def test_species_parameter_name_substrings(self):
model = Model()
rate = Parameter(name='rate', expression=1)
model.add_parameter(rate)
species1 = Species('A', initial_value=100)
species2 = Species('AA', initial_value=0)
model.add_species([species1, species2])
reaction1 = Reaction(name="reaction1",
reactants={species1: 1},
products={species2: 1},
rate=rate)
model.add_reaction(reaction1)
number_points = 11
model.timespan(np.linspace(0, 1, number_points))
from gillespy2.solvers.numpy.ssa_solver import NumPySSASolver
results = model.run(number_of_trajectories=1,
solver=NumPySSASolver,
seed=1)
self.assertTrue(len(results['time']) == number_points)
self.assertTrue(len(results[species1.name]) == number_points)
self.assertTrue(len(results[species2.name]) == number_points)
self.assertGreater(results[species1.name][0],
results[species1.name][-1])
self.assertLess(results[species2.name][0], results[species2.name][-1])
self.assertEqual(
np.sum(results[species1.name]) + np.sum(results[species2.name]),
number_points * species1.initial_value)
def test_run_nonsolver(self):
model = Model()
rate = Parameter(name='rate', expression=0.5)
model.add_parameter(rate)
species1 = Species(name='A', initial_value=0)
species2 = Species(name='B', initial_value=0)
model.add_species(species1)
model.add_species(species2)
reaction = Reaction(name='reaction1',
reactants={species1: 1},
products={species2: 1},
rate=rate)
with self.assertRaises(SimulationError):
results = model.run(number_of_trajectories=1,
solver='non_solver',
seed=1)
def test_uniform_timespan(self):
model = Model()
model.timespan(np.linspace(0, 1, 100))
with self.assertRaises(TimespanError):
model.timespan(np.array([0, 0.1, 0.5]))
model.run()
