deprecated the assess_objective function and added in a reaction module with assess functions
add conditional test for ABBREVIATION in sbml

Causes gene reading to fail when loading sbml when "ABBREVIATION" was missing
sbml loads charges from notes

If the charge is specified in the notes field, it will be saved as
metabolite.charge (which is what happens for charges specified as sbml
attributes).
unit tests are less verbose
ensure metabolites are added even with bad charge

add unit test to ensure this behavior as well
update pickles - iJO1366 should now have charge

Due to the previous commits, the iJO1366 model should now have charges
specified for the metabolites due to the structure of the xml file from
which the model was based.
install libsbml from pre-compiled tar.gz

Installs much faster since it does not need to compile
Patch that removes the independence of the reversibility and bounds attributes for a Reaction
fixed bugs introduced by changing Reaction.reversibility to a property
reaction display misinterprets reversibility

Instead of explicitly looking for 0 or 1, the arrow is now set by
evaluating if self.reversibility as expected. This makes the reactions
display correctly with the reversibility property
Reaction.boundary is now a property

If a reaction has only a single metabolite or it ONLY consumes or
produces metabolites, it is a system boundary
Remove depracated functions
update pickles
remove _boundary_metabolites
Update to latest python in INSTALL.md

now point to 2.7.6 instead of 2.7.3
brought in moma
build libSBML 5.9.0
updated the test to only allow moma to be tested if the cplex or gurobi solvers are present
Update gapAnalysis.py

Added exchange and transport reactions, as well as iterations to growMatch
clean up Jon's fixes to gap analysis