fix bugs in github actions

Author: jcharkow

.github/workflows/execute_notebooks.yml

@@ -21,72 +21,72 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - name: Checkout repository
-      uses: actions/checkout@v4
-      with:
-        token: ${{ secrets.GITHUB_TOKEN }}
-        fetch-depth: 0
+      - 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: 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: 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: 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/*ipynb -name "*.ipynb" > notebooks_to_execute.txt
-        docs/Getting\ Started.ipynb > notebooks_to_execute.txt
+      - 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
+          "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
+          echo "Found notebooks:"
+          cat notebooks_to_execute.txt
           
-          # Check if execution was successful
-          if [ $? -eq 0 ]; then
-            echo "✓ Successfully executed: $notebook"
+          # 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 "✗ Failed to execute: $notebook"
-            exit 1
+            echo "✅ Notebooks executed successfully, no changes to commit"
           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