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.
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.
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