Add weekly CI (#292)

and missing workflow for "empty" PRs (e.g. changing only CI)
workflow4metabolomics · Jan 30, 2025 · 132c30f · 132c30f
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diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
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+name: Weekly global Tool Linting and Tests
+on:
+  schedule:
+    # Run at midnight every monday
+    - cron: '0 0 * * 1'
+  repository_dispatch:
+    types: [run-all-tool-tests-command]
+env:
+  GALAXY_FORK: galaxyproject
+  GALAXY_BRANCH: release_24.2
+  MAX_CHUNKS: 40
+jobs:
+  setup:
+    name: Setup cache and determine changed repositories
+    if: ${{ github.repository_owner == 'workflow4metabolomics' }}
+    runs-on: ubuntu-latest
+    outputs:
+      galaxy-head-sha: ${{ steps.get-galaxy-sha.outputs.galaxy-head-sha }}
+      fork: ${{ steps.get-fork-branch.outputs.fork }}
+      branch: ${{ steps.get-fork-branch.outputs.branch }}
+      repository-list: ${{ steps.discover.outputs.repository-list }}
+      chunk-count: ${{ steps.discover.outputs.chunk-count }}
+      chunk-list: ${{ steps.discover.outputs.chunk-list }}
+    strategy:
+      matrix:
+        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@v4
+      with:
+        token: ${{ secrets.PAT }}
+        repository: ${{ github.event.client_payload.github.payload.repository.full_name }}
+        comment-id: ${{ github.event.client_payload.github.payload.comment.id }}
+        reactions: hooray
+    - name: Set galaxy fork and branch
+      id: get-fork-branch
+      run: |
+        TMP="${{ github.event.client_payload.slash_command.args.named.fork }}"
+        echo "fork=${TMP:-$GALAXY_FORK}" >> $GITHUB_OUTPUT
+        TMP="${{ github.event.client_payload.slash_command.args.named.branch }}"
+        echo "branch=${TMP:-$GALAXY_BRANCH}" >> $GITHUB_OUTPUT
+    - name: Determine latest commit in the Galaxy repo
+      id: get-galaxy-sha
+      run: echo "galaxy-head-sha=$(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
+      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_${{ steps.get-galaxy-sha.outputs.galaxy-head-sha }}
+    # Install the `wheel` package so that when installing other packages which
+    # 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
+      with:
+        fetch-depth: 1
+    - name: Fake a Planemo run to update cache and determine commit range, repositories, and chunks
+      uses: galaxyproject/planemo-ci-action@v1
+      id: discover
+      with:
+        create-cache: ${{ steps.cache-pip.outputs.cache-hit != 'true' || steps.cache-planemo.outputs.cache-hit != 'true' }}
+        galaxy-fork: ${{ steps.get-fork-branch.outputs.fork }}
+        galaxy-branch: ${{ steps.get-fork-branch.outputs.branch }}
+        max-chunks: ${{ env.MAX_CHUNKS }}
+        python-version: ${{ matrix.python-version }}
+    - name: Show repository list
+      run: echo '${{ steps.discover.outputs.repository-list }}'
+    - name: Show chunks
+      run: |
+        echo 'Using ${{ steps.discover.outputs.chunk-count }} chunks (${{ steps.discover.outputs.chunk-list }})'
+
+  lint:
+    name: Lint tool-list
+    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
+        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
+      if: ${{ failure() }}
+      with:
+        name: 'Tool linting output'
+        path: lint_report.txt
+
+  test:
+    name: Test tools
+    # This job runs on Linux
+    runs-on: ubuntu-latest
+    needs: setup
+    if: ${{ needs.setup.outputs.repository-list != '' }}
+    strategy:
+      fail-fast: false
+      matrix:
+        chunk: ${{ fromJson(needs.setup.outputs.chunk-list) }}
+        python-version: ['3.11']
+    services:
+      postgres:
+        image: postgres:11
+        env:
+          POSTGRES_USER: postgres
+          POSTGRES_PASSWORD: postgres
+          POSTGRES_DB: postgres
+        ports:
+          - 5432:5432
+    steps:
+    # checkout the repository
+    # and use it as the current working directory
+    - 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: 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
+      with:
+        mode: test
+        repository-list: ${{ needs.setup.outputs.repository-list }}
+        galaxy-fork: ${{ needs.setup.outputs.fork }}
+        galaxy-branch: ${{ needs.setup.outputs.branch }}
+        chunk: ${{ matrix.chunk }}
+        chunk-count: ${{ needs.setup.outputs.chunk-count }}
+        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
+
+  # - combine the results of the test chunks (which will never fail due
+  #   to `|| true`) and create a global test report as json and html which
+  #   is provided as artifact
+  # - check if any tool test actually failed (by lookup in the combined json)
+  #   and fail this step if this is the case
+  combine_outputs:
+    name: Combine chunked test results
+    needs: [setup, test]
+    strategy:
+      matrix:
+        python-version: ['3.11']
+    # This job runs on Linux
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/download-artifact@v4
+      with:
+        path: artifacts
+    - 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: Combine outputs
+      uses: galaxyproject/planemo-ci-action@v1
+      id: combine
+      with:
+        mode: combine
+        html-report: true
+        markdown-report: true
+    - 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: ${{ github.event.client_payload.slash_command.command == 'run-all-tool-tests' }}
+      id: vars
+      run: echo "run-url=https://github.com/$GITHUB_REPOSITORY/actions/runs/$GITHUB_RUN_ID" >> $GITHUB_OUTPUT
+
+    - name: Create comment
+      if: ${{ github.event.client_payload.slash_command.command == 'run-all-tool-tests' }}
+      uses: peter-evans/create-or-update-comment@v4
+      with:
+        token: ${{ secrets.PAT }}
+        repository: ${{ github.event.client_payload.github.payload.repository.full_name }}
+        issue-number: ${{ github.event.client_payload.github.payload.issue.number }}
+        body: |
+          Summary:
+
+          ${{ steps.combine.outputs.statistics }}
+
+          [Find all tool test results here][1]
+
+          [1]: ${{ steps.vars.outputs.run-url }}
+    - name: Check outputs
+      uses: galaxyproject/planemo-ci-action@v1
+      id: check
+      with:
+        mode: check
diff --git a/.github/workflows/pr_without_tool_change.yaml b/.github/workflows/pr_without_tool_change.yaml
@@ -0,0 +1,15 @@
+name: Fallback
+# Fallback workflow that provides a succeeding "Check workflow success" job
+# as this is a requirement for being able to merge a PR
+# see https://docs.github.com/en/repositories/configuring-branches-and-merges-in-your-repository/defining-the-mergeability-of-pull-requests/troubleshooting-required-status-checks#handling-skipped-but-required-checks
+on:
+  pull_request:
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+jobs:
+  determine-success:
+    name: Check workflow success
+    runs-on: ubuntu-latest
+    steps:
+      -  run: 'echo "No tool tests required for this PR"'