Use the src_paths isort config

[Stannislav]

Description

Please provide here a summary of the changes introduced by this PR.

How to test?

Please provide here instructions on how to test the changes introduced by this PR.
(if some changes cannot be tested by automated tests)

Checklist

• This PR refers to an issue from the issue tracker.
  (if it is not the case, please create an issue first).
• Unit tests added.
  (if needed)
• Documentation and whatsnew.rst updated.
  (if needed)
• setup.py and requirements.txt updated with new dependencies.
  (if needed)
• Type annotations added.
  (if a function is added or modified)
• All CI tests pass.