CUDA stream optimisation #89
Workflow file for this run
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| name: Uni-Dock Tools CI/CD | |
| on: | |
| push: | |
| branches: [ main ] | |
| pull_request: | |
| branches: [ main ] | |
| jobs: | |
| flake8: | |
| continue-on-error: true | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ["3.9"] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v3 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install flake8 | |
| - name: Run flake8 formating | |
| run: | | |
| flake8 unidock_tools/unidock_tools --exit-zero | |
| pylint: | |
| continue-on-error: true | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ["3.9"] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v3 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install pylint | |
| - name: Run pylint formating | |
| run: | | |
| pylint unidock_tools/unidock_tools --exit-zero | |
| mypy: | |
| continue-on-error: true | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ["3.9"] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v3 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install mypy | |
| - name: Run mypy check | |
| id: mypy_check | |
| run: | | |
| mypy unidock_tools/unidock_tools --ignore-missing-imports | |
| ut: | |
| if: ${{ always() }} | |
| needs: [flake8, pylint] | |
| runs-on: nvidia | |
| strategy: | |
| matrix: | |
| python-version: ["3.9"] | |
| container: | |
| image: docker.io/dptechnology/unidock:latest | |
| options: --gpus all | |
| steps: | |
| - name: checkout repo | |
| uses: actions/checkout@v3 | |
| - name: Setup conda | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| miniconda-version: "latest" | |
| python-version: ${{ matrix.python-version }} | |
| - name: install dependency | |
| run: | | |
| conda create -n mgltools mgltools -c bioconda -y | |
| conda install -n test -c conda-forge -y openbabel | |
| conda run -n test pip install --upgrade pip | |
| conda run -n test pip install pytest | |
| - name: install package | |
| working-directory: ./unidock_tools | |
| run: | | |
| export PATH=/__w/Uni-Dock/Uni-Dock/3/envs/test/bin:$PATH | |
| python setup.py install | |
| - name: perform unit-test | |
| run: | | |
| export PATH=/__w/Uni-Dock/Uni-Dock/3/envs/test/bin:$PATH | |
| pytest unidock_tools/tests/ut -v |