Update run_notebooks.yml

Organize github action workflow as multiple dependent jobs

.github/workflows/run_notebooks.yml

@@ -6,8 +6,43 @@ on:
       - 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 "[email protected]"
+          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
@@ -42,27 +77,24 @@ jobs:
             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"
+              2>&1 | tee -a notebook_execution.log || exit 1
           done
 
-      - name: List Executed Notebooks (Debug Step)
-        run: |
-          echo "Listing executed notebooks:"
-          ls -l executed_notebooks || echo "No notebooks found."
+  # 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: 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/$COMMIT_SHA/ || echo "No executed notebooks to copy."
+          cp executed_notebooks/*.ipynb gh-pages/$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
-
-      - name: Success or Failure Message
-        if: failure()
-        run: echo "Notebooks executed with errors, but pushed to GitHub Pages."