I've wrestled with this problem several times. My conclusion was mocks are just fine, but this is a wart in that there isn't "one way to do it"

For the most part I can get by with one rule: always mock the module.

  with mock.patch('os.listdir'):

will always work, even if it doesn't accomplish what you want.

  with mock.patch('mymodule.os.listdir')

will fail if that module does not explicitly import os and instead does something like from os import listdir (perhaps because a later dev did not realize importing os directly was actually a requirement for the test and changed the code).

The rule is not perfect though. In the above case, the error will actually be

  ImportError: No module named os

This can be fixed with e.g.,

  assert hasattr(module, 'os'), "os module is not explicitly imported"

as a preamble to your test but ... it is not perfect by any means.

EDIT: formatting