Add basic autodoc for API documentation

I got tired of invoking ipython to type help() for documentation.  This isn't anything fancy, but it should at least build HTML documentation for the most important parts of the code.  I tried to organize things as best as I could without making everything a top-level document.

I tested this with `make html` from inside of the doc directory.  I'm used to sphinx having its own options in `setup.cfg` so I'm not sure how you guys actually build docs.