Initial commit

start.sh

@@ -0,0 +1,65 @@
+#!/bin/bash
+# Startup script for SDF processing workflow
+
+echo "🚀 Starting SDF Processing Workflow"
+echo "===================================="
+
+# Check if we're in a pixi environment
+if [ -z "$PIXI_ENVIRONMENT_NAME" ]; then
+    echo "📦 Activating pixi environment..."
+    exec pixi run bash "$0" "$@"
+    exit $?
+fi
+
+echo "✅ Pixi environment activated: $PIXI_ENVIRONMENT_NAME"
+
+# Test the environment
+echo "🧪 Running environment test..."
+python test_environment.py
+
+if [ $? -eq 0 ]; then
+    echo ""
+    echo "🎯 Ready to start! Choose your next step:"
+    echo ""
+    echo "1. Start Jupyter Notebook (recommended):"
+    echo "   jupyter notebook notebooks/ --ip=0.0.0.0 --port=8888 --no-browser"
+    echo ""
+    echo "2. Start Jupyter Lab:"
+    echo "   jupyter lab notebooks/ --ip=0.0.0.0 --port=8888 --no-browser"
+    echo ""
+    echo "3. Run extraction script directly:"
+    echo "   python -c \"import papermill as pm; pm.execute_notebook('notebooks/01_extract_sdf_files.ipynb', 'extracted_output.ipynb')\""
+    echo ""
+    echo "4. Open interactive shell:"
+    echo "   pixi shell"
+    echo ""
+    
+    read -p "Enter your choice (1-4) or press Enter to start Jupyter: " choice
+    
+    case $choice in
+        1)
+            echo "📓 Starting Jupyter Notebook..."
+            jupyter notebook notebooks/ --ip=0.0.0.0 --port=8888 --no-browser
+            ;;
+        2)
+            echo "📓 Starting Jupyter Lab..."
+            jupyter lab notebooks/ --ip=0.0.0.0 --port=8888 --no-browser
+            ;;
+        3)
+            echo "🔄 Running extraction directly..."
+            pixi add papermill
+            python -c "import papermill as pm; pm.execute_notebook('notebooks/01_extract_sdf_files.ipynb', 'extracted_output.ipynb')"
+            ;;
+        4)
+            echo "🐚 Opening interactive shell..."
+            bash
+            ;;
+        *)
+            echo "📓 Starting Jupyter Notebook (default)..."
+            jupyter notebook notebooks/ --ip=0.0.0.0 --port=8888 --no-browser
+            ;;
+    esac
+else
+    echo "❌ Environment test failed. Please check the installation."
+    exit 1
+fi