Refine create_individual_features.py SLURM example #1305
Workflow file for this run
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| name: AlphaPulldown-CI-CD | |
| on: | |
| pull_request: | |
| push: | |
| branches: | |
| - main | |
| release: | |
| types: [published] | |
| workflow_dispatch: | |
| jobs: | |
| build-and-test: | |
| runs-on: ubuntu-20.04 | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: ["3.10", "3.11"] | |
| install-type: ['user', 'developer'] | |
| steps: | |
| - uses: webfactory/[email protected] | |
| with: | |
| ssh-private-key: ${{ secrets.SSH_PRIVATE_KEY }} | |
| - uses: actions/checkout@v4 | |
| with: | |
| submodules: recursive | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| cache: "pip" | |
| - run: python -c "import sys; print(sys.version)" | |
| - run: | | |
| echo $CONDA/bin >> $GITHUB_PATH | |
| echo "$GITHUB_WORKSPACE/alphapulldown" >> $GITHUB_PATH | |
| - if: matrix.install-type == 'user' | |
| run: | | |
| conda install -y -c conda-forge mamba | |
| mamba create -n AlphaPulldown -c omnia -c bioconda -c conda-forge python==${{ matrix.python-version }} \ | |
| openmm==8.0 pdbfixer==1.9 kalign2 hmmer hhsuite modelcif | |
| eval "$(conda shell.bash hook)" | |
| conda activate AlphaPulldown | |
| pip install alphapulldown | |
| pip install -U "jax[cuda12]" | |
| - if: matrix.install-type == 'developer' | |
| run: | | |
| conda install -y -c conda-forge mamba | |
| mamba create -n AlphaPulldown -c omnia -c bioconda -c conda-forge python==${{ matrix.python-version }} \ | |
| openmm==8.0 pdbfixer==1.9 kalign2 hmmer hhsuite modelcif | |
| eval "$(conda shell.bash hook)" | |
| conda activate AlphaPulldown | |
| pip install . | |
| pip install -U "jax[cuda12]" | |
| # export PYTHONPATH=$PWD/AlphaLink2:$PYTHONPATH | |
| # install dependencies for AlphaLink backend | |
| # pip install torch==1.13.0+cu117 --extra-index-url https://download.pytorch.org/whl/cu117 | |
| # pip install setuptools==69.5.1 # Downgrade setuptools to avoid crashes when installing unicore | |
| # git clone https://github.com/dptech-corp/Uni-Core.git | |
| # cd Uni-Core | |
| # python setup.py install --disable-cuda-ext | |
| # cd .. | |
| - run: | | |
| eval "$(conda shell.bash hook)" | |
| conda activate AlphaPulldown | |
| python test/test_python_imports.py | |
| pytest -s test/test_custom_db.py | |
| pytest -s test/test_remove_clashes_low_plddt.py | |
| pytest -s test/test_modelcif.py | |
| pytest -s test/test_features_with_templates.py | |
| pytest -s test/test_post_prediction.py | |
| pytest -s test/test_parse_fold.py | |
| #export PYTHONPATH=$PWD/alphapulldown/analysis_pipeline:$PYTHONPATH | |
| ## Test analysis pipeline | |
| #conda install -c bioconda biopandas | |
| #pip install pyrosetta-installer | |
| #python -c 'import pyrosetta_installer; pyrosetta_installer.install_pyrosetta()' | |
| #pytest -s test/test_pdb_analyser.py | |
| #pytest -s test/test_get_good_inter_pae.py | |
| build-fold-container: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: webfactory/[email protected] | |
| with: | |
| ssh-private-key: ${{ secrets.SSH_PRIVATE_KEY }} | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Free disk space | |
| run: | | |
| rm -rf /opt/hostedtoolcache | |
| - name: Login to Docker Hub | |
| uses: docker/login-action@v3 | |
| with: | |
| username: ${{ secrets.DOCKER_USERNAME }} | |
| password: ${{ secrets.DOCKER_PASSWORD }} | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v3 | |
| - name: Build and push fold container | |
| if: github.event_name == 'push' | |
| uses: docker/build-push-action@v5 | |
| with: | |
| context: . | |
| file: ./docker/pulldown.dockerfile | |
| push: true | |
| tags: ${{ secrets.DOCKER_USERNAME }}/fold:latest | |
| ssh: default | |
| - name: Build and push fold container with version | |
| if: github.event_name == 'release' && github.event.action == 'published' | |
| uses: docker/build-push-action@v5 | |
| with: | |
| context: . | |
| file: ./docker/pulldown.dockerfile | |
| push: true | |
| tags: ${{ secrets.DOCKER_USERNAME }}/fold:${{ github.event.release.tag_name }} | |
| ssh: default | |
| build-analysis-container: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Free disk space | |
| run: | | |
| rm -rf /opt/hostedtoolcache | |
| - name: Login to Docker Hub | |
| uses: docker/login-action@v3 | |
| with: | |
| username: ${{ secrets.DOCKER_USERNAME }} | |
| password: ${{ secrets.DOCKER_PASSWORD }} | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v3 | |
| - name: Build and push analysis container | |
| if: github.event_name == 'push' | |
| uses: docker/build-push-action@v5 | |
| with: | |
| context: . | |
| file: ./docker/analysis.dockerfile | |
| push: true | |
| tags: ${{ secrets.DOCKER_USERNAME }}/fold_analysis:latest | |
| - name: Build and push analysis container with version | |
| if: github.event_name == 'release' && github.event.action == 'published' | |
| uses: docker/build-push-action@v5 | |
| with: | |
| context: . | |
| file: ./docker/analysis.dockerfile | |
| push: true | |
| tags: ${{ secrets.DOCKER_USERNAME }}/fold_analysis:${{ github.event.release.tag_name }} |