[DNM] add experiment of training torsion energies #617
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [macOS-13, macOS-latest, ubuntu-latest] | |
| python-version: ["3.10", "3.11", "3.12"] | |
| pydantic-version: ["1", "2"] | |
| include-rdkit: [false, true] | |
| include-openeye: [false, true] | |
| include-dgl: [false, true] | |
| exclude: | |
| - include-rdkit: false | |
| include-openeye: false | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Build information | |
| run: | | |
| uname -a | |
| df -h | |
| ulimit -a | |
| - name: Install environment | |
| uses: mamba-org/setup-micromamba@v2 | |
| with: | |
| environment-file: devtools/conda-envs/test_env_dgl_${{ 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: ${{ env.OE_LICENSE }} | |
| - name: Uninstall OpenEye | |
| if: matrix.include-openeye == false | |
| run: micromamba remove --force openeye-toolkits --yes || echo "openeye not installed" | |
| - name: Uninstall RDKit | |
| if: matrix.include-rdkit == false | |
| run: micromamba remove --force rdkit --yes || echo "rdkit not installed" | |
| # See https://github.com/openforcefield/openff-nagl/issues/103 | |
| - name: Rewrite DGL config | |
| if: matrix.include-dgl == true | |
| run: | | |
| mkdir -p ~/.dgl | |
| echo '{"backend": "pytorch"}' > ~/.dgl/config.json | |
| - name: Check toolkit installations | |
| shell: bash -l -c "python -u {0}" | |
| run: | | |
| from openff.toolkit.utils.toolkits import OPENEYE_AVAILABLE, RDKIT_AVAILABLE | |
| assert str(OPENEYE_AVAILABLE).lower() == '${{ matrix.include-openeye }}' | |
| assert str(RDKIT_AVAILABLE).lower() == '${{ matrix.include-rdkit }}' | |
| - name: Check DGL installation | |
| if: matrix.include-dgl == true | |
| run: | | |
| python -c "import dgl" | |
| - name: Run tests | |
| run: | | |
| python -m pytest -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 $DISTRIBUTION | |
| install_from_source_conda: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: ["3.10", "3.11", "3.12"] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Install conda | |
| uses: mamba-org/setup-micromamba@v2 | |
| with: | |
| environment-name: openff-nagl | |
| create-args: >- | |
| python=${{ matrix.python-version }} | |
| - name: Build from source | |
| run: | | |
| micromamba env update --name openff-nagl --file devtools/conda-envs/docs_env.yaml | |
| python --version | |
| python -m pip install . --no-deps | |
| micromamba list | |
| - name: Check success | |
| run: | | |
| python -c "import openff.nagl ; print(openff.nagl.__version__)" |