pin biopython <=1.79 for dssp #852
Workflow file for this run
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| name: minimal_install | |
| on: | |
| push: | |
| paths-ignore: | |
| - "README.md" | |
| - "docs/**" | |
| pull_request: | |
| paths-ignore: | |
| - "README.md" | |
| - "docs/*" | |
| - "CHANGELOG.md" | |
| - "CONTRIBUTORS.md" | |
| - "CONTRIBUTING.md" | |
| - "imgs/" | |
| jobs: | |
| build_cpu: | |
| runs-on: ubuntu-latest | |
| # https://github.com/marketplace/actions/setup-miniconda#use-a-default-shell | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| strategy: | |
| matrix: | |
| python-version: [3.8, 3.9, 3.11] | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v3 | |
| # See: https://github.com/marketplace/actions/setup-miniconda | |
| - name: Setup miniconda | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| auto-update-conda: true | |
| miniforge-variant: Mambaforge | |
| conda-channels: conda-forge | |
| python-version: ${{ matrix.python-version }} | |
| use-mamba: true | |
| - name: Install Graphein | |
| run: pip install -e . | |
| - name: Install Extras | |
| run: pip install -r .requirements/extras.in | |
| - name: Install Dev Dependencies | |
| run: pip install -r .requirements/dev.in | |
| - name: Run unit tests and generate coverage report | |
| run: pytest . --ignore-glob="tests/protein/tensor" --ignore="tests/ml/test_conversion.py" --ignore="tests/ml/test_torch_geometric_dataset.py" | |
| - name: Test notebook execution | |
| run: pytest --nbval-lax notebooks/ --current-env --ignore-glob="notebooks/dataloader_tutorial.ipynb" --ignore-glob="notebooks/higher_order_graphs.ipynb" --ignore-glob="notebooks/protein_graph_analytics.ipynb" --ignore-glob="notebooks/subgraphing_tutorial.ipynb" --ignore-glob="notebooks/splitting_a_dataset.ipynb" --ignore-glob="notebooks/protein_tensors.ipynb" --ignore-glob="notebooks/datasets_and_dataloaders.ipynb" --ignore-glob="notebooks/foldcomp.ipynb" --ignore-glob="notebooks/creating_datasets_from_the_pdb.ipynb" |