<s>[INST] What is the best project structure for a Python application? Imagine that you want to develop a non-trivial end-user desktop (not web) application in Python. What is the best way to structure the project's folder hierarchy?
Desirable features are ease of maintenance, IDE-friendliness, suitability for source control branching/merging, and easy generation of install packages.
In particular:

Where do you put the source?
Where do you put application startup scripts?
Where do you put the IDE project cruft?
Where do you put the unit/acceptance tests?
Where do you put non-Python data such as config files?
Where do you put non-Python sources such as C++ for pyd/so binary extension modules?

 [/INST] Doesn't too much matter.  Whatever makes you happy will work.  There aren't a lot of silly rules because Python projects can be simple.

/scripts or /bin for that kind of command-line interface stuff
/tests for your tests
/lib for your C-language libraries
/doc for most documentation
/apidoc for the Epydoc-generated API docs.

And the top-level directory can contain README's, Config's and whatnot.
The hard choice is whether or not to use a /src tree.  Python doesn't have a distinction between /src, /lib, and /bin like Java or C has.
Since a top-level /src directory is seen by some as meaningless, your top-level directory can be the top-level architecture of your application.

/foo
/bar
/baz

I recommend putting all of this under the "name-of-my-product" directory.  So, if you're writing an application named quux, the directory that contains all this stuff is named  /quux.
Another project's PYTHONPATH, then, can include /path/to/quux/foo to reuse the QUUX.foo module.  
In my case, since I use Komodo Edit, my IDE cuft is a single .KPF file.  I actually put that in the top-level /quux directory, and omit adding it to SVN.
 </s>