Add Cython 3.0.11 generated files (#4798) #278
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| name: Build and upload to PyPI | |
| on: | |
| pull_request: | |
| branches: | |
| - "package-*" | |
| push: | |
| branches: | |
| - "package-*" | |
| tags: | |
| - "package-*" | |
| release: | |
| types: | |
| - published | |
| schedule: | |
| # 3 am Tuesdays and Fridays | |
| - cron: "0 3 * * 2,5" | |
| concurrency: | |
| group: "${{ github.ref }}-${{ github.head_ref }}-${{ github.workflow }}" | |
| cancel-in-progress: true | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| jobs: | |
| build_wheels: | |
| if: "github.repository == 'MDAnalysis/mdanalysis'" | |
| name: Build wheels | |
| runs-on: ${{ matrix.buildplat[0] }} | |
| timeout-minutes: 15 | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| buildplat: | |
| - [ubuntu-22.04, manylinux_x86_64, x86_64] | |
| - [macos-12, macosx_*, x86_64] | |
| - [windows-2019, win_amd64, AMD64] | |
| - [macos-14, macosx_*, arm64] | |
| python: ["cp310", "cp311", "cp312", "cp313"] | |
| defaults: | |
| run: | |
| working-directory: ./package | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: Build wheels | |
| uses: pypa/cibuildwheel@v2.20.0 | |
| with: | |
| package-dir: package | |
| env: | |
| CIBW_BUILD: ${{ matrix.python }}-${{ matrix.buildplat[1] }} | |
| CIBW_ARCHS: ${{ matrix.buildplat[2] }} | |
| CIBW_BUILD_VERBOSITY: 1 | |
| - name: upload artifacts | |
| if: | | |
| (github.event_name == 'push' && startsWith(github.ref, 'refs/tags/package')) || | |
| (github.event_name == 'release' && github.event.action == 'published') | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| path: wheelhouse/*.whl | |
| retention-days: 7 | |
| build_sdist: | |
| if: "github.repository == 'MDAnalysis/mdanalysis'" | |
| name: build package source distribution | |
| runs-on: ubuntu-latest | |
| timeout-minutes: 10 | |
| defaults: | |
| run: | |
| working-directory: ./package | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: Build sdist | |
| run: pipx run build --sdist | |
| - name: upload artifacts | |
| if: | | |
| (github.event_name == 'push' && startsWith(github.ref, 'refs/tags/package')) || | |
| (github.event_name == 'release' && github.event.action == 'published') | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| path: package/dist/*.tar.gz | |
| retention-days: 7 | |
| build_sdist_tests: | |
| if: "github.repository == 'MDAnalysis/mdanalysis'" | |
| name: build test source distribution | |
| runs-on: ubuntu-latest | |
| timeout-minutes: 10 | |
| defaults: | |
| run: | |
| working-directory: ./testsuite | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: Build sdist | |
| run: pipx run build --sdist | |
| - name: upload artifacts | |
| if: | | |
| (github.event_name == 'push' && startsWith(github.ref, 'refs/tags/package')) || | |
| (github.event_name == 'release' && github.event.action == 'published') | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| path: testsuite/dist/*.tar.gz | |
| retention-days: 7 | |
| upload_testpypi_mdanalysis: | |
| if: | | |
| github.repository == 'MDAnalysis/mdanalysis' && | |
| (github.event_name == 'push' && startsWith(github.ref, 'refs/tags/package')) | |
| name: testpypi_upload_mdanalysis | |
| environment: | |
| name: deploy | |
| url: https://test.pypi.org/p/mdanalysis | |
| permissions: | |
| id-token: write | |
| runs-on: ubuntu-latest | |
| needs: [build_wheels, build_sdist, build_sdist_tests] | |
| steps: | |
| - uses: actions/download-artifact@v3 | |
| with: | |
| name: artifact | |
| path: dist | |
| - name: move_test_dist | |
| run: | | |
| mkdir -p testsuite/dist | |
| mv dist/mdanalysistests-* testsuite/dist | |
| - name: upload_source_and_wheels | |
| uses: pypa/gh-action-pypi-publish@v1.11.0 | |
| with: | |
| skip_existing: true | |
| repository_url: https://test.pypi.org/legacy/ | |
| upload_testpypi_mdanalysistests: | |
| if: | | |
| github.repository == 'MDAnalysis/mdanalysis' && | |
| (github.event_name == 'push' && startsWith(github.ref, 'refs/tags/package')) | |
| name: testpypi_upload_mdanalysistests | |
| environment: | |
| name: deploy | |
| url: https://test.pypi.org/p/mdanalysis | |
| permissions: | |
| id-token: write | |
| runs-on: ubuntu-latest | |
| needs: [build_wheels, build_sdist, build_sdist_tests] | |
| steps: | |
| - uses: actions/download-artifact@v3 | |
| with: | |
| name: artifact | |
| path: dist | |
| - name: move_test_dist | |
| run: | | |
| mkdir -p testsuite/dist | |
| mv dist/mdanalysistests-* testsuite/dist | |
| - name: upload_tests | |
| uses: pypa/gh-action-pypi-publish@v1.11.0 | |
| with: | |
| packages_dir: testsuite/dist | |
| skip_existing: true | |
| repository_url: https://test.pypi.org/legacy/ | |
| upload_pypi_mdanalysis: | |
| if: | | |
| github.repository == 'MDAnalysis/mdanalysis' && | |
| github.event_name == 'release' && github.event.action == 'published' | |
| name: pypi_upload_mdanalysis | |
| environment: | |
| name: deploy | |
| url: https://pypi.org/p/mdanalysis | |
| permissions: | |
| id-token: write | |
| runs-on: ubuntu-latest | |
| needs: [build_wheels, build_sdist, build_sdist_tests] | |
| steps: | |
| - uses: actions/download-artifact@v3 | |
| with: | |
| name: artifact | |
| path: dist | |
| - name: move_test_dist | |
| run: | | |
| mkdir -p testsuite/dist | |
| mv dist/mdanalysistests-* testsuite/dist | |
| - name: upload_source_and_wheels | |
| uses: pypa/gh-action-pypi-publish@v1.11.0 | |
| upload_pypi_mdanalysistests: | |
| if: | | |
| github.repository == 'MDAnalysis/mdanalysis' && | |
| github.event_name == 'release' && github.event.action == 'published' | |
| name: pypi_upload_mdanalysistests | |
| environment: | |
| name: deploy | |
| url: https://pypi.org/p/mdanalysistests | |
| permissions: | |
| id-token: write | |
| runs-on: ubuntu-latest | |
| needs: [build_wheels, build_sdist, build_sdist_tests] | |
| steps: | |
| - uses: actions/download-artifact@v3 | |
| with: | |
| name: artifact | |
| path: dist | |
| - name: move_test_dist | |
| run: | | |
| mkdir -p testsuite/dist | |
| mv dist/mdanalysistests-* testsuite/dist | |
| - name: upload_tests | |
| uses: pypa/gh-action-pypi-publish@v1.11.0 | |
| with: | |
| packages_dir: testsuite/dist | |
| check_testpypi: | |
| if: | | |
| github.repository == 'MDAnalysis/mdanalysis' && | |
| (github.event_name == 'push' && startsWith(github.ref, 'refs/tags/package')) | |
| name: testpypi check | |
| runs-on: ${{ matrix.os }} | |
| timeout-minutes: 60 | |
| needs: [upload_testpypi_mdanalysis, upload_testpypi_mdanalysistests] | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-latest, macos-latest, windows-latest] | |
| python-version: ["3.10", "3.11", "3.12", "3.13"] | |
| type: ["FULL", "MIN"] | |
| exclude: | |
| # Multiple deps don't like windows | |
| - os: windows-latest | |
| type: "FULL" | |
| env: | |
| MPLBACKEND: agg | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: setup_micromamba | |
| uses: mamba-org/setup-micromamba@v2 | |
| with: | |
| environment-name: mda | |
| create-args: >- | |
| python=${{ matrix.python-version }} | |
| packaging | |
| pip | |
| # jaime's shim to avoid pulling down the cudatoolkit | |
| # bioconda for clustalw things | |
| condarc: | | |
| channels: | |
| - jaimergp/label/unsupported-cudatoolkit-shim | |
| - conda-forge | |
| - bioconda | |
| - name: install_full_deps | |
| uses: ./.github/actions/setup-deps | |
| if: "matrix.type == 'FULL'" | |
| with: | |
| micromamba: true | |
| full-deps: true | |
| - name: pip_install_mda | |
| run: | | |
| awk '/__version__ =/ {print $3; exit}' package/MDAnalysis/version.py | tr -d \" > version.dat | |
| ver=$(python maintainer/norm_version.py --file version.dat) | |
| pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple MDAnalysis==$ver | |
| pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple MDAnalysisTests==$ver | |
| - name: install_min_deps | |
| if: "matrix.type == 'MIN'" | |
| run: | | |
| pip install pytest-xdist pytest-timeout | |
| - name: run_tests | |
| run: | | |
| pytest --timeout=200 -n auto --pyargs MDAnalysisTests |