run_notebooks.yml

name: Run Notebooks and Save Outputs

on:
  push:
    branches:
      - main  # Trigger the action on the main branch

jobs:
  # First job: Clear outputs with nbstripout
  clear-outputs:
    runs-on: ubuntu-latest

    steps:
      - name: Checkout Repository
        uses: actions/checkout@v3

      - name: Set up Python
        uses: actions/setup-python@v4
        with:
          python-version: '3.10'

      - name: Install nbstripout
        run: |
          pip install nbstripout
          nbstripout --install

      - name: Strip notebook outputs
        run: |
          find . -name "*.ipynb" -exec nbstripout --force --keep-count {} +

      - name: Check for changes
        run: git status

      - name: Commit cleaned notebooks if needed
        run: |
          git config --global user.email "action@github.com"
          git config --global user.name "GitHub Action"
          git add .
          git commit -m "Auto-strip notebook outputs" || echo "No changes to commit"
          git push || echo "Nothing to push"

  # Second job: Run the notebooks
  run-notebooks:
    runs-on: ubuntu-latest
    needs: clear-outputs  # Ensure this job runs after 'clear-outputs'

    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
          # Make SCT callable from within the environment
          source /home/runner/.bashrc

      - 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 || exit 1
          done

  # Third job: Deploy to GitHub Pages (depends on run-notebooks)
  deploy:
    runs-on: ubuntu-latest
    needs: run-notebooks  # Ensure this job runs after 'run-notebooks'

    steps:
      - name: Checkout Repository
        uses: actions/checkout@v3

      - 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/

      - 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