Copy over FileGenerator from main branch to resolve merge conflict

This branch was created before a fix was added thats why i just commented out the code

FileGenerator.py

@@ -2,19 +2,23 @@
 from generation_utils.StructureHandler import StructureHandler
 import yaml
 from generation_utils.Logger import Logger
-import shutil
-# from precice_struct import PS_PreCICEConfig
-# from ui_struct.UI_UserInput import UI_UserInput
-# from myutils.UT_PCErrorLogging import UT_PCErrorLogging
+import sys
+# Insert controller into syspath so imports within controller submodule will still work
+sys.path.insert(0, str(( Path(__file__).parent / 'controller' ).resolve()))
+# Import controller classes
+from controller.ui_struct.UI_UserInput import UI_UserInput
+from controller.myutils.UT_PCErrorLogging import UT_PCErrorLogging
+from precice_struct import PS_PreCICEConfig
+import argparse
 
 class FileGenerator:
     def __init__(self, file: Path) -> None:
         """ Class which takes care of generating the content of the necessary files
             :param file: Input yaml file that is needed for generation of the precice-config.xml file"""
         self.input_file = file
-        #self.precice_config = PS_PreCICEConfig()
-        #self.mylog = UT_PCErrorLogging()
-        #self.user_ui = UI_UserInput()
+        self.precice_config = PS_PreCICEConfig()
+        self.mylog = UT_PCErrorLogging()
+        self.user_ui = UI_UserInput()
         self.logger = Logger()
         self.structure = StructureHandler()
 
@@ -33,26 +37,25 @@ def generate_precice_config(self) -> None:
             self.logger.error(f"Error reading input YAML file: {str(e)}")
             return
 
-        # # Build the ui
-        # self.logger.info("Building the user input info...")
-        # self.user_ui.init_from_yaml(config, self.mylog)
-        #
-        # # Generate the precice-config.xml file
-        # self.logger.info("Generating preCICE config...")
-        # self.precice_config.create_config(self.user_ui)
-        #
-        # # Set the target of the file and write out to it
-        # # Warning: self.structure.precice_config is of type Path, so it needs to be converted to str
-        # target = str(self.structure.precice_config)
-        # try:
-        #     self.logger.info(f"Writing preCICE config to {target}...")
-        #     self.precice_config.write_precice_xml_config(target, self.mylog)
-        # except Exception as e:
-        #     self.logger.error(f"Failed to write preCICE XML config: {str(e)}")
-        #     return
-        #
-        # self.logger.success(f"XML generation completed successfully: {target}")
-        self.logger.success(f"XML generation completed successfully:")
+        # Build the ui
+        self.logger.info("Building the user input info...")
+        self.user_ui.init_from_yaml(config, self.mylog)
+
+        # Generate the precice-config.xml file
+        self.logger.info("Generating preCICE config...")
+        self.precice_config.create_config(self.user_ui)
+
+        # Set the target of the file and write out to it
+        # Warning: self.structure.precice_config is of type Path, so it needs to be converted to str
+        target = str(self.structure.precice_config)
+        try:
+            self.logger.info(f"Writing preCICE config to {target}...")
+            self.precice_config.write_precice_xml_config(target, self.mylog)
+        except Exception as e:
+            self.logger.error(f"Failed to write preCICE XML config: {str(e)}")
+            return
+
+        self.logger.success(f"XML generation completed successfully: {target}")
 
     def generate_README(self) -> None:
         """Generates the README.md file"""
@@ -101,6 +104,16 @@ def generate_adapter_config(self) -> None:
         pass
 
 if __name__ == "__main__":
-    fileGenerator = FileGenerator(Path("./examples/3/topology.yaml"))
+    parser = argparse.ArgumentParser(description="Takes topology.yaml files as input and writes out needed files to start the precice.")
+    parser.add_argument(
+        "-f", "--file", 
+        type=Path, 
+        required=False, 
+        help="Input topology.yaml file",
+        default=Path("controller/examples/1/topology.yaml")
+    )
+    args = parser.parse_args()
+
+    fileGenerator = FileGenerator(args.file)
     fileGenerator.generate_precice_config()
-    fileGenerator.generate_README()
+    fileGenerator.generate_README()