prefer cglpk to glpk

cglpk is now faster, more advanced, and more robust than the bindings
through pyglpk, and will be preferred to pyglpk by the automatic solver
selection process in get_solver_name. Pyglpk will remain a solver for
legacy reasons, but has been removed from the installation instructions
page.

Also, this adds the gmp license to the cglpk docstring.
Prevent excess deepcopy using sbml io

This reduces read time by ~35% for Salmonella.
warn on more invalid formulas

The docstring has been updated to state that the only allowed characters
are letters and numbers. Warnings are explicitly raised for parenthesis
and '*' in a formula string.
SBML with metabolites on both sides of a reaction

This is case is now handled. The metabolite will not be added if it is
on both sides with the same stoichiometry.
Merge pull request #130 from aebrahim/loading_warnings

Small changes to SBML loading
DOCS: Add reaction reversibility setting to faq

Also fix a small formatting issue in simulating doc page
small updates to faq
slight change to default mosek parameters

set mosek.dparam.presolve_tol_x to 1e-15 instead of 0
cplex and mosek accept other numeric types

For example, decimal.Decimal
Merge pull request #129 from aebrahim/solver_default

prefer cglpk to glpk
small cleanup to cglpy.pyx and solver test

Solver testing now tests for an optimal solution status for each test in
the change_coefficient testing. This testing code is also now pep8
compliant.
Fixes reaction deletion/removal

This pull request is around the functions Model.remove_reactions,
Reaction.remove_from_model, and Rection.delete.

These fucnctions now all have a flag for removal of orphan
metabolites/genes. Before, this behaviro was unspecified and unclear.
Moreover, this behavior is also tested under the unit tests.

Previously, the function Reaction.delete had bugs which prevented it
from working correctly, and was not under unit testing. This has now
been corrected.
warn and skip non-ascii gene_reaction_rule in sbml
support more mosek parameters
DictList.extend duplicate id err message specific

Also include the index to make the issue easier to debug
add loopless FBA implementation

Added to the flux_analysis submodule. This commit also includes unit
tests.
add loopless FBA documentation
Merge pull request #133 from aebrahim/loopless

Add loopless FBA implementation
cobra.io.mat split read code to from_mat_struct

The function to convert the struct read in by scipy.io.loadmat has been
moved to its own function called by load_matlab model
bug in modify.convert_to_irreversible objectives

An objective reaction with a negative lower bound could cause incorrect
solutions after being made irreversible. This remedies the situation by
setting the objective coefficient of the reflection to -1 * the original
objective coefficient