Add JSON artifact reader for inference #181
Workflow file for this run
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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", "3.13"] | |
| fail-fast: false | |
| runs-on: ${{ matrix.os }} | |
| name: Tutorials Python ${{ matrix.python-version }} on ${{ matrix.os }} | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v6 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v6 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install OpenMP (macOS only) | |
| if: runner.os == 'macOS' | |
| run: brew install libomp | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install papermill ipykernel | |
| - name: Install my package from source | |
| run: python -m pip install -e . | |
| - name: Install Jupyter Kernel | |
| run: | | |
| python -m ipykernel install --user --name my_env_kernel --display-name "my_env_kernel" | |
| - name: Create papermill wrapper | |
| run: | | |
| cat > run_nb.py << 'EOF' | |
| import sys | |
| import papermill as pm | |
| notebook = sys.argv[1] | |
| pm.execute_notebook( | |
| f'examples/tutorials/{notebook}.ipynb', | |
| f'examples/tutorials/{notebook}_out.ipynb', | |
| parameters={ | |
| 'HPO_ITER': 1, | |
| 'TOP_PERCENTILE': 0.5, | |
| 'PLOT_LOSSES': False, | |
| 'EARLY_STOP_PATIENCE': 1 | |
| }, | |
| kernel_name='my_env_kernel', | |
| execution_timeout=3600, | |
| iopub_timeout=3600 | |
| ) | |
| EOF | |
| - name: Compile brca_subtypes.ipynb | |
| run: python run_nb.py brca_subtypes | |
| - name: Compile lgg_gbm.ipynb | |
| run: python run_nb.py survival_subtypes_LGG_GBM | |
| - name: Compile unsupervised-analysis | |
| run: python run_nb.py unsupervised_analysis_single_cell | |
| - name: Compile cbioportal | |
| run: python run_nb.py cbioportal | |
| - name: Compile gnn_custom_networks | |
| run: python run_nb.py gnn_custom_networks |