upgrade cobra.external.six to 1.7.3
Update version.py

Update to aebrahim/python-git-version@e4b1833
cplex bug when setting paramter in solve_problem
cobra.io.mat dict construction is its own function

The create_mat_dict function may be useful when using sosmethig other
than scipy to write the mat file. The dict created contains vectors
matching the structure of the MATLAB COBRA toolbox struct.
README.md points to github site

Replaces the link to the older sourceforge site.
load_matlab_model reads subsystem
Improve setup.py on MacOS X

Running bdist_wheel will now append additional tag versions
automatically. Additionally, warnings for unused functions in clang are
now silenced to highlight other wanings which may signal issues.
update VERSION file on sdist/bdist_wheel
DictList Exception incorrectly formatted

The exception printed out the repr of the id function instead of the id
of the object which could not be added.
fix misspelling in documentation conf.py

mathjax cdn url was not being set to https because of this.
DOC: add faq and bugfixes

Add an FAQ notebook to answer common questions. It now answeres the
question of how to rename reactions/metabolites, which fixes #78.

The QP example now also has figures to better illustrate the problems.
cglpk: add function to write problem to LP file
quadratic_component is an optional keyeword arg

No longer pass quadratic_component=None to all solvers by default and
force them to implement code to ignore it if they do not support
quadratic programming. When specified, it is still passed on.
cglpk: bugfix to LP file writing with python 3
Add exact solving to cglpk

This is controlled by the exact=True parameter. However, this requires
an additional dependency on libgmp (which can also be statically
linked).
add bindings to QSopt_ex aka esolver

The solver uses cglpk to construct the problem and write out an LP, and
the command line interface to esolver is used to solve it. Esolver can
use rational math to solve an LP exactly.
test esolver on travis
Merge pull request #126 from aebrahim/exact

Add exact solving to cobrapy
Prevent excess deepcopy using sbml io

This reduces read time by ~35% for Salmonella.
Follow SBML Rerversibility tag guidelines

SBML requires that an irreversible rection never be negative. However,
cobrapy's definition of reversibility is more consistent with the
biochemical definition that flux flows both ways. Therefore, set the
SBML reversibility flag when writing out a file by using the criteria of
lower_bound < 0 instead of the Reaction.reversibility property.

This fixes #114.