The topic of how to structure your project invokes lots of opinions.  Generally speaking, the relatively agreed guidelines include:

 * if the project is a single source file, put it in the top level.
 * if you have tests, put them in a tests/ subdirectory (even if the project is a single source file), or if you have subdirectories and prefer to keep unit tests with code, put them there.
 * if you have an executable script to run your project, put it in a bin/ subdirectory, without the .py suffix even if it's a Python script
 * if you have many source files, create a subdirectory with the name of the project, and start populating there
 * include a doc/ directory (you have docs, right?)
 * create module directories as needed

These guidelines are partly convention, partly because they align well with Python packaging tools.

The Python tutorial shows an example of a more complex layout: https://docs.python.org/3/tutorial/modules.html#packages


There are many many other places that describe a layout, not all agreeing. Here are a couple:
 * [[https://www.cmi.ac.in/~madhavan/courses/prog2-2012/docs/diveintopython3/packaging.html|packaging chapter]] of [[https://www.cmi.ac.in/~madhavan/courses/prog2-2012/docs/diveintopython3/packaging.html#structure|Dive Into Python 3]] for some useful information.
 * https://realpython.com/python-application-layouts