Use empty arrays when there are no observables or expressions (#481)

* Use empty arrays when there are no observables or expressions
* Add unit test

pysb/simulator/base.py

@@ -805,14 +805,15 @@ def __init__(self, simulator, tout, trajectories=None,
                 len(tout[n]) * len(expr_names)).view(dtype=yexpr_dtype) for n
                           in range(self.nsims)]
         else:
-            self._yobs = [np.ndarray((len(self.tout[n]),),
-                                     dtype=yobs_dtype) for n in range(self.nsims)]
+            self._yobs = [np.ndarray((len(self.tout[n]),), dtype=yobs_dtype) if obs_names
+                          else np.ndarray((len(self.tout[n]), 0), dtype=yobs_dtype)
+                          for n in range(self.nsims)]
             self._yobs_view = [self._yobs[n].view(float).
-                               reshape(len(self._yobs[n]), -1) for n in range(
-                self.nsims)]
-            self._yexpr = [np.ndarray((len(self.tout[n]),),
-                                      dtype=yexpr_dtype) for n in range(
+                                   reshape(len(self._yobs[n]), -1) for n in range(
                 self.nsims)]
+            self._yexpr = [np.ndarray((len(self.tout[n]),), dtype=yexpr_dtype) if expr_names
+                           else np.ndarray((len(self.tout[n]), 0), dtype=yexpr_dtype)
+                           for n in range(self.nsims)]
             self._yexpr_view = [self._yexpr[n].view(float).reshape(len(
                 self._yexpr[n]), -1) for n in range(self.nsims)]
 

pysb/tests/test_simulationresult.py

@@ -11,6 +11,7 @@
 from pysb.pattern import SpeciesPatternMatcher
 import collections
 import copy
+import io
 import pandas as pd
 
 
@@ -190,6 +191,18 @@ def test_save_load():
     _check_resultsets_equal(nfres2, nfres2_load)
 
 
+def test_save_load_observables_expressions():
+    buff = io.BytesIO()
+    tspan = np.linspace(0, 100, 100)
+    sim = ScipyOdeSimulator(tyson_oscillator.model, tspan).run()
+    sim.save(buff, include_obs_exprs=True)
+
+    sim2 = SimulationResult.load(buff)
+    assert len(sim2.observables) == len(tspan)
+    # Tyson oscillator doesn't have expressions
+    assert_raises(ValueError, lambda: sim2.expressions)
+
+
 def _check_resultsets_equal(res1, res2):
     try:
         assert np.allclose(res1.species, res2.species)