more tries #352
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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", "3.12"] | ||
| runner: ["ubuntu-latest"] | ||
| include: | ||
| - runner: "ubuntu-20.04" | ||
| python-version: "3.8" | ||
| outputs: | ||
| python-version: ${{ matrix.python-version }} | ||
| runner: ${{ matrix.runner }} | ||
| test: | ||
| name: Test with Python ${{ needs.setup.outputs.python-version }} on ${{ needs.setup.outputs.runner }} | ||
| needs: setup | ||
| if: ${{ github.ref == 'refs/heads/master' || (needs.setup.outputs.python-version == 'ubuntu-20.04' && needs.setup.outputs.runner == '3.8') }} | ||
| runs-on: ${{ needs.setup.outputs.runner }} | ||
| steps: | ||
| - uses: actions/checkout@v2 | ||
| name: Check out source-code repository | ||
| - name: Set up Python ${{ needs.setup.outputs.python-version }} | ||
| uses: actions/setup-python@v2 | ||
| 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 }} | ||
