When running the test command, or any other command that invokes with_project_on_sys_path, setuptools ensures those projects are on sys.path, but if a subprocess is launched that relies on those dependencies such as tox does or any other project that launches subprocesses to create fixtures or launch services, that subprocess won't have the projects on sys.path so will fail, as reported in tox-dev/tox#360.

On project I maintain works around this issue by adding all of sys.path to PYTHONPATH for the subprocesses. Setuptools should do something similar (though more elegant by matching only those projects added), enabling this use case in general.