guess and filebonds options for Molecule.get #753
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| name: Test code and publish package | |
| on: [push] | |
| jobs: | |
| test: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: ["ubuntu-latest", "macos-latest", "macos-13", "windows-2019"] | |
| python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"] | |
| defaults: # Needed for conda | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| lfs: true | |
| submodules: true | |
| - uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| mamba-version: "*" | |
| miniforge-variant: Mambaforge | |
| channels: acellera,conda-forge,defaults | |
| - name: Lint with flake8 | |
| run: | | |
| pip install flake8 coverage pytest-cov pytest pytest-subtests | |
| # stop the build if there are Python syntax errors or undefined names | |
| flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics | |
| # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide | |
| flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics | |
| - name: Install moleculekit conda deps. Force rdkit version for tests | |
| run: | | |
| mamba install -y -q --file extra_requirements.txt python=${{ matrix.python-version }} -c acellera -c conda-forge | |
| mamba install -y rdkit=2024.03.4 | |
| # scikit-learn, joblib, biopython are only used for rarely-used functions in smallmol | |
| mamba install -y -q scikit-learn joblib biopython -c conda-forge | |
| # - name: Install cdpkit | |
| # if: ${{ matrix.os == 'ubuntu-latest' }} | |
| # run: | | |
| # # for testing CDPKit SmallMol | |
| # pip install cdpkit | |
| - name: Install moleculekit | |
| run: | | |
| pip install "numpy>=1.18.5" "Cython>=0.29.21" | |
| pip install . | |
| pip install "versioneer==0.28" | |
| python setup.py build_ext --inplace | |
| - name: List conda environment | |
| run: mamba list | |
| - name: Test | |
| run: | | |
| pytest ./moleculekit | |
| env: | |
| GITHUB_ACTIONS: 1 | |
| # - name: Upload coverage to Codecov | |
| # uses: codecov/codecov-action@v3 | |
| deploypypi: | |
| if: startsWith(github.event.ref, 'refs/tags/') | |
| needs: test | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: ["ubuntu-latest"] | |
| python-version: ["3.9"] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| activate-environment: deploy | |
| python-version: ${{ matrix.python-version }} | |
| - name: Build PyPI 📦 | |
| run: | | |
| pip install numpy>=1.18.5 Cython>=0.29.21 build | |
| python -m build --sdist --outdir dist/ . | |
| - name: Publish distribution 📦 to PyPI | |
| uses: pypa/gh-action-pypi-publish@release/v1 | |
| with: | |
| password: ${{ secrets.PUBLIC_PYPI_API_TOKEN }} | |
| skip_existing: true | |
| deploy_linux: | |
| if: startsWith(github.event.ref, 'refs/tags/') | |
| needs: test | |
| runs-on: ${{ matrix.os }} | |
| container: ${{ matrix.container }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: ["ubuntu-latest"] | |
| python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"] | |
| container: ["quay.io/pypa/manylinux_2_28_x86_64"] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| miniconda-version: "latest" | |
| activate-environment: ../deploy-env | |
| python-version: ${{ matrix.python-version }} | |
| - name: Build moleculekit package | |
| shell: bash -l {0} | |
| run: | | |
| git config --global --add safe.directory '*' | |
| conda install anaconda-client conda-build python=${{ matrix.python-version }} toml | |
| pip install versioneer==0.28 | |
| python package/moleculekit/insert_placeholder_values.py | |
| conda build --python ${{ matrix.python-version }} package/moleculekit/ --output-folder ./pkg/ --no-include-recipe --no-anaconda-upload -c acellera -c conda-forge | |
| - name: Upload to conda | |
| shell: bash -l {0} | |
| run: | | |
| anaconda -t ${{ secrets.ANACONDA_TOKEN_BASIC }} upload -u acellera ./pkg/*/moleculekit-*.tar.bz2 | |
| deploy_osx_win: | |
| if: startsWith(github.event.ref, 'refs/tags/') | |
| needs: test | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: ["macos-latest", "macos-13", "windows-2019"] | |
| python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| miniconda-version: "latest" | |
| activate-environment: ../deploy-env | |
| python-version: ${{ matrix.python-version }} | |
| - name: Build moleculekit package | |
| shell: bash -l {0} | |
| run: | | |
| git config --global --add safe.directory '*' | |
| conda install anaconda-client conda-build python=${{ matrix.python-version }} toml | |
| pip install versioneer==0.28 | |
| python package/moleculekit/insert_placeholder_values.py | |
| conda build --python ${{ matrix.python-version }} package/moleculekit/ --output-folder ./pkg/ --no-include-recipe --no-anaconda-upload -c acellera -c conda-forge | |
| - name: Upload to conda | |
| shell: bash -l {0} | |
| run: | | |
| anaconda -t ${{ secrets.ANACONDA_TOKEN_BASIC }} upload -u acellera ./pkg/*/moleculekit-*.tar.bz2 |