PEP8 fixes Bio, Scripts
PEP8 on test_KEGG.py
Remove trailing whitespace from QueryResult.__str__ (Fixes #418)
Added a KEGG API Wrapper, docs, and tests

Take into account Peter's suggestions in PR#152. Move functions out of
KEGG/__init__.py and rename them to include "kegg_" prefixes. Change
function param names to better reflect KEGG endpoint params. Update
interface to include new KEGG functionality. Attempt to add more
argument validation with richer error messages.
KEGG get also supports kgml output
PEP8 tweaks to KEGG REST code
KEGG REST API tests using unittest.

Based on the print-and-compare tests prepared by Kevin Wu
(which I did not commit), plus an example using KGML originally
using Leighton's KGML_scrape.py for online access.
Thank Kevin and mention KEGG REST API in NEWS file.

This closes PR #152.
Basic docstrings for KEGG REST API.
Revert accidental whitespace change to test output
Fix common PEP8 violation in unittest verbosity argument
PEP8 work on test_prodoc.py
Interface specific adapter class for mysql.connector in BioSQL

BioSQL will use a specific MySQL adapter class when
necessary but in other cases it will default to the
general Adapter class. This closes issue #370.

Additionally, Adapter now inherits from object and
some docstrings were added to existing classes and
methods.
Addressed TODO's -use_index -soft_masking (BLAST+ wrappers)
BLAST+ wrappers now have -soft_masking and -use_index

Closes #328
Deal with dead URL (closes #404)
Fix typo; wonder if get_matrices.py still exists?