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You should read this.

By putting the files at the same level, you put them is the same package level. In your case, you need to get this architecture:

mypackage
├── __init__.py
├── one.py # contains "import two"
└── two
 ├── __init__.py
 ├── three
 │  ├── __init__.py
 │  └── three.py
 └── two.py # contains "import three"

And then, you can access the package with:

import mypackage.one
import mypackage.one.two
import mypackage.one.two.three