I have a project in Pycharm organized as follows:
-- Sources
|--__init__.py
|--Calculators
|--__init__.py
|--Filters.py
|--Controllers
I know this is old, but Google sent me here so I guess others will come too like me.
The answer on 2018 is the selected one here: Pycharm: "unresolved reference" error on the IDE when opening a working project
Just be aware that you can only add one Content Root
but you can add several Source Folders
. No need to touch __init__.py
files.