the underlying code has this assumption when writing it

That means that you want to make things work not in a standard Python way ... In which case you need to do "non-standard" things to make it work.
You can do this for example in the beginning of your run.py

import sys
import os
sys.path.append(os.path.abspath(os.path.join(os.path.dirname(__file__), '..')))

In this way, you not relying on a non-standard feature to be implemented by your tool like pycharm or clearml