Handle multi-molecule structures in openmm, with host-guest example. #355
Workflow file for this run
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| name: Tests | |
| on: | |
| push: | |
| branches: | |
| - master | |
| pull_request: | |
| workflow_dispatch: | |
| jobs: | |
| ruff: | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.11" | |
| cache: "pip" | |
| - run: "pip install '.[dev]'" | |
| - run: ruff check . | |
| mypy: | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.11" | |
| cache: "pip" | |
| - run: "pip install -e '.[dev]'" | |
| - run: mypy src examples | |
| ruff-format: | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.11" | |
| cache: "pip" | |
| - run: "pip install -e '.[dev]'" | |
| - run: ruff format --check . | |
| pytest: | |
| # https://ericmjl.github.io/blog/2021/12/30/better-conda-environments-on-github-actions/ | |
| runs-on: ubuntu-22.04 | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| auto-update-conda: true | |
| miniforge-variant: Mambaforge | |
| channels: conda-forge,defaults | |
| python-version: 3.11 | |
| activate-environment: pytest | |
| use-mamba: true | |
| - name: Build environment | |
| run: | | |
| conda activate pytest | |
| conda install -c conda-forge openff-toolkit openmm openmmtools dgl rdkit==2024.3.4 espaloma_charge | |
| python -m pip install --upgrade pip | |
| python -m pip install --upgrade setuptools | |
| python -m pip install -e '.[dev]' | |
| - run: pytest | |
| example-tests: | |
| # https://ericmjl.github.io/blog/2021/12/30/better-conda-environments-on-github-actions/ | |
| runs-on: ubuntu-22.04 | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| auto-update-conda: true | |
| miniforge-variant: Mambaforge | |
| channels: conda-forge,defaults | |
| python-version: 3.11 | |
| activate-environment: pytest | |
| use-mamba: true | |
| - name: Build environment | |
| run: | | |
| conda activate pytest | |
| conda install -c conda-forge openff-toolkit openmm openmmtools dgl rdkit==2024.3.4 espaloma_charge | |
| conda install -c conda-forge mdanalysis openbabel | |
| python -m pip install --upgrade pip | |
| python -m pip install --upgrade setuptools | |
| python -m pip install -e '.[dev]' | |
| - name: Run script | |
| run: python examples/testable_example.py | |
| doctest: | |
| runs-on: ubuntu-22.04 | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| auto-update-conda: true | |
| miniforge-variant: Mambaforge | |
| channels: conda-forge,defaults | |
| python-version: 3.11 | |
| activate-environment: pytest | |
| use-mamba: true | |
| - name: Build environment | |
| run: | | |
| conda activate pytest | |
| conda install -c conda-forge openff-toolkit openmm openmmtools dgl rdkit==2024.3.4 espaloma_charge | |
| conda install -c conda-forge mdanalysis openbabel | |
| python -m pip install --upgrade pip | |
| python -m pip install --upgrade setuptools | |
| python -m pip install -e '.[dev]' | |
| - run: make -C docs doctest |