def test_parse_last_state():
raw_last_state = [
"RNA(solution) -1 -4 6 191",
"RNA(solution) 1 2 3 193",
"Gf(solution) 0 0 0 192",
]
last_state = parse_last_state(raw_last_state)
assert Mol("RNA", -1.0, -4.0, 6.0) in last_state
assert Mol("RNA", 1.0, 2.0, 3.0) in last_state
assert Mol("Gf", 0.0, 0.0, 0.0) in last_state
def test_smoldyn_run_trajectory(self, template, parameters):
""" Test smoldyn runs and terminates in threshold mode
"""
n_points = 500
initial_state = [Mol("Gf", 0.0, 0.0, 0.0)]
model = Cell(template, parameters)
history, _ = run_trajectory(
model.model,
time_stop=10.,
time_step=0.01,
initial_state=initial_state,
seed=0,
n_points=n_points)
assert len(history['P']) == n_points + 1
#if it works, rerun with smaller tstep and retest
history, _ = run_trajectory(
model.model,
time_stop=10.,
time_step=0.01/4,
initial_state=initial_state,
seed=0,
n_points=n_points)
assert len(history['P']) == n_points + 1
def test_smoldyn_parallel(self, template, parameters):
""" Test smoldyn parallel run using dask
"""
import time
from dask.distributed import LocalCluster, Client
cluster = LocalCluster(processes=False)
client = Client(cluster)
initial_state = [Mol("Gf", 0.0, 0.0, 0.0)]
model = Cell(template, parameters)
s_start = time.time()
model.run(initial_state, 100., n_trajectories=32)
s_end = time.time()
p_start = time.time()
model.run(initial_state, 100., n_trajectories=32, client=client)
p_end = time.time()
assert s_end - s_start > 0.8 * 2 * (p_end - p_start)
# Minimal speed up is a trade off here between garanteed performance
# and time necessary to run the test
client.close()
cluster.close()
def test_smoldyn(self, template, parameters):
""" Test smoldyn is running without raising exceptions
"""
initial_state = [Mol("Gf", 0.0, 0.0, 0.0)]
model = Cell(template, parameters)
model.run(initial_state, 10., n_trajectories=1)
def test_seed(self, template, parameters):
""" Test results are the same when the same seed is provided
"""
initial_state = [Mol("Gf", 0.0, 0.0, 0.0)]
model = Cell(template, parameters)
results = [
model.run(initial_state, 10., n_trajectories=1, seed=0)
for _ in range(2)]
assert results[0] == results[1]
def test_noseed(self, template, parameters):
""" Test results are different when no seed is provided
"""
initial_state = [Mol("Gf", 0.0, 0.0, 0.0)]
model = Cell(template, parameters)
# Run models one after the other to ensure timebased seed is different
results = [model.run(initial_state, 10., n_trajectories=1)]
results.append(model.run(initial_state, 10., n_trajectories=1))
assert results[0] != results[1]
def test_smoldyn_threshold(self, template, parameters):
""" Test smoldyn runs and terminates in threshold mode
"""
n_points = 500
initial_state = [Mol("Gf", 0.0, 0.0, 0.0)]
model = Cell(template, parameters)
data, time = model.run_threshold(initial_state, 10.,
n_trajectories=10, threshold=0.25, n_points=n_points)
for tstep in data:
assert len(tstep['P'][0]) == n_points + 1
def test_npoints(self, template, parameters):
""" Test timeseries have the specified length
"""
import numpy as np
initial_state = [Mol("Gf", 0.0, 0.0, 0.0)]
# Vary tstop
n_points = 100
model = Cell(template, parameters)
for tstop in [1., 10., 100.]:
results = model.run(
initial_state, tstop,
n_trajectories=1, n_points=n_points, seed=0)
for species in results[0]:
assert len(results[0][species]) == n_points + 1
# Vary tstep
n_points = 500
tstop = 1000
for tstep in [0.01, 0.02, 0.04]:
parameters['time_step'] = tstep
model = Cell(template, parameters)
results = model.run(
initial_state, tstop,
n_trajectories=1, n_points=n_points, seed=0)
for species in results[0]:
assert len(results[0][species]) == n_points + 1
# Test with many trajectories
n_points = 500
tstop = 1000
n_traj = 10
for tstep in [0.01, 0.02, 0.04]:
parameters['time_step'] = tstep
model = Cell(template, parameters)
results = model.run(
initial_state, tstop,
n_trajectories=n_traj, n_points=n_points, seed=0)
for species in results:
assert np.array(results[species]).shape == (n_traj, n_points + 1)
def test_smoldyn_input(self):
assert Mol("RNA", 1.0, 2.0, 3.0).to_smoldyn_input() == "mol 1 RNA 1.0 2.0 3.0"
assert Mol("P", 5, -10.0, 0.0).to_smoldyn_input() == "mol 1 P 5.0 -10.0 0.0"
assert Mol("Gf", -0.2, -250, -1).to_smoldyn_input() == "mol 1 Gf -0.2 -250.0 -1.0"
def test_repr(self):
assert str(Mol("RNA", 1.0, 2.0, 3.0)) == "{'name': 'RNA', 'x': 1.0, 'y': 2.0, 'z': 3.0}"