tracks reasons for _not_executed
copyright fix
pep8 complaints
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
removing files
Port safe_md5 to bipy

This includes the required additions to the documentation and pertinent
tests.
Remove whitespace
Added class FastqParseError to exception.py
added newline character
Change link to avoid the redirection

make checklink complained about the link doing a redirection.
fixes #138, but I'd rather it be a little smarter
Fixes #120.
made pep8 compliant
Fix PEP8 complaints
fixing code to not use unit tests from bipy
Merge branch 'master' of github.com:biocore/bipy into issue-138

Conflicts:
	bipy/core/sequence.py