Update GitHub Actions (major) #10249
Workflow file for this run
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| name: Python tests | |
| # This workflow is triggered on pushes and PRs to the repository. | |
| # Only run if we changed a Python file | |
| on: | |
| push: | |
| branches: | |
| - dev | |
| # https://docs.renovatebot.com/key-concepts/automerge/#branch-vs-pr-automerging | |
| - "renovate/**" # branches Renovate creates | |
| paths-ignore: | |
| - "docs/**" | |
| - "CHANGELOG.md" | |
| pull_request: | |
| paths-ignore: | |
| - "docs/**" | |
| - "CHANGELOG.md" | |
| # ignore github workflows except for the current one | |
| - ".github/**" | |
| - "!.github/workflows/pytest.yml" | |
| release: | |
| types: [published] | |
| workflow_dispatch: | |
| # Cancel if a newer run with the same workflow name is queued | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| jobs: | |
| setup: | |
| runs-on: "ubuntu-latest" | |
| strategy: | |
| matrix: | |
| python-version: ["3.10", "3.14"] | |
| runner: ["ubuntu-latest"] | |
| steps: | |
| - name: Check conditions | |
| id: conditions | |
| run: echo "run-tests=${{ github.ref == 'refs/heads/main' || (matrix.runner == 'ubuntu-20.04' && matrix.python-version == '3.10') }}" >> "$GITHUB_OUTPUT" | |
| outputs: | |
| python-version: ${{ matrix.python-version }} | |
| runner: ${{ matrix.runner }} | |
| run-tests: ${{ steps.conditions.outputs.run-tests }} | |
| # create a test matrix based on all python files in /tests | |
| list_tests: | |
| name: Get test file matrix | |
| runs-on: "ubuntu-latest" | |
| steps: | |
| - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5 | |
| name: Check out source-code repository | |
| - name: List tests | |
| id: list_tests | |
| run: | | |
| echo "tests=$(find tests -type f -name "test_*.py" | tac | sed 's/tests\///g' | jq -R -s -c '{test: (split("\n")[:-1])}')" >> $GITHUB_OUTPUT | |
| outputs: | |
| tests: ${{ steps.list_tests.outputs.tests }} | |
| test: | |
| name: Run ${{matrix.test}} with Python ${{ needs.setup.outputs.python-version }} on ${{ needs.setup.outputs.runner }} | |
| needs: [setup, list_tests] | |
| if: ${{ needs.setup.outputs.run-tests }} | |
| runs-on: | |
| - runs-on=${{ github.run_id }}-run-test | |
| - runner=4cpu-linux-x64 | |
| strategy: | |
| matrix: ${{ fromJson(needs.list_tests.outputs.tests) }} | |
| fail-fast: false # run all tests even if one fails | |
| steps: | |
| - name: go to subdirectory and change nextflow workdir | |
| run: | | |
| mkdir -p pytest | |
| cd pytest | |
| export NXF_WORK=$(pwd) | |
| - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5 | |
| name: Check out source-code repository | |
| - name: Set up Python ${{ needs.setup.outputs.python-version }} | |
| uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6 | |
| with: | |
| python-version: ${{ needs.setup.outputs.python-version }} | |
| cache: "pip" | |
| token: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip -r requirements-dev.txt | |
| pip install -e . | |
| - name: Set up Singularity | |
| if: ${{ matrix.test == 'test_download.py'}} | |
| uses: eWaterCycle/setup-singularity@931d4e31109e875b13309ae1d07c70ca8fbc8537 # v7 | |
| with: | |
| singularity-version: 3.8.3 | |
| - name: Get current date | |
| id: date | |
| run: echo "date=$(date +'%Y-%m')" >> $GITHUB_ENV | |
| - name: Install Nextflow | |
| uses: nf-core/setup-nextflow@v2 | |
| - name: Install nf-test | |
| uses: nf-core/setup-nf-test@v1 | |
| - name: move coveragerc file up | |
| run: | | |
| mv .github/.coveragerc . | |
| - name: Test with pytest | |
| id: pytest | |
| run: | | |
| python3 -m pytest tests/${{matrix.test}} --color=yes --cov --cov-config=.coveragerc --durations=0 -n auto && exit_code=0|| exit_code=$? | |
| # don't fail if no tests were collected, e.g. for test_licence.py | |
| if [ "${exit_code}" -eq 5 ]; then | |
| echo "No tests were collected" | |
| exit 0 | |
| elif [ "${exit_code}" -ne 0 ]; then | |
| echo "Tests failed with exit code ${exit_code}" | |
| exit 1 | |
| fi | |
| - name: remove slashes from test name | |
| run: | | |
| test=$(echo ${{ matrix.test }} | sed 's/\//__/g') | |
| echo "test=${test}" >> $GITHUB_ENV | |
| - name: Store snapshot report | |
| uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5 | |
| if: always() && contains(matrix.test, 'test_create_app') && steps.pytest.outcome == 'failure' | |
| with: | |
| include-hidden-files: true | |
| name: Snapshot Report ${{ env.test }} | |
| path: ./snapshot_report.html | |
| - name: Upload coverage | |
| uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5 | |
| with: | |
| include-hidden-files: true | |
| name: coverage_${{ env.test }} | |
| path: .coverage | |
| coverage: | |
| needs: test | |
| runs-on: | |
| - runs-on=${{ github.run_id }}-coverage | |
| - runner=2cpu-linux-x64 | |
| steps: | |
| - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5 | |
| - name: Set up Python 3.14 | |
| uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6 | |
| with: | |
| python-version: "3.14" | |
| cache: "pip" | |
| - name: Install coverage | |
| run: | | |
| python -m pip install --upgrade pip coverage | |
| - name: move coveragerc file up | |
| run: | | |
| mv .github/.coveragerc . | |
| - name: Download all artifacts | |
| uses: actions/download-artifact@018cc2cf5baa6db3ef3c5f8a56943fffe632ef53 # v6 | |
| with: | |
| pattern: coverage_* | |
| - name: Run coverage | |
| run: | | |
| coverage combine --keep coverage_*/.coverage* | |
| coverage report | |
| coverage xml | |
| - uses: codecov/codecov-action@5a1091511ad55cbe89839c7260b706298ca349f7 # v5 | |
| with: | |
| files: coverage.xml | |
| disable_search: true # we already know the file to upload | |
| env: | |
| CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} |