Update alphalink2 inference integration #110
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 "$(conda shell.bash hook)" | |
| conda activate AlphaPulldown | |
| conda install -c anaconda conda-build | |
| conda develop alphapulldown | |
| conda develop alphapulldown/ColabFold | |
| conda develop alphafold | |
| python -c "import alphafold; import os; print('Alphafold module is located at:', alphafold.__file__); alphafold_dir = os.path.dirname(alphafold.__file__); print('Contents of the Alphafold directory:', os.listdir(alphafold_dir))" | |
| - name: Install dependencies in unifold setup.py | |
| run: | | |
| eval "$(conda shell.bash hook)" | |
| export WORKDIRPATH=$PWD | |
| conda activate AlphaPulldown | |
| cd $WORKDIRPATH/unifold && python3 setup.py install | |
| - name: Install dependencies in AlphaFold setup.py | |
| run: | | |
| eval "$(conda shell.bash hook)" | |
| export WORKDIRPATH=$PWD | |
| conda activate AlphaPulldown | |
| pip install protobuf==4.23.0 | |
| cd $WORKDIRPATH/alphafold && python3 setup.py install | |
| python -c "import tree" | |
| - name: Install Dependencies | |
| run: | | |
| eval "$(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 | |
| #conda install -c bioconda hmmer hhsuite #this causes conda conflicts | |
| 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: Check imports of submodules | |
| # run : | | |
| # eval "$(conda shell.bash hook)" | |
| # conda activate AlphaPulldown | |
| # # install PyTorch | |
| # pip install torch --pre -f https://download.pytorch.org/whl/nightly/cu121/torch_nightly.html | |
| # # setup unicore | |
| # git clone https://github.com/dptech-corp/Uni-Core.git | |
| # cd Uni-Core | |
| # python3 setup.py install --disable-cuda-ext | |
| # python -c "from unifold.alphalink_inference import alphalink_prediction" | |
| # python -c "from unifold.dataset import process_ap" | |
| # python -c "from unifold.config import model_config" | |
| # python -c "from colabfold.batch import get_queries, unserialize_msa, get_msa_and_templates, msa_to_str, build_monomer_feature, parse_fasta" | |
| - name: Run Tests | |
| run: | | |
| eval "$(conda shell.bash hook)" | |
| conda activate AlphaPulldown | |
| pytest -s test/test_custom_db.py | |
| pytest -s test/test_remove_clashes_low_plddt.py | |
| # python3 -m unittest test/test_crosslink_input.py |