Fix bug in PDB DataFrame (e.g. when using add_distance_threshold edges in construct_graph)
#2283
Workflow file for this run
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| name: build | |
| on: | |
| push: | |
| paths-ignore: | |
| - "README.md" | |
| - "CHANGELOG.md" | |
| - "CONTRIBUTORS.md" | |
| - "CONTRIBUTING.md" | |
| - "docs/**" | |
| pull_request: | |
| paths-ignore: | |
| - "README.md" | |
| - "CHANGELOG.md" | |
| - "CONTRIBUTORS.md" | |
| - "CONTRIBUTING.md" | |
| - "docs/*" | |
| jobs: | |
| build_cpu: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: [3.8, 3.9, "3.10", "3.11"] | |
| torch: [1.13.0, 2.1.0, 2.2.0, 2.3.0, 2.4.0, 2.5.0] | |
| # https://github.com/marketplace/actions/setup-miniconda#use-a-default-shell | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v3 | |
| # See: https://github.com/mamba-org/setup-micromamba/tree/main | |
| - name: Setup micromamba | |
| - uses: mamba-org/setup-micromamba@v2 | |
| with: | |
| micromamba-version: 'latest' | |
| init-shell: bash | |
| cache-environment: true | |
| cache-environment-key: environment-${{ steps.date.outputs.date }} | |
| cache-downloads-key: downloads-${{ steps.date.outputs.date }} | |
| post-cleanup: 'all' | |
| - name: Install setuptools | |
| run: pip install setuptools==69.5.1 | |
| - name: Install Boost 1.7.3 (for DSSP) | |
| run: mamba install -c anaconda libboost=1.73.0 | |
| - name: Install DSSP | |
| run: mamba install dssp -c salilab | |
| - name: Install mmseqs | |
| run: mamba install -c conda-forge -c bioconda mmseqs2 | |
| - name: Install PyTorch (1.13.0) | |
| if: matrix.torch == '1.13.0' | |
| run: pip install torch==${{matrix.torch}}+cpu --extra-index-url https://download.pytorch.org/whl/cpu | |
| - name: Install PyTorch (2.0+) | |
| if: matrix.torch != '1.13.0' | |
| run: pip install torch==${{matrix.torch}} -f https://download.pytorch.org/whl/cpu | |
| - name: Install PyG | |
| #run: mamba install -c pyg pyg | |
| run: pip install torch_geometric | |
| - name: Install torch-cluster | |
| #run: mamba install pytorch-cluster -c pyg | |
| run: pip install torch_scatter torch_sparse torch_cluster torch_spline_conv -f https://data.pyg.org/whl/torch-${{matrix.torch}}+cpu.html | |
| - name: Install BLAST | |
| run: sudo apt install ncbi-blast+ | |
| - 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: Install doc dependencies | |
| run: pip install -r .requirements/docs.in | |
| - name: Run unit tests and generate coverage report | |
| run: pytest . | |
| - name: Test notebook execution | |
| run: pytest --nbval-lax notebooks/ --nbval-current-env --ignore-glob="notebooks/dataloader_tutorial.ipynb" --ignore-glob="notebooks/datasets_and_dataloaders.ipynb" --ignore-glob="notebooks/foldcomp.ipynb" --ignore-glob="notebooks/grn_tutorial.ipynb" |