Unit tests (closes #28) and standardize cupsoda run signature (fixes …

…#26)

Note that cupsoda unit tests are not run on travis due to lack of GPU/CUDA
infrastructure. Developers should run the tests locally before committing
to github.

pysb/cupsoda.py

@@ -235,7 +235,7 @@ def __init__(self, model, tspan=None, cleanup=True, verbose=False,
         # overwrite default integrator options
         self.options.update(integrator_options)
 
-    def run(self, param_values, y0, tspan=None, outdir=None,
+    def run(self, tspan=None, param_values=None, y0=None, outdir=None,
             prefix=None, **integrator_options):
         """Perform a set of integrations.
 
@@ -274,6 +274,29 @@ def run(self, param_values, y0, tspan=None, outdir=None,
         """
 
         start_time = time.time()
+
+        if y0 is None and param_values is None:
+            warnings.warn("Neither 'y0' nor 'param_values' were supplied. "
+                          "Running a single simulation with model defaults.")
+
+        if y0 is None:
+            # Run simulation using same parameters, varying initial conditions
+            species_names = [str(s) for s in self.model.species]
+            y0 = np.zeros(len(species_names))
+            for ic in self.model.initial_conditions:
+                y0[species_names.index(str(ic[0]))] = ic[1].value
+            y0 = np.repeat([y0],
+                           1 if param_values is None else
+                           param_values.shape[0],
+                           axis=0)
+
+        if param_values is None:
+            # Run simulation using same initial conditions, varying parameters
+            param_values = np.repeat(np.array([[p.value for p in
+                                              self.model.parameters]]),
+                                     y0.shape[0],
+                                     axis=0)
+
         # make sure tspan is defined somewhere
         if tspan is not None:
             self.tspan = tspan