cobra_pie_0.2.0-alpha02.patch:
   Includes cobra_pie_0.2.alpha01.patch and
   Fixed cobra.mlab bugs
   Fixed MIP support for new style solvers and java solvers
   Fixed parameter setting bug for new style solvers
   Added MIP and minimize tests to cobra.test.solvers
   TODO: fix cobra.test.flux_variability


cobra_pie_0.2.alpha01.patch:
  Adds support for gurobi, cplex, and libglpk-java solvers through jython and moves towards the new style solvers.  
  Adds sbml support for jython via jsbml.
  Adds get_model to Reaction and Metabolite/Gene which returns the Model object that contains the calling Object.
  Adds get_reaction to Metabolite/Gene which returns a list of Reaction Objects that contain the calling Object.
  Started to remove numpy/scipy dependencies from core objects / functions as they aren't really essential.


DictList_tab_complete  
Allows tab completion on a DictList, such as model.reactions.PG<TAB> will
autocomplete to model.reactions.PGI
   STATUS: 04 June 2012: Applied


convert_back_to_reversible  
Adds a function to cobra.manipulation.modify which can undo the changes made by convert_to_irreversible.
   STATUS: 04 June 2012: A different method has been applied 



mlab
Make improvements to the mlab module. MATLAB commands can be called using cobra.matlab Creates a function init_matlab_toolbox, which calls the initCobraToolbox function in MATLAB and scans through the cobra matlab functions for faster use.
   STATUS: 04 June 2012: Applied

store_solution_in_model 
Store the flux of the reaction in the reaction object itself. This allows commands like:
[r for r in reactions if r.x > 2.0 and r.id.startswith("EX_")]
model.reactions.query(lambda r : r.x > 2.0 and r.id.startswith("EX_"), None)
   STATUS: 04 June 2012: This degrades performance when running lots of simulations (FVA, double deletion, ...).  Possibly add
as an option to the optimize call, a separate function, or in a solver-specific fashion to minimize performance issues.

test_directory_improvement
Defines platform-independent paths to test files
   STATUS: 04 June 2012: Applied
