setup.py always rebuilds cglpk.c

 - uses force=True in cythonize.
 - cython is required to use the develop option
 - misc changes to setup.py (passes pep8 now)
Fix cobra.io.json types and attributes

This fixes issue #98 where numpy objects failed to be saved.

The exclude_attributes functionality was also removed. This will cause
the json input and output to be consistent and reproducible, reducing
the possibility of generating malformed files. The module will export
the minimal amount of information needed to rebuild the cobra model.

In addition, the module can now load and dump json strings. The code
also passes pep8.
Add unit test for cobra.Gene.remove_form_model

This function raises an Exception while running (issue #119)
Fix cobra.Gene.remove_from_model

Going through the gene reaction rule setter caused all the gene
associations to be recomputed, causing an error when attempting to
remove the gene. Because the association does not need to be entirely
recomputed, setting the underlying _gene_reaction_rule instead fixes
this issue. This closes #119 on github.

In addition, the model parameter was unecessary to this function and has
been deprecated.
Finish implementation of Model.repair

This will:
 - recompute the relationship between genes and metabolites and their
   respecitve reactions.
 - Rebuild indexes for DictList
 - Point _model of genes, metabolites, and reactions to the model
Support for coveralls.io

Author:  Nikolaus Sonnenschein <niko.sonnenschein@gmail.com>

Use coveralls to determine unit test coverage
expand coveralls ignore list