COG-945 Add pandas utility examples #12
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| name: Run Jupyter Notebooks | |
| on: | |
| push: | |
| branches: | |
| - "**" | |
| pull_request: | |
| types: [opened, synchronize, reopened] | |
| jobs: | |
| run-notebooks: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.13" | |
| - name: Install dependencies | |
| run: | | |
| pip install --upgrade pip | |
| pip install chemaxon jupyter nbconvert ipykernel | |
| python -m ipykernel install --user --name python3 | |
| - name: Run 01_basic_functions.ipynb | |
| run: | | |
| jupyter nbconvert --to notebook --execute \ | |
| --ExecutePreprocessor.timeout=600 \ | |
| --output /tmp/01_basic_functions_executed.ipynb \ | |
| jupyter/01_basic_functions.ipynb | |
| - name: Run 02_calculators.ipynb | |
| run: | | |
| jupyter nbconvert --to notebook --execute \ | |
| --ExecutePreprocessor.timeout=600 \ | |
| --output /tmp/02_calculators_executed.ipynb \ | |
| jupyter/02_calculators.ipynb | |
| - name: Run 03_molecular_similarity.ipynb | |
| run: | | |
| jupyter nbconvert --to notebook --execute \ | |
| --ExecutePreprocessor.timeout=600 \ | |
| --output /tmp/03_molecular_similarity_executed.ipynb \ | |
| jupyter/03_molecular_similarity.ipynb | |
| - name: Run 04_standardizer.ipynb | |
| run: | | |
| jupyter nbconvert --to notebook --execute \ | |
| --ExecutePreprocessor.timeout=600 \ | |
| --output /tmp/04_standardizer_executed.ipynb \ | |
| jupyter/04_standardizer.ipynb | |
| - name: Run 05_structure_checker.ipynb | |
| run: | | |
| jupyter nbconvert --to notebook --execute \ | |
| --ExecutePreprocessor.timeout=600 \ | |
| --output /tmp/05_structure_checker_executed.ipynb \ | |
| jupyter/05_structure_checker.ipynb | |
| - name: Run 06_molecule_search.ipynb | |
| run: | | |
| jupyter nbconvert --to notebook --execute \ | |
| --ExecutePreprocessor.timeout=600 \ | |
| --output /tmp/06_molecule_search_executed.ipynb \ | |
| jupyter/06_molecule_search.ipynb | |
| - name: Run 07_pandas_integration_examples.ipynb | |
| run: | | |
| jupyter nbconvert --to notebook --execute \ | |
| --ExecutePreprocessor.timeout=600 \ | |
| --output /tmp/07_pandas_integration_examples_executed.ipynb \ | |
| jupyter/07_pandas_integration_examples.ipynb | |
| - name: Run 08_fingerprint_calculations.ipynb | |
| run: | | |
| jupyter nbconvert --to notebook --execute \ | |
| --ExecutePreprocessor.timeout=600 \ | |
| --output /tmp/08_fingerprint_calculations_executed.ipynb \ | |
| jupyter/08_fingerprint_calculations.ipynb | |
| - name: Upload executed notebooks as artifacts | |
| if: always() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: executed-notebooks | |
| path: /tmp/*_executed.ipynb | |
| retention-days: 7 |