- the application now uses only the default values from the app.options dict, the app.defaults dict holds the definitive default values

- fixed some outstanding issues from the PyQt6 port
- PEP8 fixes
- minor fixes
- updated the saving of Preferences to update the self.options too: the `Apply` action will update the self.options but the `Save` action will save the updated preferences to the file on disk

tclCommands/TclCommandIsolate.py

@@ -84,7 +84,7 @@ class TclCommandIsolate(TclCommandSignaled):
                 par = args['combine']
             args['combine'] = bool(eval(str(par)))
         else:
-            args['combine'] = bool(eval(str(self.app.defaults["tools_iso_combine_passes"])))
+            args['combine'] = bool(eval(str(self.app.options["tools_iso_combine_passes"])))
 
         obj = self.app.collection.get_by_name(name)
         if obj is None: