Add general linear fit target (#131) #535
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| name: GH Actions CI | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| branches: | |
| - main | |
| schedule: | |
| # weekly tests, Sundays at midnight | |
| - cron: "0 0 * * 0" | |
| concurrency: | |
| # Specific group naming so CI is only cancelled | |
| # within same PR or on merge to main | |
| group: ${{ github.ref }}-${{ github.head_ref }}-${{ github.workflow }} | |
| cancel-in-progress: true | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| env: | |
| OE_LICENSE: ${{ github.workspace }}/oe_license.txt | |
| jobs: | |
| main_tests: | |
| name: CI (${{ matrix.os }}, py-${{ matrix.python-version }}, rdkit=${{ matrix.include-rdkit }}, openeye=${{ matrix.include-openeye }}, dgl=${{ matrix.include-dgl }}), pydantic=${{ matrix.pydantic-version }} | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [macOS-12, ubuntu-latest] | |
| python-version: ["3.10", "3.11", "3.12"] | |
| pydantic-version: ["1", "2"] | |
| include-rdkit: [false, true] | |
| include-openeye: [false, true] | |
| include-dgl: [false, true] | |
| exclude: | |
| - include-rdkit: false | |
| include-openeye: false | |
| # no openeye for 3.12 yet | |
| - include-openeye: true | |
| python-version: "3.12" | |
| # no builds? | |
| - include-dgl: true | |
| python-version: "3.12" | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Build information | |
| run: | | |
| uname -a | |
| df -h | |
| ulimit -a | |
| - name: Install environment | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: devtools/conda-envs/test_env_dgl_${{ matrix.include-dgl }}.yaml | |
| create-args: >- | |
| python=${{ matrix.python-version }} | |
| pydantic=${{ matrix.pydantic-version }} | |
| - name: Install package | |
| run: | | |
| python -m pip install . --no-deps | |
| - uses: ./.github/actions/include-openeye | |
| if: matrix.include-openeye == true | |
| with: | |
| openeye-license-text: ${{ secrets.OE_LICENSE }} | |
| openeye-license-file: ${{ env.OE_LICENSE }} | |
| - name: Uninstall OpenEye | |
| if: matrix.include-openeye == false | |
| run: conda remove --force openeye-toolkits --yes || echo "openeye not installed" | |
| - name: Uninstall RDKit | |
| if: matrix.include-rdkit == false | |
| run: conda remove --force rdkit --yes || echo "rdkit not installed" | |
| # See https://github.com/openforcefield/openff-nagl/issues/103 | |
| - name: Rewrite DGL config | |
| if: matrix.include-dgl == true | |
| run: | | |
| mkdir -p ~/.dgl | |
| echo '{"backend": "pytorch"}' > ~/.dgl/config.json | |
| - name: Python information | |
| run: | | |
| which python | |
| conda info | |
| conda list | |
| - name: Check toolkit installations | |
| shell: bash -l -c "python -u {0}" | |
| run: | | |
| from openff.toolkit.utils.toolkits import OPENEYE_AVAILABLE, RDKIT_AVAILABLE | |
| assert str(OPENEYE_AVAILABLE).lower() == '${{ matrix.include-openeye }}' | |
| assert str(RDKIT_AVAILABLE).lower() == '${{ matrix.include-rdkit }}' | |
| - name: Run tests | |
| run: | | |
| python -m pytest -n 4 -v --cov=openff/nagl --cov-config=setup.cfg --cov-append --cov-report=xml --color=yes openff/nagl/ | |
| - name: codecov | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| file: ./coverage.xml | |
| verbose: True | |
| # name: codecov-${{ matrix.os }}-py${{ matrix.python-version }} | |
| pylint_check: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.10" | |
| - name: Install Pylint | |
| run: | | |
| which pip | |
| which python | |
| pip install pylint | |
| - name: Run Pylint | |
| env: | |
| PYLINTRC: .pylintrc | |
| run: | | |
| pylint openff-nagl | |
| pypi_check: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.10" | |
| - name: Install dependencies | |
| run: | | |
| pip install setuptools twine | |
| - name: Build package | |
| run: | | |
| python setup.py sdist | |
| - name: Check package build | |
| run: | | |
| DISTRIBUTION=$(ls -t1 dist/openff-nagl-*.tar.gz | head -n 1) | |
| test -n "${DISTRIBUTION}" || { echo "no distribution dist/openff-nagl-*.tar.gz found"; exit 1; } | |
| echo "twine check $DISTRIBUTION" | |
| twine check $DISTRIBUTION | |
| install_from_source_conda: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: ["3.10", "3.11", "3.12"] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Install conda | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| add-pip-as-python-dependency: true | |
| architecture: x64 | |
| miniforge-variant: Mambaforge | |
| use-mamba: true | |
| auto-update-conda: true | |
| show-channel-urls: true | |
| channels: conda-forge, defaults | |
| - name: Build from source | |
| run: | | |
| conda create --name openff-nagl | |
| conda activate openff-nagl | |
| conda list | |
| mamba env update --name openff-nagl --file devtools/conda-envs/docs_env.yaml | |
| python --version | |
| python -m pip install . --no-deps | |
| conda list | |
| - name: Check success | |
| run: | | |
| conda activate openff-nagl | |
| python -c "import openff.nagl ; print(openff.nagl.__version__)" |