docs: do not execute notebooks (#93) #4
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| # .github/workflows/execute-notebooks.yml | |
| name: Execute Notebooks | |
| on: | |
| push: | |
| branches: [ main ] | |
| paths: | |
| - 'docs/Data Formatting/*ipynb' | |
| - 'docs/*ipynb' | |
| - '.github/workflows/execute_notebooks.yml' | |
| pull_request: | |
| branches: [ main ] | |
| paths: | |
| - 'docs/Data Formatting/*ipynb' | |
| - 'docs/*ipynb' | |
| - '.github/workflows/execute_notebooks.yml' | |
| workflow_dispatch: # Allow manual trigger | |
| jobs: | |
| execute-notebooks: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| with: | |
| token: ${{ secrets.GITHUB_TOKEN }} | |
| fetch-depth: 0 | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.12' | |
| cache: 'pip' | |
| - name: Install dependencies | |
| run: | | |
| # Install system dependencies | |
| sudo apt update | |
| sudo apt install pandoc | |
| # Install Python dependencies | |
| python -m pip install --upgrade pip | |
| pip install jupyter nbconvert nbformat | |
| pip install -r requirements.txt | |
| pip install ipykernel rdkit cairosvg pymzml | |
| pip install . | |
| - name: Configure git | |
| run: | | |
| git config --local user.email "action@github.com" | |
| git config --local user.name "GitHub Action" | |
| - name: Find and execute notebooks | |
| run: | | |
| # Find all notebooks that need to execute (adjust paths as needed) | |
| find "docs/Data Formatting/" -name "*.ipynb" > notebooks_to_execute.txt | |
| echo "docs/Getting Started.ipynb" >> notebooks_to_execute.txt | |
| echo "Found notebooks:" | |
| cat notebooks_to_execute.txt | |
| # Execute each notebook | |
| while IFS= read -r notebook; do | |
| echo "Executing: $notebook" | |
| # Clear outputs first (optional) | |
| jupyter nbconvert --clear-output --inplace "$notebook" | |
| # Execute notebook | |
| jupyter nbconvert --execute --to notebook --inplace "$notebook" \ | |
| --ExecutePreprocessor.timeout=300 \ | |
| --ExecutePreprocessor.kernel_name=python3 | |
| # Check if execution was successful | |
| if [ $? -eq 0 ]; then | |
| echo "✓ Successfully executed: $notebook" | |
| else | |
| echo "✗ Failed to execute: $notebook" | |
| exit 1 | |
| fi | |
| done < notebooks_to_execute.txt | |
| - name: Push changes | |
| if: steps.verify-changed-files.outputs.changed == 'true' && github.event_name != 'pull_request' | |
| run: | | |
| git push origin ${{ github.ref_name }} | |
| - name: Summary | |
| run: | | |
| if [ "${{ steps.verify-changed-files.outputs.changed }}" == "true" ]; then | |
| echo "✅ Notebooks executed successfully and changes committed" | |
| else | |
| echo "✅ Notebooks executed successfully, no changes to commit" | |
| fi |