Update run_notebooks.yml #21
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| name: Run Notebooks and Save Outputs | |
| on: | |
| push: | |
| branches: | |
| - main # Trigger the action on the main branch | |
| jobs: | |
| run-notebooks: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v3 | |
| - name: Clear GitHub Action Caches | |
| run: | | |
| echo "Clearing caches..." | |
| sudo rm -rf ~/.cache/pip | |
| sudo rm -rf executed_notebooks | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.10' | |
| - name: Install Python dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install -r requirements.txt | |
| - name: Install SCT | |
| run: | | |
| git clone --depth 1 https://github.com/spinalcordtoolbox/spinalcordtoolbox.git | |
| yes | spinalcordtoolbox/install_sct | |
| - name: Run Jupyter Notebooks | |
| continue-on-error: true # Allow workflow to continue even if notebook execution fails | |
| run: | | |
| mkdir -p executed_notebooks | |
| for notebook in $(find . -name "*.ipynb"); do | |
| echo "Executing $notebook" | |
| jupyter nbconvert --to notebook --execute --allow-errors --inplace \ | |
| --output executed_notebooks/$(basename $notebook) $notebook \ | |
| 2>&1 | tee -a notebook_execution.log || echo "Execution failed for $notebook" | |
| done | |
| - name: List Executed Notebooks (Debug Step) | |
| run: | | |
| echo "Listing executed notebooks:" | |
| ls -l executed_notebooks || echo "No notebooks found." | |
| - name: Copy Executed Notebooks to Pages Directory | |
| run: | | |
| COMMIT_SHA=$(git rev-parse --short HEAD) | |
| mkdir -p gh-pages/$COMMIT_SHA | |
| cp executed_notebooks/*.ipynb gh-pages/$COMMIT_SHA/ || echo "No executed notebooks to copy." | |
| - name: Deploy to GitHub Pages | |
| uses: peaceiris/actions-gh-pages@v3 | |
| with: | |
| github_token: ${{ secrets.GITHUB_TOKEN }} | |
| publish_dir: gh-pages | |
| publish_branch: gh-pages | |
| - name: Success or Failure Message | |
| if: failure() | |
| run: echo "Notebooks executed with errors, but pushed to GitHub Pages." |