Modified pysb.bng.run_ssa to fill in the model elements 'species', 'reactions', 'observables', and 'odes' by parsing the NET file generated by BNG. To accomplish this, pysb.bng.generate_equations had to be refactored. Specifically, the majority of the code was moved into a new function named '_parse_netfile'. This allows this function to be called at the end of pysb.bng.run_ssa.
Modified pysb.bng.run_ssa to fill in the model elements 'species',
'reactions', 'observables', and 'odes' by parsing the NET file generated
by BNG. To accomplish this, pysb.bng.generate_equations had to be
refactored. Specifically, the majority of the code was moved into a new
function named '_parse_netfile'. This allows this function to be called
at the end of pysb.bng.run_ssa.

johnbachman/pysb,alubbock/pysb,johnbachman/pysb,LoLab-VU/pysb,pysb/pysb,LoLab-VU/pysb,jmuhlich/pysb