Update README.md #226
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"] | |
| 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" >> $GITHUB_PATH | |
| - name: Install AlphaPulldown without dependencies | |
| run: | | |
| conda create -n AlphaPulldown -c omnia -c bioconda -c conda-forge python==${{ matrix.python-version }} openmm==8.0 pdbfixer==1.9 kalign2 cctbx-base pytest importlib_metadata | |
| eval "$(conda shell.bash hook)" | |
| conda activate AlphaPulldown | |
| #python3 -m pip install alphapulldown==1.0.1 | |
| conda install -c bioconda hmmer hhsuite | |
| pip install -e . | |
| pip install -e alphapulldown/ColabFold --no-deps | |
| pip install -e alphafold --no-deps | |
| python -c "import alphafold; import os; print('Alphafold module is located at:', alphafold.__file__); alphafold_dir = os.path.dirname(alphafold.__file__); print('Contents of the Alphafold directory:', os.listdir(alphafold_dir))" | |
| - name: Install dependencies in AlphaLink2 setup.py | |
| run: | | |
| eval "$(conda shell.bash hook)" | |
| export WORKDIRPATH=$PWD | |
| conda activate AlphaPulldown | |
| cd $WORKDIRPATH/AlphaLink2 && python3 setup.py install | |
| - name: Install dependencies in AlphaFold setup.py | |
| run: | | |
| eval "$(conda shell.bash hook)" | |
| export WORKDIRPATH=$PWD | |
| conda activate AlphaPulldown | |
| pip install protobuf==4.23.0 ml-dtypes==0.2.0 | |
| - name: Install Pytorch Dependencies | |
| run: | | |
| eval "$(conda shell.bash hook)" | |
| conda activate AlphaPulldown | |
| # install PyTorch | |
| pip install torch --pre -f https://download.pytorch.org/whl/nightly/cu121/torch_nightly.html | |
| #pip install jax==0.4.20 jaxlib==0.4.16+cuda11.cudnn86 -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==5.9.2" "py3Dmol==2.0.4" ipython appdirs jupyterlab ipywidgets pytest | |
| - name: Check imports of submodules | |
| run : | | |
| eval "$(conda shell.bash hook)" | |
| conda activate AlphaPulldown | |
| # install PyTorch | |
| pip install torch --pre -f https://download.pytorch.org/whl/nightly/cu121/torch_nightly.html | |
| # setup unicore | |
| git clone https://github.com/dptech-corp/Uni-Core.git | |
| cd Uni-Core | |
| python3 setup.py install --disable-cuda-ext | |
| python -c "from colabfold.batch import get_queries, unserialize_msa, get_msa_and_templates, msa_to_str, build_monomer_feature, parse_fasta" | |
| # python -c "from unifold.alphalink_inference import alphalink_prediction" | |
| # python -c "from unifold.dataset import process_ap" | |
| # python -c "from unifold.config import model_config" | |
| - name: Run Tests | |
| run: | | |
| eval "$(conda shell.bash hook)" | |
| conda activate AlphaPulldown | |
| pytest -s test/test_custom_db.py | |
| pytest -s test/test_features_with_templates.py | |
| pytest -s test/test_remove_clashes_low_plddt.py | |
| # python3 -m unittest test/test_crosslink_input.py | |