A good IDE will keep that structure simple and organized, too. The problem with python is more that its dynamic, duck typing type system hinders some of the great benefits that "modern" (as in, from the past ~2 decades) IDEs bring. Since the IDE can hardly infer any type, and since even the ones it could infer can dynamically change in shape at any time, the IDE cannot provide as helpful suggestions and as powerful navigation as IDEs for other languages can.
For the same reason, compile time almost exclusively tells you about crass syntax errors only, which further diminishes an IDE's helpfulness.
I'd be curious to know if there are python IDEs who integrate with mypy (or the underlying static typing PEP) to bring some of the lost magic back to python IDEs.