You need to make sure your PYTHONPATH is set correctly so the command-line interpreter can find your packages, or run your test cases from within Eclipse Pydev. Update: Another option: running your tests using nose might make things a bit easier, since it can auto-discover packages and test cases.
If your project is laid out like so:
/home/user/dev/ src/pkg1/ mod1.py test/ mod1_test.py Use: PYTHONPATH=$HOME/dev/src python test/mod1_test.py. I'd also recommend using distribute and virtualenv to set up your project for development.