Read bonds from CIF/BCIF file #29
Workflow file for this run
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| # Based on the workflow from https://github.com/biotite-dev/biotite/ | |
| # contributed by Daniel Farrell (danpf) and published under the same license | |
| name: "CI & CD" | |
| on: | |
| workflow_dispatch: | |
| pull_request: | |
| release: | |
| types: | |
| - published | |
| env: | |
| CIBW_BUILD: cp310-* cp311-* cp312-* | |
| CIBW_ARCHS_LINUX: "x86_64" | |
| CIBW_ARCHS_MACOS: "x86_64 arm64" | |
| CIBW_ARCHS_WINDOWS: "x86 AMD64" | |
| # Skip musllinux because it takes too long to compile on GHA | |
| # since it is emulated. (6+ hours) | |
| # *note* most of the build time is actually numpy for musllinux | |
| CIBW_SKIP: "*musllinux* *-manylinux_i686 *-musllinux_i686 *-win32 pp*" | |
| CIBW_TEST_EXTRAS: test | |
| CIBW_TEST_COMMAND: pytest {project} --durations=50 | |
| CIBW_DEPENDENCY_VERSIONS: "pinned" | |
| # Runtime too long due to architecture emulation | |
| CIBW_TEST_SKIP: "*-macosx_arm64" | |
| jobs: | |
| lint: | |
| name: Check code style | |
| 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==0.5.2 | |
| - name: Check code formatting | |
| run: ruff format --diff | |
| - name: Lint code base | |
| run: ruff check | |
| test-and-build: | |
| name: "Build & Test" | |
| strategy: | |
| matrix: | |
| os: [ubuntu-latest, windows-latest, macos-latest] | |
| runs-on: ${{ matrix.os }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up QEMU | |
| if: runner.os == 'Linux' | |
| uses: docker/setup-qemu-action@v2 | |
| with: | |
| platforms: all | |
| - name: Build & (optionally) test wheels | |
| uses: pypa/cibuildwheel@v2.19.1 | |
| - uses: actions/upload-artifact@v3 | |
| with: | |
| name: dist | |
| path: ./wheelhouse/*.whl | |
| if-no-files-found: error | |
| make-sdist: | |
| name: Build source distribution | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| submodules: true | |
| - name: Build source distribution | |
| run: pipx run build --sdist | |
| - uses: actions/upload-artifact@v3 | |
| with: | |
| name: dist | |
| path: dist/*.tar.gz | |
| if-no-files-found: error | |
| make-doc: | |
| name: Build documentation | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| activate-environment: hydride | |
| auto-update-conda: true | |
| python-version: '3.11' | |
| - name: Installing dependencies | |
| run: conda install -c conda-forge sphinx cython numpy numpydoc biotite | |
| - name: Building documentation | |
| run: sphinx-build ./doc ./build/doc | |
| - name: Zipping documentation | |
| run: cd .//build; zip -r doc.zip doc; cd .. | |
| - uses: actions/upload-artifact@v3 | |
| with: | |
| name: doc | |
| path: build//doc.zip | |
| if-no-files-found: error | |
| upload: | |
| name: Upload to GitHub Releases & PyPI | |
| permissions: | |
| contents: write | |
| needs: | |
| - lint | |
| - test-and-build | |
| - make-sdist | |
| - make-doc | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/download-artifact@v3 | |
| - name: List distributions to be uploaded | |
| run: ls dist | |
| - name: Upload to GitHub Releases | |
| uses: softprops/action-gh-release@de2c0eb89ae2a093876385947365aca7b0e5f844 | |
| if: github.event_name == 'release' && github.event.action == 'published' | |
| with: | |
| files: | | |
| dist//* | |
| doc//* | |
| - name: Upload to PyPI | |
| uses: pypa/gh-action-pypi-publish@c7f29f7adef1a245bd91520e94867e5c6eedddcc | |
| if: github.event_name == 'release' && github.event.action == 'published' | |
| with: | |
| password: ${{ secrets.PYPI_TOKEN }} |