I have an application at work that is set up with the following structure.
/project_root
/applications
/app1
__init__.py
/app2
The solution to this was a two step process:
pkg directory as a source root. Do this by selecting File -> Settings -> Project -> (select the project) -> Project Structure then select the pkg directory and add by clicking the Sources button. Click Ok.File -> Invalidate Caches / Restart -> Invalidate and RestartWait for PyCharm to restart and rebuild it's cache / scan the indexes. Now the pkg directory is detected as a source root and my errors are gone.