Modular

Hi Andrew,

I have just been looking through your modular branch with the eye to start implementing the proposed changes in my email to the NineML mailing list from there. However, since I have configured my editor to flag all non-pep8 compliant code as I was going through it I cleaned up all the warnings (it has been a slow day as I get my head back into coding after OCNS). Since this meant touching a lot of files I thought I would make a pull request soon to avoid a headache merging them later on. 

All the unittests still pass, so I am assuming that I haven't broken anything in the process (not that I should have).

Cheers,

Tom