Merge dae388f into c267f1e

pysb/bng.py

@@ -225,7 +225,7 @@ def read_simulation_results_multi(base_filenames):
 
             # Read concentrations data
             try:
-                cdat_arr = numpy.loadtxt(base_filename + '.cdat', skiprows=1)
+                cdat_arr = numpy.loadtxt(base_filename + '.cdat', skiprows=1, ndmin=2)
                 # -1 for time column
                 names += ['__s%d' % i for i in range(cdat_arr.shape[1] - 1)]
             except IOError:
@@ -237,7 +237,7 @@ def read_simulation_results_multi(base_filenames):
                     # Exclude \# and time column
                     names += f.readline().split()[2:]
                     # Exclude first column (time)
-                    gdat_arr = numpy.loadtxt(f)
+                    gdat_arr = numpy.loadtxt(f, ndmin=2)
                     if cdat_arr is None:
                         cdat_arr = numpy.ndarray((len(gdat_arr), 0))
                     else:

pysb/simulator/bng.py

@@ -228,7 +228,10 @@ def run(self, tspan=None, initials=None, param_values=None, n_runs=1,
                                    1:(len(self.model.species) + 1)])
                 if len(self.model.observables) or len(self.model.expressions):
                     obs_exp_out.append(yfull_view[:,
-                                       (len(self.model.species) + 1):])
+                                        (len(self.model.species) + 1):
+                                        (len(self.model.species) + 1) +
+                                        len(self.model.observables) +
+                                        len(self.model.expressions_dynamic())])
 
         return SimulationResult(self, tout=tout, trajectories=species_out,
                                 observables_and_expressions=obs_exp_out,

pysb/tests/test_simulator_bng.py

@@ -1,6 +1,6 @@
 from pysb.testing import *
 import numpy as np
-from pysb import Monomer, Parameter, Initial, Observable, Rule
+from pysb import Monomer, Parameter, Initial, Observable, Rule, Expression
 from pysb.simulator.bng import BngSimulator, PopulationMap
 from pysb.bng import generate_equations
 from pysb.examples import robertson, expression_observables, earm_1_0
@@ -122,3 +122,21 @@ def test_hpp():
                 seed=_BNG_SEED)
     observables = np.array(x.observables)
     assert len(observables) == 50
+
+
+def test_stop_if():
+    Model()
+    Monomer('A')
+    Rule('A_synth', None >> A(), Parameter('k', 1))
+    Observable('Atot', A())
+    Expression('exp_const', k + 1)
+    Expression('exp_dyn', Atot + 1)
+    sim = BngSimulator(model, verbose=5)
+    tspan = np.linspace(0, 100, 101)
+    x = sim.run(tspan, stop_if='Atot>9', seed=_BNG_SEED)
+    # All except the last Atot value should be <=9
+    assert all(x.observables['Atot'][:-1] <= 9)
+    assert x.observables['Atot'][-1] > 9
+    # Starting with Atot > 9 should terminate simulation immediately
+    y = sim.run(tspan, initials=x.species[-1], stop_if='Atot>9')
+    assert len(y.observables) == 1