JarRunner initializes sys (PySystemState), passing args in (including the name "__run__" as arg 0 for consistancy with Python expectations), and import __run__. It is intended to be used to allow an application jarred up with Jython's runtime to run like "java -jar foo.jar". It requires a __run__.py in the jar that will execute the program, and the following entry in the manifest: Main-Class: org.python.util.JarRunner XXX: For the moment it should be considered experimental, but it is simple enough that I expect to be able to remove this warning pretty quickly.