deprecated the assess_objective function and added in a reaction module with assess functions
update_pickles.py now uses legacy sbml for iJO1366

This prevents reaction names with _LPAREN_e_RPAREN_ for exchange
reactions.

The pickles were also all updated.
update file permissions
add conditional test for ABBREVIATION in sbml

Causes gene reading to fail when loading sbml when "ABBREVIATION" was missing
Merge pull request #37 from pillmill/sbml_bugfix

add conditional test for ABBREVIATION in sbml
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
Merge pull request #38 from aebrahim/sbml_charge

sbml loads charges from notes
Merge pull request #39 from aebrahim/travis_faster_libsbml

install libsbml from pre-compiled tar.gz in travis
Merge pull request #35 from danielhyduke/issue_34

Deprecations of assess_objective and introduction of cobra.flux_analysis.reaction.assess*
Merge pull request #2 from opencobra/master

Updates from opencobra:master
Patch that removes the independence of the reversibility and bounds attributes for a Reaction
fixed bugs introduced by changing Reaction.reversibility to a property
Merge pull request #41 from danielhyduke/patches

Reaction reversibility patch
Merge pull request #3 from opencobra/master

Back merging reaction patch from opencobra:master
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
Merge pull request #42 from aebrahim/reaction_display_fix

reaction display misinterprets reversibility