fix bug in pFBA from oven
move pFBA from oven to mainline
fix revert_to_reversible rxn/met relationship

need to use model.remove_reactions to make sure reaction/metabolite
awareness is updated
relative imports in parsimonious.py

now that it has been moved out of the oven
unit tests and bugfixes for pFBA/make_reversible
Merge pull request #61 from aebrahim/pFBA

Move pFBA from oven to mainline
Merge pull request #60 from afif-elghraoui/master

Minor Bug Fix in write_cobra_model_to_sbml_file to Allow Default Compartments to be created
small doc formatting bugfixes
reran autodoc script
update pickles
begin separating glpk for cpython and jython
glpk solver uses comprehensions in format solution
split cplex and gurobi java solvers off
glpk solver uses izip in create_problem

speeds up problem_creation by 9% while using less memory
gurobi_solver now has change_variable_bounds

gurobipy does not allow getting variables by index, but does by name
(for some strange reason). Therefore, this now uses the index as the
name (ugh) so we can get this functionality. Otherwise, we would need to
index the specific variable out of the entire list of lp.getVars(),
which takes nearly 500us every time.
add change_variable_bounds to cplex
small bugfix for glpk and glpk_java
single deletion fba fast method

Single reaction deletions with this function are 20x faster

This speedup comes from using the solver specific functions
add change_variable_objective to cpython solvers
implement fva using optimized solver functions

speedup of 3.5x