Update checknb.yml

Convert nb to .jl and run individually

.github/workflows/checknb.yml

@@ -38,7 +38,7 @@ jobs:
         run: python -m pip install -U pip
 
       - name: Install Python dependencies
-        run: python -m pip install -U -r requirements.txt
+        run: python -m pip install nbconvert
 
       - uses: julia-actions/setup-julia@v2
         with:
@@ -51,16 +51,29 @@ jobs:
         env:
           PYTHON: python
 
-      # Install Papermill for executing notebooks
-      - name: Install Papermill
-        run: python -m pip install papermill
+      # Convert notebooks to .jl files using nbconvert
+      - name: Convert Notebooks to Julia Scripts
+        run: |
+          for notebook in $(find notebooks -name "*.ipynb"); do
+            echo "Converting $notebook to Julia script"
+            jupyter nbconvert --to script "$notebook" --output-dir=. --output "$notebook.jl"
+          done
 
-      # Run all Jupyter notebooks using the wildcard, capture errors
-      - name: Run Jupyter Notebooks
+      # Update HOME variable in nb => .jl scripts
+      # HOME = "../.." => "."
+      - name: Update Paths in Converted Julia Scripts
+        run: |
+          for script in $(find converted_notebooks -maxdepth 1 -name "*.jl"); do
+            echo "Updating paths in $script"
+            sed -i 's|\.\./\.\.|.|g' "$script"
+          done
+
+      # Run converted .jl files using Julia
+      - name: Run Julia Scripts
         run: |
           EXIT_CODE=0
-          for notebook in $(find notebooks -name "*.ipynb"); do
-            echo "Running notebook: $notebook"
-            papermill "$notebook" /dev/null || EXIT_CODE=$?
+          for script in $(find . -maxdepth 1 -name "*.jl"); do
+            echo "Running Julia script: $script"
+            julia --project=. "$script" || EXIT_CODE=$?
           done
           exit $EXIT_CODE