Thanks for sending the patch! Would you mind telling me more about how you're using the custom fixtures? I want to test this locally and my fixture setup happens in conftest.py which is working for me.
I am also using conftest.py, however it is in a sub-folder. My layout is something like root -> nsp -> app -> tests -> func -> conftest.py, test_app.py; so the fixtures are meant for functional tests of the app. The root is where pytest.el will cd to, as it contains setup.py. The nsp level is a namespace package which contains the package app. If I am in test_app.py and do pytest-module, py.test complains that a fixture was not found.