Use pre commit for linting jobs #5839
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 | |
| paths-ignore: | |
| - "docs/**" | |
| - "CHANGELOG.md" | |
| pull_request: | |
| paths-ignore: | |
| - "docs/**" | |
| - "CHANGELOG.md" | |
| release: | |
| types: [published] | |
| # Cancel if a newer run is started | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| jobs: | |
| setup: | |
| runs-on: ["ubuntu-latest"] | |
| strategy: | |
| matrix: | |
| python-version: ["3.8", "3.11"] | |
| runner: ["ubuntu-latest"] | |
| include: | |
| - python-version: "3.8" | |
| runner: "ubuntu-20.04" | |
| steps: | |
| - name: Check conditions | |
| id: conditions | |
| run: echo "run-tests=${{ github.ref == 'refs/heads/master' || (matrix.runner == 'ubuntu-20.04' && matrix.python-version == '3.8') }}" >> "$GITHUB_OUTPUT" | |
| outputs: | |
| python-version: ${{ matrix.python-version }} | |
| runner: ${{ matrix.runner }} | |
| run-tests: ${{ steps.conditions.outputs.run-tests }} | |
| test: | |
| name: Test with Python ${{ needs.setup.outputs.python-version }} on ${{ needs.setup.outputs.runner }} | |
| needs: setup | |
| if: ${{ needs.setup.outputs.run-tests}} | |
| runs-on: ${{ needs.setup.outputs.runner }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| name: Check out source-code repository | |
| - name: Set up Python ${{ needs.setup.outputs.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ needs.setup.outputs.python-version }} | |
| cache: "pip" | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip -r requirements-dev.txt | |
| pip install -e . | |
| - name: Downgrade git to the Ubuntu official repository's version | |
| if: ${{ needs.setup.outputs.runner == 'ubuntu-20.04' && needs.setup.outputs.python-version == '3.8' }} | |
| run: | | |
| sudo apt update | |
| sudo apt remove -y git git-man | |
| sudo add-apt-repository --remove ppa:git-core/ppa | |
| sudo apt install -y git | |
| - name: Get current date | |
| id: date | |
| run: echo "date=$(date +'%Y-%m')" >> $GITHUB_ENV | |
| - name: Install Nextflow | |
| uses: nf-core/setup-nextflow@v1 | |
| with: | |
| version: "latest-everything" | |
| - name: Cache nf-test installation | |
| id: cache-software | |
| uses: actions/cache@v3 | |
| with: | |
| path: | | |
| /usr/local/bin/nf-test | |
| /home/runner/.nf-test/nf-test.jar | |
| key: ${{ runner.os }}-nftest-${{ env.date }} | |
| - name: Install nf-test | |
| if: steps.cache-software.outputs.cache-hit != 'true' | |
| run: | | |
| wget -qO- https://code.askimed.com/install/nf-test | bash | |
| sudo mv nf-test /usr/local/bin/ | |
| - name: Test with pytest | |
| run: python3 -m pytest tests/ --color=yes --cov-report=xml --cov-config=.github/.coveragerc --cov=nf_core | |
| - uses: codecov/codecov-action@v1 | |
| name: Upload code coverage report | |
| with: | |
| if: success() | |
| token: ${{ secrets.CODECOV_TOKEN }} |