Major update of dependencies and structure #52
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 | |
| #conda info | |
| #conda list | |
| #python -c "import sys; print(sys.path)" | |
| #echo "Python path: $PYTHONPATH" | |
| python -c "import alphafold; import os; print('Alphafold module is located at:', alphafold.__file__); alphafold_dir = os.path.dirname(alphafold.__file__); print('Contents of the Alphafold directory:', os.listdir(alphafold_dir))" | |
| - name: Install Dependencies | |
| run: | | |
| eval "$(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 | |
| #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: Run Tests | |
| run: | | |
| eval "$(conda shell.bash hook)" | |
| conda activate AlphaPulldown | |
| pytest test/ | |
| - name: Build and Push to Docker Hub | |
| uses: mr-smithers-excellent/docker-build-push@v5 | |
| with: | |
| image: dmolodenskiy/AlphaPulldown | |
| registry: docker.io | |
| dockerfile: docker/Dockerfile | |
| username: ${{ secrets.DOCKER_USERNAME }} | |
| password: ${{ secrets.DOCKER_PASSWORD }} | |
| tags: latest |