Python’s import system is weird but it does make sense when you use absolute imports:

  project
  ├── main.py
  ├── package1
  │   ├── module1.py
  │   └── module2.py
  └── package2
      ├── __init__.py
      ├── module3.py
      ├── module4.py
      └── subpackage1
          └── module5.py

As long as the file containing the main() function resides in the top-level folder you can use absolute imports in every file, e.g.

  from package1 import module1
  from package1.module2 import function1
  from package2.subpackage1.module5 import function2