- 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

appCommon/Common.py

@@ -588,8 +588,8 @@ class ExclusionAreas(QtCore.QObject):
 
             self.app.app_cursor.set_data(np.asarray([(curr_pos[0], curr_pos[1])]),
                                          symbol='++', edge_color=self.app.cursor_color_3D,
-                                         edge_width=self.app.defaults["global_cursor_width"],
-                                         size=self.app.defaults["global_cursor_size"])
+                                         edge_width=self.app.options["global_cursor_width"],
+                                         size=self.app.options["global_cursor_size"])
 
         # update the positions on status bar
         if self.cursor_pos is None: