Remove bipy prefix from doc filenames

Fixes #131.
Support for documenting private/special methods

Adding numpydoc source so that we can extend/customize as necessary (see licenses/numpydoc.txt for license).

Added an extension to the numpydoc standard that allows a developer to tag a method to be included in the built documentation, when it would have otherwise been ignored. This is necessary in order to have special methods (e.g.  __getitem__, __str__, etc.) included in the built docs.
remove numpydoc dep from setup.py and Travis conf
Merge pull request #134 from jrrideout/issue-129

DOC: remove 'bipy.' prefix and add support for documenting special/private methods
Merge branch 'master' of github.com:biocore/bipy