Changed netgen_args={} to netgen_args=None in the call signature for

`BngSimulator.run` and added a simple validation test to
test_simulator_bng.py.

pysb/simulator/bng.py

@@ -25,7 +25,7 @@ def __init__(self, model, tspan=None, cleanup=True, verbose=False):
 
     def run(self, tspan=None, initials=None, param_values=None, n_runs=1,
             method='ssa', output_dir=None, output_file_basename=None,
-            cleanup=None, population_maps=None, netgen_args={}, 
+            cleanup=None, population_maps=None, netgen_args=None, 
             **additional_args):
         """
         Simulate a model using BioNetGen
@@ -177,6 +177,8 @@ def run(self, tspan=None, initials=None, param_values=None, n_runs=1,
                     f.write(hpp_bngl)
             if method != 'nf':
                 # TODO: Write existing netfile if already generated
+                if netgen_args is None:
+                    netgen_args = {}
                 bngfile.action('generate_network', overwrite=True,
                                verbose=extended_debug, **netgen_args)
             if output_file_basename is None:

pysb/tests/test_simulator_bng.py

@@ -122,3 +122,20 @@ def test_hpp():
                 seed=_BNG_SEED)
     observables = np.array(x.observables)
     assert len(observables) == 50
+
+def test_bng_netgen_args():
+    Model()
+    N_STATES=10
+    Monomer('A', ['state'], {'state' : ['_{}'.format(i) 
+                                        for i in range(N_STATES)]})
+    Initial(A(state='_0'), Parameter('A0'))
+    Parameter('k', 1)
+    [Rule('State_{}_to_{}'.format(i,i+1), 
+          A(state='_{}'.format(i)) >> A(state='_{}'.format(i+1)), k) 
+          for i in range(N_STATES-1)]
+    sim = BngSimulator(model)
+    sim.run(tspan=[0,1], netgen_args={'max_iter':1})
+    assert len(model.species) == 2
+    model.reset_equations()
+    sim.run(tspan=[0,1], netgen_args={'max_iter':2})
+    assert len(model.species) == 3