Major refractor

Author: RobbinBouwmeester

.gitignore

@@ -4,6 +4,15 @@ workflow_visualization/*.svg
 workflow_visualization/*.pdf
 workflow_visualization/plantuml.jar
 workflow_visualization/*.class
+*.png
+*.puml
+
+# Pipeline output and intermediate files
+test_results.txt
+.benchmarks/
+mumdia.egg-info/
+mzml_files/
+notebook_helpers/
 
 # Byte-compiled / optimized / DLL files
 __pycache__/

config.py

@@ -103,7 +103,7 @@ def load_config_from_json(json_path: str) -> 'MuMDIAConfig':
 
     # Check if this is the old nested format
     if "sage_basic" in config_data or "sage" in config_data or "mumdia" in config_data:
-        print(f"🔄 Converting legacy config format to new simplified format...")
+        print("Converting legacy config format to new simplified format...")
         config_data = convert_legacy_config(config_data)
 
     # Filter out comment fields (fields starting with _comment)
@@ -532,9 +532,9 @@ def get_config() -> MuMDIAConfig:
         print(f"  deisotope: {full['deisotope']}")
         print()
 
-        print("✅ Simplified configuration with smart defaults!")
-        print("✅ Automatic initial vs full search differentiation!")
-        print("✅ Override system working!")
-        
+        print("Simplified configuration with smart defaults!")
+        print("Automatic initial vs full search differentiation!")
+        print("Override system working!")
+
     except SystemExit:
-        print("❌ Configuration validation failed")
+        print("Configuration validation failed")