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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,247 @@ | ||
| name: Build and upload to PyPI | ||
|
|
||
| on: | ||
| pull_request: | ||
| branches: | ||
| - "package-*" | ||
| push: | ||
| branches: | ||
| - "package-*" | ||
| tags: | ||
| - "package-*" | ||
| release: | ||
| types: | ||
| - published | ||
|
|
||
|
|
||
| concurrency: | ||
| group: "${{ github.ref }}-${{ github.head_ref }}-${{ github.workflow }}" | ||
| cancel-in-progress: true | ||
|
|
||
|
|
||
| defaults: | ||
| run: | ||
| shell: bash -l {0} | ||
|
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||
|
|
||
| jobs: | ||
| build_wheels: | ||
| if: "github.repository == 'MDAnalysis/mdanalysis'" | ||
| name: Build wheels | ||
| runs-on: ${{ matrix.buildplat[0] }} | ||
| strategy: | ||
| fail-fast: false | ||
| matrix: | ||
| buildplat: | ||
| - [ubuntu-18.04, manylinux_x86_64] | ||
| - [macos-10.15, macosx_*] | ||
| - [windows-2019, win_amd64] | ||
| python: ["cp38", "cp39", "cp310"] | ||
| defaults: | ||
| run: | ||
| working-directory: ./package | ||
| steps: | ||
| - uses: actions/checkout@v3 | ||
| with: | ||
| fetch-depth: 0 | ||
|
|
||
| - name: Build wheels | ||
| uses: pypa/[email protected] | ||
| with: | ||
| package-dir: package | ||
| env: | ||
| CIBW_BUILD: ${{ matrix.python }}-${{ matrix.buildplat[1] }} | ||
| 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@v2 | ||
| with: | ||
| path: wheelhouse/*.whl | ||
| retention-days: 7 | ||
|
|
||
| build_sdist: | ||
| if: "github.repository == 'MDAnalysis/mdanalysis'" | ||
| name: build package source distribution | ||
| runs-on: ubuntu-latest | ||
| defaults: | ||
| run: | ||
| working-directory: ./package | ||
| steps: | ||
| - uses: actions/checkout@v3 | ||
| 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@v2 | ||
| 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 | ||
| defaults: | ||
| run: | ||
| working-directory: ./testsuite | ||
| steps: | ||
| - uses: actions/checkout@v3 | ||
| 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@v2 | ||
| with: | ||
| path: testsuite/dist/*.tar.gz | ||
| retention-days: 7 | ||
|
|
||
| upload_testpypi: | ||
| if: | | ||
| github.repository == 'MDAnalysis/mdanalysis' && | ||
| (github.event_name == 'push' && startsWith(github.ref, 'refs/tags/package')) | ||
| name: testpypi upload | ||
| environment: deploy | ||
| runs-on: ubuntu-latest | ||
| needs: [build_wheels, build_sdist, build_sdist_tests] | ||
| steps: | ||
| - uses: actions/download-artifact@v2 | ||
| 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/[email protected] | ||
| with: | ||
| user: __token__ | ||
| password: ${{ secrets.TESTPYPI_API_TOKEN_SRC }} | ||
| skip_existing: true | ||
| repository_url: https://test.pypi.org/legacy/ | ||
|
|
||
| - name: upload_tests | ||
| uses: pypa/[email protected] | ||
| with: | ||
| user: __token__ | ||
| password: ${{ secrets.TESTPYPI_API_TOKEN_TEST }} | ||
| packages_dir: testsuite/dist | ||
| skip_existing: true | ||
| repository_url: https://test.pypi.org/legacy/ | ||
|
|
||
| upload_pypi: | ||
| if: | | ||
| github.repository == 'MDAnalysis/mdanalysis' && | ||
| github.event_name == 'release' && github.event.action == 'published' | ||
| name: pypi upload | ||
| environment: deploy | ||
| runs-on: ubuntu-latest | ||
| needs: [build_wheels, build_sdist, build_sdist_tests] | ||
| steps: | ||
| - uses: actions/download-artifact@v2 | ||
| 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/[email protected] | ||
| with: | ||
| user: __token__ | ||
| password: ${{ secrets.PYPI_API_TOKEN_SRC }} | ||
|
|
||
| - name: upload_tests | ||
| uses: pypa/[email protected] | ||
| with: | ||
| user: __token__ | ||
| password: ${{ secrets.PYPI_API_TOKEN_TEST }} | ||
| 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 }} | ||
| needs: upload_testpypi | ||
| strategy: | ||
| fail-fast: false | ||
| matrix: | ||
| os: [ubuntu-latest, macos-latest, windows-latest] | ||
| python-version: ["3.8", "3.9", "3.10"] | ||
| type: ["FULL", "MIN"] | ||
| exclude: | ||
| # Multiple deps don't like windows | ||
| - os: windows-latest | ||
| python-version: "3.8" | ||
| type: "FULL" | ||
| - os: windows-latest | ||
| python-version: "3.9" | ||
| type: "FULL" | ||
| - os: windows-latest | ||
| python-version: "3.10" | ||
| type: "FULL" | ||
| # OpenMM isn't available for this yet | ||
| - os: macos-latest | ||
| python-version: "3.10" | ||
| type: "FULL" | ||
| env: | ||
| MPLBACKEND: agg | ||
|
|
||
| steps: | ||
| - uses: actions/checkout@v3 | ||
|
|
||
| - name: setup_miniconda | ||
| uses: conda-incubator/setup-miniconda@v2 | ||
| with: | ||
| python-version: ${{ matrix.python-version }} | ||
| auto-update-conda: true | ||
| channel-priority: flexible | ||
| channels: conda-forge, bioconda | ||
| add-pip-as-python-dependency: true | ||
| mamba-version: "*" | ||
| architecture: x64 | ||
|
|
||
| - name: install_full_deps | ||
| uses: ./.github/actions/setup-deps | ||
| if: "matrix.type == 'FULL'" | ||
| with: | ||
| mamba: true | ||
| full-deps: true | ||
|
|
||
| - name: install_min_deps | ||
| if: "matrix.type == 'MIN'" | ||
| run: | | ||
| pip install pytest pytest-xdist | ||
| - name: pip_install_mda | ||
| run: | | ||
| awk '/__version__ =/ {print $3; quit}' package/MDAnalysis/version.py | tr -d \" > version.dat | ||
| ver=$(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: run_tests | ||
| run: | | ||
| pytest -n2 --pyargs MDAnalysisTests |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,32 @@ | ||
| from packaging.version import Version | ||
|
|
||
|
|
||
| def norm_version(version_str: str): | ||
| """ | ||
| Normalize an input version string in the same way that setuptools' dist | ||
| does. | ||
| Parameters | ||
| ---------- | ||
| version_str : str | ||
| A version string to normalize. | ||
| Returns | ||
| ------- | ||
| str | ||
| Normalised version string | ||
| """ | ||
| return str(Version(version_str)) | ||
|
|
||
|
|
||
| if __name__ == "__main__": | ||
| import argparse | ||
|
|
||
| parser = argparse.ArgumentParser() | ||
| parser.add_argument('--file', type=str, help="file with version to parse") | ||
| args = parser.parse_args() | ||
|
|
||
| with open(args.file) as filed: | ||
| ver = filed.readlines()[0].strip("\n") | ||
|
|
||
| print(norm_version(version_str=ver)) |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,32 @@ | ||
| DL_POLY Classic: example of HISTORY | ||
| 0 1 3 | ||
| timestep 1 3 0 1 0.000500 | ||
| 35.607 0.000 0.000 | ||
| 0.000 35.607 0.000 | ||
| 0.000 0.000 35.607 | ||
| C 1 39.098300 0.994000 | ||
| -1.3006E+01 1.1459E+01 -1.6983E+01 | ||
| B 2 39.098300 0.994000 | ||
| -1.1628E+01 1.0204E+01 -1.7025E+01 | ||
| A 3 39.098300 0.994000 | ||
| -1.4345E+01 1.2719E+01 -1.6813E+01 | ||
| timestep 2001 3 0 1 0.000500 | ||
| 35.607 0.000 0.000 | ||
| 0.000 35.607 0.000 | ||
| 0.000 0.000 35.607 | ||
| C 1 39.098300 0.994000 | ||
| -1.2998E+01 1.1186E+01 -1.7425E+01 | ||
| B 1 39.098300 0.994000 | ||
| -1.1677E+01 9.9189E+00 -1.7225E+01 | ||
| A 1 39.098300 0.994000 | ||
| -1.4141E+01 1.2646E+01 -1.7451E+01 | ||
| timestep 4001 3 0 1 0.000500 | ||
| 35.607 0.000 0.000 | ||
| 0.000 35.607 0.000 | ||
| 0.000 0.000 35.607 | ||
| C 1 39.098300 0.994000 | ||
| -1.3124E+01 1.1173E+01 -1.7308E+01 | ||
| B 1 39.098300 0.994000 | ||
| -1.1651E+01 1.0041E+01 -1.7020E+01 | ||
| A 1 39.098300 0.994000 | ||
| -1.4614E+01 1.2287E+01 -1.7416E+01 |
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