Skip test_bgzf.py if Python's gzip is broken
Skip Bio.bgzf doctest if gzip broken http://bugs.python.org/issue17666
Can't import anything from Bio in run_tests.py
Revert moving import (must be after edit PYTHONPATH)
Stupid typo, broken under Python 3
Skip BGZF tests in test_SeqIO_index.py if issue 17666
Updated FastaWriter documentation to reflect reality

Someone must have edited the code and didn't update the documentation for FastaWriter.
Added color_scheme keyword to weblogo to allow users to set their own colors (suggested by Anthony Mathelier of UBC)
added a gc_content method method to the GenericPositionMatrix in Bio.motifs (contributed by Anthony Mathelier of UBC)
removed some whitespace
Avoid NaN results if p is zero
Two blank lines between classes (PEP8)
Fix lots of overly long lines, try to follow PEP8 for property docstrings
Omit argument with default value
Adding static argument to Bio.Application, use for BWA
Fix for missing isnan on Python 2.5
Clarify docstring import for newcomers.

This wasn't needed for the doctest to work (by default a
doctest has the module's namespace preloaded). See:
http://lists.open-bio.org/pipermail/biopython/2013-May/008578.html
optionalcascade now requires container and item attr names as args

Hit has also been updated to initialize with some default values
Remove explicit '._items' slicing in optionalcascade

For QueryResult to use optionalcascade instead of partialcascade, this is
needed; as explicit '._items' indexing will return the Hit key instead of the
Hit object.
Merge partialcascade into optionalcascade