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Just some thoughts as we embark on the PyQt-based GUI:

The second example in the PyQt Designer documentation illustrates a controller separated from the view (the third example uses multiple inheritance, binding the controller and view into a single class). The uic.loadUi function allows directly loading the ui from a .ui file, without needing to explicitly compiling a .py file first via pyuic.

This Apple developer page has a nice short discussion about the various kinds of controllers we need: coordinating controllers, view controllers, and mediating controllers.