add utility to fix legacy id compartment

Changes style from [c] or (c) to _c
Implemented as fix_compartments flag on cobra.io.fix_legacy_id
check id length before trying to fix it
build cglpk with function signatures
version pep440 compliance added, not used yet

Instead of just using the as-is output of git describe, which is
```tag-N-commit```
Now use
```tag.postN-commit```
The option pep440=True will make this pep440 compliant
```tag.postN```
sbml import checks on bounds

This fixes #46.

 - a formula not parsing correctly is downgraded to a warning
 - check that lower and upper bounds are not nan or inf
 - io_test runs fba and chekcs solution
fix #77 removing _b mets in read_legacy_sbml
Initial documentation cleanup

Clean up docstring formatting for most of core docs.
Merge pull request #71 from aebrahim/sbml_id_compartment_fix_util

add utility to fix legacy id compartment
gurobi and cplex use 1/2 coefficient in quad obj

Prior to v0.3.0b1, gurobi used v^T Q v and cplex used 1/2 v^T Q v.
In v0.3.0b1, this was switched to both using v^T Q v. However, the
convention appears to be to use the 1/2 (so what users will expect):
https://en.wikipedia.org/wiki/Quadratic_programming
Therefore, the 1/2 convention will be used for all solvers.
remove cobra.stats

The code was not referenced anywhere else in cobrapy. It provided a set
of convenient wrappers to statistical functions like p value adjustment
in rpy. However, that functionality can now be replaced by native python
implementations like statsmodels
doc update: phenotype phase plane

Added an example notebook for phenotype phase plane

Also fixed a few docstrings in core.
some rst docs built directly from notebooks

The rst produced by ipython nbconvert can be used directly for
metabolites, reactions, and phenotype_phase_plane. The autodoc script
will also run nbconvert.
Include license and readme with installation
Make installation more robust

* Cython is no longer required to build the cglpk extension
* ez_setup only used when required (and ships correctly)
* extras_require updated
INSTALL.md gives beta instructions (temporarily)

The instructions listed are for v0.3.0, so they recommend the use of pip
install --pre (for now) so the beta will be installed. This should be
revereted when the final version is released, and these instructions
will work correctly without the --pre tag.
setup uses pep440 compliant version
Merge pull request #97 from aebrahim/install

Improve installation
prettier warnings

Warning filenames replace the full cobra path with just cobra, allowing
the messages to fit on asingle line. Additionally, on posix systems,
ansi color excapes are used to color warning messages for increased
visibility.
add inequality unit tests for lp solvers
improve cglpk accuracy by using double (not float)