Add cpdb support to speed up parsing #1774
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| name: build | |
| on: | |
| push: | |
| paths-ignore: | |
| - "README.md" | |
| - "docs/**" | |
| pull_request: | |
| paths-ignore: | |
| - "README.md" | |
| - "docs/*" | |
| jobs: | |
| build_cpu: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: [3.8, 3.9] | |
| torch: [1.12.0, 1.13.0, 2.0.0] | |
| #include: | |
| # - torch: 1.6.0 | |
| # torchvision: 0.7.0 | |
| # - torch: 1.7.0 | |
| # torchvision: 0.8.1 | |
| # - torch: 1.8.0 | |
| # torchvision: 0.9.0 | |
| # - torch: 1.9.0 | |
| # torchvision: 0.10.0 | |
| # - torch: 1.8.0 | |
| # torchvision: 0.9.0 | |
| # python-version: 3.9 | |
| # - torch: 1.9.0 | |
| # torchvision: 0.10.0 | |
| # python-version: 3.8 | |
| # - torch: 1.9.0 | |
| # torchvision: 0.10.0 | |
| # python-version: 3.9 | |
| # 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: Set up Python ${{ matrix.python-version }} | |
| # uses: actions/setup-python@v2 | |
| # with: | |
| #python-version: ${{ matrix.python-version }} | |
| #- name: Setup conda environment | |
| # run: conda env create -n graphein-dev python=${{ matrix.python-version }} | |
| #- name: Activate Conda Environment | |
| # run: source activate graphein-dev | |
| - name: Install DSSP | |
| run: conda install -c salilab dssp | |
| - 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 torchvision==${{matrix.torchvision}}+cpu -f https://download.pytorch.org/whl/torch_stable.html | |
| - name: Install PyG | |
| run: mamba install -c pyg pyg | |
| - name: Install torch-cluster | |
| run: mamba install pytorch-cluster -c pyg | |
| - 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" |