EDITED to provide better clarity of question
Is there a recommended or standard way to organize a large python application -- as in, requires multiple files in different sub directories for a clearly organization project.
All the documentation I have been able to find talk about packages, which to my eye are what in any other language would be called a library. i.e. code that is included / required by the main program. The setup.py in a package adds to this confusion because it looks like it should be the main program/script for the entire application, but is used to "Install" the modules as a library instead.
In short, standards/recommendations for organizing code to be a application(a program that you actually run). Not a library/package(something which is included/used by an application)