[pre-commit.ci] pre-commit autoupdate #2320
This file contains hidden or 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: [3.9, "3.10", "3.11"] | |
| torch: [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' | |
| environment-name: test_env | |
| init-shell: bash | |
| create-args: python=${{matrix.python-version}} | |
| #cache-environment: true | |
| #cache-environment-key: environment-${{ steps.date.outputs.date }} | |
| #cache-downloads-key: downloads-${{ steps.date.outputs.date }} | |
| post-cleanup: 'all' | |
| - name: Install setuptools | |
| run: pip install setuptools==69.5.1 | |
| - name: Update build tools | |
| run: pip install --upgrade pip setuptools wheel | |
| - name: Install DSSP | |
| run: micromamba install dssp -c salilab | |
| - name: Install mmseqs | |
| run: micromamba install -c conda-forge -c bioconda mmseqs2 | |
| - name: Install Boost 1.7.3 (for DSSP) | |
| run: micromamba install -c anaconda libboost=1.73.0 | |
| - name: Install PyTorch (1.13.0) | |
| if: matrix.torch == '1.13.0' | |
| run: pip install torch==${{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==${{matrix.torch}} -f https://download.pytorch.org/whl/cpu | |
| - name: Install PyG | |
| #run: micromamba install -c pyg pyg | |
| run: pip install torch_geometric | |
| - name: Install torch-cluster | |
| #run: micromamba install pytorch-cluster -c pyg | |
| run: pip install torch_scatter torch_sparse torch_cluster torch_spline_conv -f https://data.pyg.org/whl/torch-${{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" |