignore:
+      - '.github/**'
+      - 'deprecated/**'
+      - 'docs/**'
+      - '*'
 env:
   GALAXY_FORK: galaxyproject
-  GALAXY_BRANCH: release_23.0
+  GALAXY_BRANCH: release_23.2
   MAX_CHUNKS: 4
   MAX_FILE_SIZE: 1M
 concurrency:
@@ -35,7 +45,7 @@ jobs:
       commit-range: ${{ steps.discover.outputs.commit-range }}
     strategy:
       matrix:
-        python-version: ['3.7']
+        python-version: ['3.11']
     steps:
     - name: Print github context properties
       run: |
@@ -101,7 +111,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.7']
+        python-version: ['3.11']
     steps:
     - uses: actions/checkout@v3
       with:
@@ -115,11 +125,21 @@ jobs:
       with:
         path: ~/.cache/pip
         key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }}
+
+    - name: Set fail level for pull request
+      if: ${{ github.event_name == 'pull_request' }}
+      run:
+        echo "FAIL_LEVEL=warn" >> "$GITHUB_ENV"
+    - name: Set fail level for merge
+      if: ${{ github.event_name != 'pull_request' }}
+      run:
+        echo "FAIL_LEVEL=error" >> "$GITHUB_ENV"
     - name: Planemo lint
       uses: galaxyproject/planemo-ci-action@v1
       id: lint
       with:
         mode: lint
+        fail-level: ${{ env.FAIL_LEVEL }}
         repository-list: ${{ needs.setup.outputs.repository-list }}
         tool-list: ${{ needs.setup.outputs.tool-list }}
     - uses: actions/upload-artifact@v3
@@ -132,12 +152,12 @@ jobs:
   flake8:
     name: Lint Python scripts
     needs: setup
-    if: ${{ needs.setup.outputs.repository-list != '' }}
+    if: ${{ github.event_name == 'pull_request' && needs.setup.outputs.repository-list != '' }}
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.7']
+        python-version: ['3.11']
     steps:
     - uses: actions/checkout@v3
       with:
@@ -164,7 +184,7 @@ jobs:
   lintr:
     name: Lint R scripts
     needs: setup
-    if: ${{ needs.setup.outputs.repository-list != '' }}
+    if: ${{ github.event_name == 'pull_request' && needs.setup.outputs.repository-list != '' }}
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
@@ -258,7 +278,7 @@ 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
@@ -290,6 +310,8 @@ jobs:
     - name: Get number of CPU cores
       uses: SimenB/github-actions-cpu-cores@v1
       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
@@ -316,11 +338,11 @@ jobs:
   combine_outputs:
     name: Combine chunked test results
     needs: [setup, test]
-    if: ${{ needs.setup.outputs.repository-list != '' }}
+    if: ${{ always() && needs.setup.outputs.repository-list != '' }}
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.7']
+        python-version: ['3.11']
     steps:
     - uses: actions/download-artifact@v3
       with:
@@ -340,6 +362,7 @@ jobs:
       with:
         mode: combine
         html-report: true
+        markdown-report: true
     - uses: actions/upload-artifact@v3
       with:
         name: 'All tool test results'
@@ -349,16 +372,44 @@ jobs:
       id: check
       with:
         mode: check
+    - name: Check if all test chunks succeeded
+      run: |
+        NFILES=$(ls artifacts/ | grep "Tool test output" | wc -l)
+        if [[ "${{ needs.setup.outputs.chunk-count }}" != "$NFILES" ]]; then
+          exit 1
+        fi
+    - run: cat upload/tool_test_output.md >> $GITHUB_STEP_SUMMARY
+    # the following only works for PRs opened from the main fork
+    # which we should not do (but lets leave this here until we have a
+    # solution)
+    - name: Get PR object
+      if: failure()
+      uses: 8BitJonny/[email protected]
+      id: failed_pr_number
+      with:
+        sha: ${{ github.event.pull_request.head.sha }}
+    - name: Debug GetPR output
+      if: failure()
+      run: |
+          echo ${{ steps.failed_pr_number.outputs.number }}
+    - name: Post comment with test report
+      if: failure()
+      uses: peter-evans/create-or-update-comment@v3
+      with:
+        token: ${{ secrets.PAT }}
+        issue-number: ${{ steps.failed_pr_number.outputs.number }}
+        body-path: upload/tool_test_output.md
+
 
   # deploy the tools to the toolsheds (first TTS for testing)
   deploy:
     name: Deploy
-    needs: [setup, lint, flake8, lintr, combine_outputs]
+    needs: [setup, lint, combine_outputs]
     if: ${{ (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main' ) && github.repository_owner == 'bgruening' }}
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.7']
+        python-version: ['3.11']
     steps:
     - uses: actions/checkout@v3
       with: