feat: Adds optional param to translate_cds to allow for positional overrides #2
Workflow file for this run
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| # https://packaging.python.org/en/latest/guides/publishing-package-distribution-releases-using-github-actions-ci-cd-workflows/ | |
| name: Python package | |
| on: | |
| push: | |
| tags: | |
| - '[0-9]+.[0-9]+.[0-9]+' # release | |
| - '[0-9]+.[0-9]+.[0-9]+a[0-9]+' # alpha | |
| - '[0-9]+.[0-9]+.[0-9]+b[0-9]+' # beta | |
| - '[0-9]+.[0-9]+.[0-9]+rc[0-9]+' # release candidate | |
| - '[0-9]+.[0-9]+.[0-9]+.dev[0-9]+' # dev (not semver compliant) | |
| - '[0-9]+.[0-9]+.[0-9]+.post[0-9]+' # post (not semver compliant) | |
| pull_request: | |
| jobs: | |
| cqa: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: awalsh128/cache-apt-pkgs-action@latest | |
| with: | |
| packages: zsh | |
| version: 1.0 | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.12" | |
| cache: pip | |
| cache-dependency-path: '**/pyproject.yaml' | |
| - name: Install test dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install --use-deprecated=legacy-resolver -e .[dev,test] | |
| - name: Lint with Ruff | |
| run: | | |
| ruff check . | |
| - name: Format check with Ruff | |
| run: | | |
| ruff format --check . | |
| test: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: ["3.10", "3.11", "3.12"] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: awalsh128/cache-apt-pkgs-action@latest | |
| with: | |
| packages: zsh | |
| version: 1.0 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| cache: pip | |
| cache-dependency-path: '**/setup.cfg' | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| make develop | |
| - name: Test with pytest | |
| run: | | |
| make test | |
| - name: Upload coverage data to Codecov | |
| run: | | |
| # Verify integrity of codecov download | |
| curl https://uploader.codecov.io/verification.gpg | gpg --no-default-keyring --keyring trustedkeys.gpg --import | |
| curl -Os https://uploader.codecov.io/latest/linux/codecov | |
| curl -Os https://uploader.codecov.io/latest/linux/codecov.SHA256SUM | |
| curl -Os https://uploader.codecov.io/latest/linux/codecov.SHA256SUM.sig | |
| gpgv codecov.SHA256SUM.sig codecov.SHA256SUM | |
| shasum -a 256 -c codecov.SHA256SUM | |
| # Upload coverage report | |
| chmod +x codecov | |
| ./codecov | |
| build: | |
| name: Build distribution | |
| if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags') | |
| runs-on: ubuntu-latest | |
| needs: | |
| - cqa | |
| - test | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.12" | |
| cache: pip | |
| cache-dependency-path: '**/setup.cfg' | |
| - name: Install pypa/build | |
| run: >- | |
| python3 -m | |
| pip install | |
| build | |
| --user | |
| - name: Build a binary wheel and a source tarball | |
| run: python3 -m build | |
| - name: Store the distribution packages | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: python-package-distributions | |
| path: dist/ | |
| publish-to-pypi: | |
| name: >- | |
| Publish Python distribution to PyPI | |
| needs: | |
| - build | |
| runs-on: ubuntu-latest | |
| environment: | |
| name: pypi | |
| url: https://pypi.org/p/bioutils | |
| permissions: | |
| id-token: write # IMPORTANT: mandatory for trusted publishing | |
| steps: | |
| - name: Download all the dists | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: python-package-distributions | |
| path: dist/ | |
| - name: Publish distribution to PyPI | |
| uses: pypa/gh-action-pypi-publish@release/v1 |