I'm not sure if it matters but 'kwcoco' is being imported inside one of the repo's functions and not on the script's header.

Should work.
when you run pip freeze inside the same env what are you getting ?
Also, is there anyother import that is missing? (basically 'clearml' tryies to be smart, and see if maybe the script itself, even though inside a repo, is not actually importing anything from the repo itself, and if this is the case it will only analyze the original script. Basically are you importing any "local" modules inside the original script is the way it detects it)