EMAN2 use Boost.python to wrap c++ function to Python. Pyste is a Boost.Python code generator. In EMAN2 there is a script create_boost_python in /eman2/libpyEM directory to create c++ wrapping file linpy***.cpp. Then the c++ compiler will create libraries which contain all the Python function call of EMAN2. Current release of Pyste has a dificit for the default argument handling. So please replace two of your Pyste files in Python site-packages with attached files.