def test_stdout(self):
sim = core.Simulation(k_syn=1, k_deg=0.25, verbose=True)
with capturer.CaptureOutput() as captured:
sim.run(value_init=4, time_max=10)
stdout = captured.get_text()
lines = stdout.rstrip().split('\n')
for line in lines:
self.assertRegex(line, r'^Time \d+: \d+ molecules$')
def test_invalid_inputs(self):
sim = core.Simulation()
with self.assertRaisesRegex(
ValueError, '`value_init` must be a non-negative integer'):
sim.run(value_init=-1, time_max=10)
with self.assertRaisesRegex(
ValueError, '`time_max` must be a non-negative integer'):
sim.run(value_init=4, time_max=-1)
def test_statistics(self):
sim = core.Simulation(k_syn=1, k_deg=0.25)
time_max = 100
n_sample = 100
values = numpy.full((time_max + 1, n_sample), numpy.nan)
for i_sample in range(n_sample):
hist = sim.run(value_init=4, time_max=time_max)
values[:, i_sample] = hist.values
numpy.testing.assert_allclose(numpy.mean(values[:]), 4., rtol=1e-1)
def test_run(self):
sim = core.Simulation(k_syn=1, k_deg=0.25)
hist = sim.run(value_init=4, time_max=10)
# the result is an instance of core.Trajectory
self.assertIsInstance(hist, core.Trajectory)
# the timepoints are 0, 1, 2, ..., 10
numpy.testing.assert_equal(hist.times, numpy.arange(0., 11., 1.))
# all of the predicted values are positive
self.assertTrue(numpy.all(hist.values >= 0))
def test_invalid_inputs(self):
sim = core.Simulation()
def test_stdout(self):
sim = core.Simulation()
def test_statistics(self):
sim = core.Simulation()