Small changes to 'BngSimulator.run' to support optional arguments to

[lh64]

BNG's 'generate_network' method. Added a new optional argument, 'netgen_args', to the 'BngSimulator.run' call signature. This is a dictionary that gets passed to 'bngfile.action' when the 'generate_network' command is called.

[coveralls]

Coverage increased (+0.03%) to 79.232% when pulling 0a151fc on netgen_args into c267f1e on master.

[alubbock]

Thanks for the PR. Two issues and a question:

1. It's not a good idea to have a mutable default argument, in this case a dictionary (see here for explanation). The simplest solution is to make to write netgen_args=None, and then add if netgen_args is None: netgen_args = {}.
2. A small test or two would help. I'd suggest one with a working netgen argument, and an invalid one to test that an error is raised.
3. Should this be extended to other simulators, or is there no need, since generate_equations can be called beforehand with arguments in those cases?

[lh64]

Ok, thanks.

1. I'll change netgen_args={} to netgen_args=None, as you suggest.
2. I'll also add a test. The only issue here is that it's not actually possible to pass an argument that will cause an error. BNG doesn't check that your arguments are valid, so unrecognized arguments just end up getting ignored. I suppose we could fix that on the PySB side but it's true of all BNG methods (including simulate, etc.), so I'm not sure it makes sense. What do you think?
3. I think we can just pass kwargs to generate_equations for the other simulators. But those will need to be updated. ScipyOdeSimulator, for example, doesn't provide any way to pass kwargs over to generate_equations.

[alubbock]

One other thing: netgen_kwargs is ignored if method=='nf'. Should probably raise a ValueError in that case, stating that the arguments are incompatible.