I want diagrams of my modules and how things are connected, such as one that shows "types defined in foo.py are used in bar.py". While you're generating docs from code, might think about diagrams.
Have you tried Pyreverse[1]? I used it for my Software Engineering course. From the documentation - Pyreverse analyses Python code and extracts UML class diagrams and package dependencies.
[1] https://www.logilab.org/blogentry/6883