Correct the judgment of hydrogen bonds #1983
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: 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"] | |
| torch: [1.13.0, 2.1.0, 2.2.0] | |
| # 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/marketplace/actions/setup-miniconda | |
| - name: Setup miniconda | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| auto-update-conda: true | |
| miniforge-variant: Mambaforge | |
| channels: "conda-forge, salilab, pytorch, pyg" | |
| python-version: ${{ matrix.python-version }} | |
| use-mamba: true | |
| - name: Install Boost 1.7.3 (for DSSP) | |
| run: conda install -c anaconda libboost=1.73.0 | |
| - name: Install DSSP | |
| run: conda install dssp -c salilab | |
| - name: Install mmseqs | |
| run: mamba install -c conda-forge -c bioconda mmseqs2 | |
| - name: Install PyTorch | |
| #run: mamba install -c pytorch pytorch==${{matrix.torch}} cpuonly | |
| run: pip install torch==${{matrix.torch}}+cpu -f https://download.pytorch.org/whl/torch_stable.html | |
| - name: Install PyG | |
| #run: mamba install -c pyg pyg | |
| run: pip install torch_geometric | |
| - name: Install torch-cluster | |
| #run: mamba install pytorch-cluster -c pyg | |
| run: pip install pyg_lib torch_scatter torch_sparse torch_cluster torch_spline_conv -f https://data.pyg.org/whl/torch-${{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/ --current-env --ignore-glob="notebooks/dataloader_tutorial.ipynb" --ignore-glob="notebooks/datasets_and_dataloaders.ipynb" --ignore-glob="notebooks/foldcomp.ipynb" |