Fix docs

[dwhswenson]

Resolves #49.

Had to pin almost everything (I couldn't get a pip install of MDTraj working on RTD). The things specific to docs (like the nbsphinx extension) are not pinned, but all the scientific things (MDTraj, numpy, etc) are pinned in the RTD environment.

Note that these pins only affect the doc building environment, not the testing environment.

I also left things in place to again attempt a pip-based install at a later date.

Only affects things specific to how RTD builds the docs.