As of r95, the code produces passable doxygen docs. I made sure that the documentation of the function variables was at least enumerated properly using markdown functionality available only in python >= 1.8 (so that it still looks okay using standard pydoc routines).

Would be nice at some point to introduce proper context highlighted for examples using ~_~~~~~~~~ flag and formula markups for the formulae so they get parsed properly... but this is a good start. Also I couldnt figure out how to persuade doxygen to group documentation together...