Check Tutorials #25
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| name: Check Tutorials | |
| on: | |
| workflow_dispatch: # This line enables manual triggering of the workflow | |
| schedule: | |
| # Runs at 00:00 UTC every Sunday | |
| - cron: '0 0 * * 0' | |
| jobs: | |
| check_tutorials: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v2 | |
| - name: Set up Python | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: '3.11' | |
| - name: Set up Miniconda | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| auto-update-conda: true | |
| python-version: '3.11' | |
| - name: Cache Conda environment | |
| uses: actions/cache@v2 | |
| with: | |
| path: ~/miniconda/envs | |
| key: ${{ runner.os }}-conda-${{ hashFiles('spec-file.txt') }} | |
| restore-keys: | | |
| ${{ runner.os }}-conda- | |
| - name: Create environment with dependencies | |
| shell: bash -l {0} | |
| run: | | |
| conda create --name my_env --file spec-file.txt | |
| conda activate my_env | |
| - name: Install my package from source | |
| shell: bash -l {0} | |
| run: | | |
| conda activate my_env | |
| pip install -e . | |
| - name: Install Jupyter Kernel | |
| shell: bash -l {0} | |
| run: | | |
| conda activate my_env | |
| python -m ipykernel install --user --name my_env_kernel --display-name "my_env_kernel" | |
| - name: Compile brca_subtypes.ipynb | |
| shell: bash -l {0} | |
| run: | | |
| conda activate my_env | |
| notebook='examples/tutorials/brca_subtypes' | |
| papermill "${notebook}.ipynb" "${notebook}_out.ipynb" -p HPO_ITER 1 -k my_env_kernel | |
| - name: Compile modeling_drug_response | |
| shell: bash -l {0} | |
| run: | | |
| conda activate my_env | |
| notebook='examples/tutorials/modeling_drug_response' | |
| papermill "${notebook}.ipynb" "${notebook}_out.ipynb" -p HPO_ITER 1 -k my_env_kernel | |
| - name: Compile survival_subtypes_LGG_GBM | |
| shell: bash -l {0} | |
| run: | | |
| conda activate my_env | |
| notebook='examples/tutorials/survival_subtypes_LGG_GBM' | |
| papermill "${notebook}.ipynb" "${notebook}_out.ipynb" -p HPO_ITER 1 -k my_env_kernel | |
| - name: Compile scrnaseq_bonemarrow | |
| shell: bash -l {0} | |
| run: | | |
| conda activate my_env | |
| notebook='examples/tutorials/scrnaseq_bonemarrow' | |
| papermill "${notebook}.ipynb" "${notebook}_out.ipynb" -p HPO_ITER 1 -k my_env_kernel | |
| - name: Compile neuroblastoma_data_integration | |
| shell: bash -l {0} | |
| run: | | |
| conda activate my_env | |
| notebook='examples/tutorials/neuroblastoma_data_integration' | |
| papermill "${notebook}.ipynb" "${notebook}_out.ipynb" -p HPO_ITER 1 -k my_env_kernel | |
| - name: Compile unsupervised_analysis_single_cell | |
| shell: bash -l {0} | |
| run: | | |
| conda activate my_env | |
| notebook='examples/tutorials/unsupervised_analysis_single_cell' | |
| papermill "${notebook}.ipynb" "${notebook}_out.ipynb" -p HPO_ITER 1 -k my_env_kernel |