The reason that pythoscope overwrites test/test_pydoc.py is because it hasn't been properly inspected. If you turn on --verbose flag you'll see:
135709.880 inspector:36 INFO: Inspecting module test/test_pydoc.py.
135709.966 astbuilder:84 DEBUG: Had problems parsing:
Also notice that Pythoscope adds a test to the test/test_iterlen.py file and there everything is fine.
This is still an ugly bug - Pythoscope should *never* touch and uninspected module.
I don't want to delay 0.4.2 any more, but I will probably make 0.4.3 release for this fix alone. Thank you for the report!