Clean dependencies #1269
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 | |
| - name: Set up Miniconda | |
| id: setup_miniconda | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| miniconda-version: "latest" | |
| auto-update-conda: true | |
| channel-priority: flexible | |
| use-mamba: true | |
| python-version: ${{ matrix.python-version }} | |
| - name: Create Conda Environment | |
| shell: bash | |
| run: | | |
| source "${{ steps.setup_miniconda.outputs.conda-prefix }}/etc/profile.d/conda.sh" | |
| mamba create -y -n AlphaPulldown -c omnia -c bioconda -c conda-forge \ | |
| python=${{ matrix.python-version }} \ | |
| openmm==8.0 pdbfixer==1.9 kalign2 hmmer hhsuite modelcif biopandas | |
| - name: Install Pip Dependencies | |
| shell: bash | |
| run: | | |
| source "${{ steps.setup_miniconda.outputs.conda-prefix }}/etc/profile.d/conda.sh" | |
| conda activate AlphaPulldown | |
| pip install -U "jax[cuda12]" pyrosetta-installer | |
| python -c 'import pyrosetta_installer; pyrosetta_installer.install_pyrosetta()' | |
| - name: Install AlphaPulldown (User) | |
| if: matrix.install-type == 'user' | |
| shell: bash | |
| run: | | |
| source "${{ steps.setup_miniconda.outputs.conda-prefix }}/etc/profile.d/conda.sh" | |
| conda activate AlphaPulldown | |
| pip install alphapulldown==2.0.0b6 | |
| - name: Install AlphaPulldown (Developer) | |
| if: matrix.install-type == 'developer' | |
| shell: bash | |
| run: | | |
| source "${{ steps.setup_miniconda.outputs.conda-prefix }}/etc/profile.d/conda.sh" | |
| conda activate AlphaPulldown | |
| pip install -e . | |
| pip install -e ColabFold --no-deps | |
| pip install -e alphafold --no-deps | |
| - name: Set Environment Variables | |
| shell: bash | |
| run: | | |
| source "${{ steps.setup_miniconda.outputs.conda-prefix }}/etc/profile.d/conda.sh" | |
| conda activate AlphaPulldown | |
| export PYTHONPATH=$PWD/alphapulldown/analysis_pipeline:$PYTHONPATH | |
| export PYTHONPATH=$PWD/AlphaLink2:$PYTHONPATH | |
| - name: Install Optional Dependencies | |
| shell: bash | |
| run: | | |
| source "${{ steps.setup_miniconda.outputs.conda-prefix }}/etc/profile.d/conda.sh" | |
| conda activate AlphaPulldown | |
| # Install dependencies for AlphaLink backend if needed | |
| # Uncomment the following lines if required | |
| # mamba install -y -c pytorch pytorch==1.13.0 | |
| # 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 .. | |
| - name: Run Tests | |
| shell: bash | |
| run: | | |
| source "${{ steps.setup_miniconda.outputs.conda-prefix }}/etc/profile.d/conda.sh" | |
| 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_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 }} |