I think in the interest of ploughing ahead I'd prefer to keep the implementation as-is. We'd need a better sense of what it means to have dependencies "for the purpose of running a tool".

__init__.py

is a simpler case - it is true in some sense that those are deps. But

conftest.py

isn't really a dep of the code under test, it's config for the pytest runner itself. So I'm not sure modeling it as a dep is even the right thing to do.