Question: I have read several similar topics but haven't succeeded yet. I feel I miss or misunderstand some fundamental thing and this is the reason of my failure. I have an 'application' written in a python which I want to deploy with help of standard setup.py. Due to complex functionality it consists of different python modules. But there is no sense in separate release of this modules as they are too specific. Expected result is to have package installed in a system with help of pip install and be available from OS command line with simple app command. Simplifying long story to reproducible example - I have following directory structure: <root> ├─ app | ├─ aaa | | └── module_a.py | ├─ bbb | | └── module_b.py | └── app.py ├─ docs | └── ..... ├─ tests | └── ..... └─ setup.py  Below is code of modules: app.py #!/usr/bin/python from aaa.module_a import method1 from bbb.module_b import method2 def main(): print("APP main executed") method1() method2() if __name__ == '__main__': main()  module_a.py def method1(): print("A1 executed")  module_b.py def method2(): print("B2 executed")  When I run app.py from console it works fine and gives expected output: APP main executed A1 executed B2 executed  So, this simple 'application' works fine and I want to distribute it with help of following setup.py from setuptools import setup setup( name="app", version="1.0", packages=['app', 'app.aaa', 'app.bbb'], package_dir={'app': 'app'}, entry_points={ 'console_scripts': ['app=app.app:main', ] } )  Again, everything looks good and test installation looks good: (venv) [user@test]$ pip install <root> Processing /home/user/<root> Using legacy 'setup.py install' for app, since package 'wheel' is not installed. Installing collected packages: app Running setup.py install for app ... done Successfully installed app-1.0 (venv) [user@test]$  And now comes the problem. With aforementioned entry_points from setup.py I expect to be able execute my application with ./app command. Indeed it works. But application itself fails with error message: File "/test/venv/lib/python3.9/site-packages/app/app.py", line 3, in <module> from aaa.module_a import method1 ModuleNotFoundError: No module named 'aaa'  I understand the reason of the error - it is because pip install put directories aaa and bbb together with app.py in one directory app. I.e. from this point of view app.py should use import app.aaa instead of import aaa. But if I do so then my app during development runs with error: ModuleNotFoundError: No module named 'app.aaa'; 'app' is not a package  that is also logical as there are no app package available at that time... (it is under development and isn't installed in the system...) Finally. The question is - what is a correct way to create directory structure and setup.py for standalone python application that consist of several own modules? UPD The most promising result (but proved to be wrong after discussion in coments) that I have now came after following changes:  moved app.py from <root>/app into <root> itself I referenced it in setup.py by py_modules=['app'] I changed imports from import aaa.method1 to import app.aaa.method1 etc.  This way package works both in my development environment and after installation. But I got a problem with entry_points - I see no way how to configure entry point to use main() from app.py that is not a part of app package but is a separate module.... I.e. new structure is <root> ├─ app | ├─ aaa | | └── module_a.py | ├─ bbb | | └── module_b.py | └──__init__.py ├─ docs | └── ..... ├─ tests | └── ..... ├─ app.py └─ setup.py  I.e. the logic here - to have 2 separate entities:  An empty package app (consists of init.py only) with subpackages aaa, bbb etc. A script app.py that uses functions from subpackages app.aaa, app.bbb  But as I wrote - I see no way how to define entry point for app.py to allow it's run from OS command line directly.

Answer: With that directory (package) structure, in your app.py you should import as one of the following: from app.aaa.module_a import method1  from .aaa.module_a import method1  Then make sure to call you application like one of the following: app  (this should work thanks to the console entry point) python -m app.app  (this should work even without the console entry point)  I try to recreate the complete project here Directory structure: . ├── app │ ├── aaa │ │ └── module_a.py │ ├── app.py │ └── bbb │ └── module_b.py └── setup.py  setup.py import setuptools setuptools.setup( name="app", version="1.0", packages=['app', 'app.aaa', 'app.bbb'], entry_points={ 'console_scripts': ['app=app.app:main', ] }, )  app/app.py #!/usr/bin/env python from .aaa.module_a import method1 from .bbb.module_b import method2 def main(): print("APP main executed") method1() method2() if __name__ == '__main__': main()  app/aaa/module_a.py def method1(): print("A1 executed")  app/bbb/module_b.py def method2(): print("B2 executed")  Then I run following commands: $ python3 -V Python 3.6.9  $ python3 -m venv .venv  $ .venv/bin/python -m pip install -U pip setuptools wheel # [...]  $ .venv/bin/python -m pip list Package Version ------------- ------------------- pip 20.3.3 pkg-resources 0.0.0 setuptools 51.1.0.post20201221 wheel 0.36.2  $ .venv/bin/python -m pip install . # [...]  $ .venv/bin/python -m app.app APP main executed A1 executed B2 executed  $ .venv/bin/app APP main executed A1 executed B2 executed  $ .venv/bin/python -m pip uninstall app # [...]  $ .venv/bin/python -m pip install --editable . # [...]  $ .venv/bin/python -m app.app APP main executed A1 executed B2 executed  $ .venv/bin/app APP main executed A1 executed B2 executed