Test for gappy pdb #96
Workflow file for this run
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| name: AlphaPulldown-github-CI | |
| on: [pull_request, push] | |
| jobs: | |
| build: | |
| runs-on: ubuntu-20.04 | |
| strategy: | |
| matrix: | |
| python-version: ["3.10.12", "3.11"] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| submodules: recursive | |
| - name: Debug List Directory | |
| run: ls -la -R | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| cache: "pip" | |
| - name: Display Python version | |
| run: python -c "import sys; print(sys.version)" | |
| - name: Add Conda to System Path | |
| run: | | |
| pwd | |
| echo $CONDA/bin >> $GITHUB_PATH | |
| echo "$GITHUB_WORKSPACE/alphapulldown" >> $GITHUB_PATH | |
| - name: Install AlphaPulldown without dependencies | |
| run: | | |
| conda create --name AlphaPulldown python=${{ matrix.python-version }} | |
| eval "$(conda shell.bash hook)" | |
| conda activate AlphaPulldown | |
| conda install -c anaconda conda-build | |
| conda develop alphapulldown | |
| conda develop alphapulldown/ColabFold | |
| conda develop alphafold | |
| python -c "import alphafold; import os; print('Alphafold module is located at:', alphafold.__file__); alphafold_dir = os.path.dirname(alphafold.__file__); print('Contents of the Alphafold directory:', os.listdir(alphafold_dir))" | |
| - name: Install Dependencies | |
| run: | | |
| eval "$(conda shell.bash hook)" | |
| conda activate AlphaPulldown | |
| conda install -c omnia -c bioconda -c conda-forge openmm==8.0 pdbfixer==1.9 kalign2 cctbx-base importlib_metadata | |
| pip install jax==0.3.25 jaxlib==0.3.25+cuda11.cudnn805 -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html | |
| pip install "absl-py>=0.13.0" dm-haiku "dm-tree>=0.1.6" "h5py>=3.1.0" "ml-collections>=0.1.0" "pandas>=1.3.4" tensorflow "importlib-resources==5.8.0" "nbformat==5.4.0" "py3Dmol==2.0.1" ipython appdirs jupyterlab ipywidgets pytest | |
| - name: Run Tests | |
| run: | | |
| eval "$(conda shell.bash hook)" | |
| conda activate AlphaPulldown | |
| pytest -s test/test_custom_db.py | |
| pytest -s test/test_remove_clashes_low_plddt.py | |
| #TODO: mock AF dbs and add other tests | |
| publish: | |
| runs-on: ubuntu-latest | |
| if: github.event_name == 'release' && github.event.action == 'published' | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - run: python3 -m pip install --upgrade build && python3 -m build | |
| - name: Publish package | |
| uses: pypa/gh-action-pypi-publish@release/v1 | |
| with: | |
| user: ${{ secrets.PYPI_LOGIN_DIMA }} | |
| password: ${{ secrets.PYPI_PASSWORD_DIMA }} | |
| repository_url: https://test.pypi.org/legacy/ |