Improve documentation and code of ancestry readers/writers. Solve variants_alt inconsistency. Rename phased to sum_strands and set default to False #22
Workflow file for this run
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| # File: .github/workflows/release.yml | |
| # This workflow handles: | |
| # 1. For Pull Requests: | |
| # - Runs all tests | |
| # - Verifies documentation builds | |
| # 2. For Pre-releases: | |
| # - Runs all tests | |
| # - Builds documentation | |
| # - Deploys documentation to GitHub Pages | |
| # - Publishes package to PyPI | |
| # - If everything passes: | |
| # - Updates the release to a full release (removes pre-release status) | |
| name: Test, Docs & Publish | |
| on: | |
| # Run on pull requests to main branch to verify changes | |
| pull_request: | |
| branches: | |
| - main | |
| # Run when a new release is published to deploy docs and package | |
| release: | |
| types: [published] | |
| permissions: | |
| contents: write # Needed to update release status | |
| pages: write # Needed for docs deployment | |
| id-token: write # Needed for docs deployment | |
| jobs: | |
| test: | |
| if: github.event_name == 'pull_request' || (github.event_name == 'release' && github.event.release.prerelease == true) | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ['3.8', '3.13'] # Test on limit versions (3.8 and latest) | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 # Fetch full repository history, including all tags | |
| - name: Verify available tags | |
| run: git tag -l | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| cache: "pip" # Enables automatic pip caching | |
| # Cache test data | |
| - name: Cache test data | |
| uses: actions/cache@v4 | |
| with: | |
| path: data/ | |
| key: snputils-test-data-${{ hashFiles('snputils/snp/io/read/__test__/conftest.py') }} | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install tox tox-gh-actions | |
| - name: Run tests | |
| run: python -m tox | |
| build-docs: | |
| # Only build documentation after tests have passed | |
| needs: test | |
| if: needs.test.result == 'success' && (github.event_name == 'pull_request' || (github.event_name == 'release' && github.event.release.prerelease == true)) | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 # Fetch full repository history, including all tags | |
| - name: Verify available tags | |
| run: git tag -l | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.13' # Ensure this is the latest Python version so the cached deps are used | |
| cache: 'pip' | |
| - name: Install package with docs dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install '.[docs]' | |
| # Build documentation and verify it builds correctly | |
| # DOC_ALLOW_EXEC=1 allows executing code examples in docstrings | |
| - name: Build documentation | |
| run: DOC_ALLOW_EXEC=1 pdoc --docformat google -o docs/ snputils | |
| # Upload Pages artifact if this is a release | |
| - name: Upload Pages artifact | |
| if: github.event_name == 'release' | |
| uses: actions/upload-pages-artifact@v3 | |
| with: | |
| path: docs/ | |
| deploy: | |
| needs: [test, build-docs] | |
| if: needs.build-docs.result == 'success' && github.event_name == 'release' && github.event.release.prerelease == true | |
| runs-on: ubuntu-latest | |
| environment: | |
| name: github-pages | |
| url: ${{ steps.deployment.outputs.page_url }} | |
| steps: | |
| # Deploy documentation to GitHub Pages | |
| - name: Deploy to GitHub Pages | |
| id: deployment | |
| uses: actions/deploy-pages@v4 | |
| # Build and publish to PyPI | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 # Fetch full repository history, including all tags | |
| - name: Verify available tags | |
| run: git tag -l | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.13' # Ensure this is the latest Python version so the cached deps are used | |
| cache: 'pip' | |
| - name: Install build dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install build | |
| - name: Build package | |
| run: python -m build | |
| - name: Publish package to PyPI | |
| uses: pypa/gh-action-pypi-publish@release/v1 | |
| with: | |
| user: __token__ | |
| password: ${{ secrets.PYPI_API_TOKEN }} | |
| # Update the release to a full release and mark it as latest | |
| - name: Mark Release as Final and Latest | |
| if: success() | |
| env: | |
| GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| run: | | |
| gh release edit ${{ github.event.release.tag_name }} --prerelease=false --latest |