Check Tutorials #110
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| name: Check Tutorials | |
| on: | |
| workflow_dispatch: # allow manual runs | |
| schedule: | |
| # Runs at 00:00 UTC every Sunday | |
| - cron: '0 0 * * 0' | |
| pull_request: | |
| branches: | |
| - main | |
| paths: | |
| - 'flexynesis/**' | |
| - '.github/workflows/models.yml' | |
| - 'pyproject.toml' | |
| - 'manifest.scm' | |
| - 'guix.scm' | |
| jobs: | |
| check_tutorials: | |
| strategy: | |
| matrix: | |
| os: [ubuntu-latest, macos-latest] | |
| python-version: ["3.11", "3.12", "3.x"] | |
| runs-on: ${{ matrix.os }} | |
| name: Tutorials Python ${{ matrix.python-version }} on ${{ matrix.os }} | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install papermill ipykernel | |
| - name: Install my package from source | |
| run: | | |
| pip install -e . | |
| - name: Install Jupyter Kernel | |
| run: | | |
| python -m ipykernel install --user --name my_env_kernel --display-name "my_env_kernel" | |
| - name: Compile brca_subtypes.ipynb | |
| run: | | |
| notebook='examples/tutorials/brca_subtypes' | |
| papermill "${notebook}.ipynb" "${notebook}_out.ipynb" -p HPO_ITER 1 -k my_env_kernel | |
| - name: Compile lgg_gbm.ipynb | |
| run: | | |
| notebook='examples/tutorials/survival_subtypes_LGG_GBM' | |
| papermill "${notebook}.ipynb" "${notebook}_out.ipynb" -p HPO_ITER 1 -k my_env_kernel | |
| - name: Compile unsupervised-analysis | |
| run: | | |
| notebook='examples/tutorials/unsupervised_analysis_single_cell' | |
| papermill "${notebook}.ipynb" "${notebook}_out.ipynb" -p HPO_ITER 1 -k my_env_kernel | |
| - name: Compile cbioportal | |
| run: | | |
| notebook='examples/tutorials/cbioportal' | |
| papermill "${notebook}.ipynb" "${notebook}_out.ipynb" -p HPO_ITER 1 -k my_env_kernel |