Merge pull request #176 from teepean/plink_support #326
Workflow file for this run
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| # https://docs.github.com/en/actions | |
| # https://github.com/codecov/example-python | |
| # https://stackoverflow.com/a/3237883 | |
| # https://stackoverflow.com/a/5688592 | |
| # https://stackoverflow.com/a/6270803 | |
| # https://github.com/actions/virtual-environments/issues/1341 | |
| name: CI | |
| on: | |
| schedule: | |
| - cron: '37 4 * * 0' | |
| push: | |
| branches: | |
| - '**' | |
| pull_request: | |
| branches: | |
| - '**' | |
| jobs: | |
| enable-workflow: | |
| runs-on: ubuntu-latest | |
| if: ${{ github.event_name == 'push' || github.event_name == 'pull_request' || (github.event_name == 'schedule' && github.repository == 'apriha/snps') }} | |
| steps: | |
| - name: Enable workflow based on preconditions | |
| run: echo "Workflow enabled." | |
| lint-format: | |
| needs: [enable-workflow] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.12' | |
| - name: Install Ruff | |
| run: | | |
| pip install ruff | |
| - name: Lint with Ruff | |
| run: | | |
| ruff check | |
| - name: Format with Ruff | |
| run: | | |
| ruff format --check | |
| build-docs: | |
| needs: [enable-workflow] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.12' | |
| - name: Install Sphinx | |
| run: | | |
| pip install -r docs/requirements.txt | |
| pip install . | |
| - name: Build docs with Sphinx | |
| run: | | |
| sphinx-build -W --keep-going -T -E -D language=en docs docs/_build | |
| test: | |
| needs: [lint-format, build-docs] | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: [ubuntu-latest] | |
| python-version: ['3.8', '3.9', '3.10', '3.11', '3.12'] | |
| include: | |
| - os: macos-latest | |
| python-version: '3.12' | |
| - os: windows-latest | |
| python-version: '3.12' | |
| env: | |
| JOB_ID: ${{ strategy.job-index }} | |
| NUM_JOBS: ${{ strategy.job-total }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| persist-credentials: false | |
| - name: Setup Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Ensure Python and source code are on same drive (Windows) | |
| if: ${{ matrix.os == 'windows-latest' }} | |
| shell: cmd | |
| run: | | |
| mkdir C:\a | |
| xcopy D:\a C:\a /s /e | |
| - name: Determine if downloads are enabled for this job | |
| # for testing, limit downloads from the resource servers to only the selected job for | |
| # PRs and the master branch; note that the master branch is tested weekly via `cron`, | |
| # so this ensures all Python versions will be periodically integration tested with the | |
| # resource servers | |
| if: ${{ github.event_name == 'pull_request' || github.ref == 'refs/heads/master' }} | |
| shell: bash | |
| run: | | |
| SELECTED_JOB=$((10#$(date +%V) % $NUM_JOBS)) | |
| if [[ $SELECTED_JOB == $JOB_ID ]]; then | |
| # set environment variable to download resources for selected job | |
| echo "DOWNLOADS_ENABLED=true" >> $GITHUB_ENV | |
| fi | |
| - name: Install dependencies | |
| run: | | |
| pip install pytest-cov | |
| pip install . | |
| - name: Test with pytest (Ubuntu & macOS) | |
| if: ${{ matrix.os != 'windows-latest' }} | |
| run: | | |
| pytest --cov=snps tests | |
| - name: Test with pytest (Windows) | |
| if: ${{ matrix.os == 'windows-latest' }} | |
| working-directory: C:\a\snps\snps | |
| run: | | |
| pytest --cov=snps tests | |
| - name: Upload coverage to Codecov | |
| uses: codecov/codecov-action@v4 | |
| test-extras: | |
| needs: [lint-format, build-docs] | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: [ubuntu-latest] | |
| python-version: ['3.8', '3.9', '3.10', '3.11'] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| persist-credentials: false | |
| - name: Setup Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: | | |
| pip install --upgrade pip setuptools wheel | |
| pip install pytest-cov | |
| pip install .[ezancestry] | |
| - name: Test with pytest | |
| run: | | |
| pytest --cov=snps tests |