def test_to_csv_single_result_no_stamp(self):
test_data = {'time': [0]}
result = Results(data=[test_data])
test_nametag = "test_nametag"
with tempfile.TemporaryDirectory() as tempdir:
result.to_csv(nametag=test_nametag, path=tempdir)
assert len(os.listdir(tempdir)) is not 0
def test_to_csv_single_result_no_data(self):
result = Results(data=None)
test_nametag = "test_nametag"
test_stamp = "test_stamp"
with tempfile.TemporaryDirectory() as tempdir:
result.to_csv(stamp=test_stamp, nametag=test_nametag, path=tempdir)
test_path = tempdir + "/" + test_nametag + test_stamp
assert not os.path.isdir(test_path)
def test_to_csv_single_result_no_nametag(self):
test_model = Model('test_model')
test_data = Trajectory(data={'time': [0]}, model=test_model)
result = Results(data=[test_data])
result.solver_name = 'test_solver'
test_stamp = "test_stamp"
with tempfile.TemporaryDirectory() as tempdir:
result.to_csv(stamp=test_stamp, path=tempdir)
assert len(os.listdir(tempdir)) is not 0
def test_to_csv_single_result_file_exists(self):
test_data = {'time': [0]}
result = Results(data=[test_data])
test_nametag = "test_nametag"
test_stamp = "test_stamp"
with tempfile.TemporaryDirectory() as tempdir:
result.to_csv(stamp=test_stamp, nametag=test_nametag, path=tempdir)
test_path = tempdir + "/" + test_nametag + test_stamp + "/" + test_nametag + "0.csv"
assert os.path.isfile(test_path)
def test_xscale_plot(self):
from unittest import mock
trajectory = Trajectory(data={
'time': [0.],
'foo': [1.]
},
model=Model('test_model'))
results = Results(data=[trajectory])
with mock.patch('matplotlib.pyplot.xscale') as mock_xscale:
results.plot(xscale='log')
mock_xscale.assert_called_with('log')
def test_to_csv_single_result_no_path(self):
test_data = Trajectory({'time': [0]},
model=Model('test_model'),
solver_name='test_solver_name')
result = Results(data=[test_data])
test_nametag = "test_nametag"
test_stamp = "test_stamp"
def test_plotly_layout_args(self):
from unittest import mock
trajectory = Trajectory(data={
'time': [0.],
'foo': [1.]
},
model=Model('test_model'))
results = Results(data=[trajectory])
with mock.patch('plotly.offline.init_notebook_mode') as mock_notebook:
with mock.patch('plotly.graph_objs.Scatter') as mock_scatter:
with mock.patch('plotly.graph_objs.Layout') as mock_layout:
results.plotplotly(return_plotly_figure=True, xscale='log')
mock_layout.assert_called_with(showlegend=True,
title='',
xaxis_title='Time ',
xscale='log',
yaxis_title='Species Population')
def test_plotly_std_dev_range_layout_args(self):
from unittest import mock
from unittest.mock import MagicMock
trajectory = Trajectory(data={
'time': [0.],
'foo': [1.]
},
model=Model('test_model'))
results = Results(data=[trajectory])
_plotly_iterate = MagicMock()
with mock.patch('plotly.offline.init_notebook_mode') as mock_notebook:
with mock.patch('plotly.graph_objs.Scatter') as mock_scatter:
with mock.patch('plotly.graph_objs.Layout') as mock_layout:
results.plotplotly_std_dev_range(return_plotly_figure=True,
xscale='log')
mock_layout.assert_called_with(legend={'traceorder': 'normal'},
showlegend=True,
title='Standard Deviation Range',
xaxis_title='Time ',
xscale='log',
yaxis_title='Species Population')
def run(self,
solver=None,
timeout=0,
t=None,
show_labels=True,
cpp_support=False,
**solver_args):
"""
Function calling simulation of the model. There are a number of
parameters to be set here.
:param solver: The solver by which to simulate the model. This solver object may
be initialized separately to specify an algorithm. Optional,
defaults to ssa solver.
:type solver: gillespy.GillesPySolver
:param timeout: Allows a time_out value in seconds to be sent to a signal handler, restricting simulation run-time
:type timeout: int
:param t: End time of simulation
:type t: int
:param solver_args: Solver-specific arguments to be passed to solver.run()
:return If show_labels is False, returns a numpy array of arrays of species population data. If show_labels is
True,returns a Results object that inherits UserList and contains one or more Trajectory objects that
inherit UserDict. Results object supports graphing and csv export.
To pause a simulation and retrieve data before the simulation, keyboard interrupt the simulation by pressing
control+c or pressing stop on a jupyter notebook. To resume a simulation, pass your previously ran results
into the run method, and set t = to the time you wish the resuming simulation to end (run(resume=results, t=x)).
Pause/Resume is only supported for SINGLE TRAJECTORY simulations. T MUST BE SET OR UNEXPECTED BEHAVIOR MAY OCCUR.
"""
if not show_labels:
from gillespy2.core import log
log.warning('show_labels = False is deprecated. Future releases '
'of GillesPy2 may not support this feature.')
if t is None:
t = self.tspan[-1]
if solver is None:
solver = self.get_best_solver()
try:
solver_results, rc = solver.run(model=self,
t=t,
increment=self.tspan[-1] -
self.tspan[-2],
timeout=timeout,
**solver_args)
except Exception as e:
if cpp_support is False:
if not isinstance(solver, str):
if solver.name == 'SSACSolver' or solver.name == 'VariableSSACSolver':
from gillespy2.core import log
log.warning(
"Please install/configure 'g++' and 'make' on your"
" system, to ensure that GillesPy2 C solvers will"
" run properly.")
raise SimulationError(
"argument 'solver={}' to run() failed. Reason Given: {}".
format(solver, e))
if rc == 33:
from gillespy2.core import log
log.warning('GillesPy2 simulation exceeded timeout.')
if hasattr(solver_results[0], 'shape'):
return solver_results
if len(solver_results) > 0:
results_list = []
for i in range(0, len(solver_results)):
temp = Trajectory(data=solver_results[i],
model=self,
solver_name=solver.name,
rc=rc)
results_list.append(temp)
results = Results(results_list)
if show_labels == False:
results = results.to_array()
return results
if len(solver_results) > 0:
results_list = []
for i in range(0, len(solver_results)):
temp = Trajectory(data=solver_results[i],
model=self,
solver_name=solver.name,
rc=rc)
results_list.append(temp)
results = Results(results_list)
if show_labels == False:
results = results.to_array()
return results
else:
raise ValueError(
"number_of_trajectories must be non-negative and non-zero")
def run(self=None, model=None, t=None, number_of_trajectories=1, increment=None, seed=None,
debug=False, profile=False, live_output=None, live_output_options={},
timeout=None, resume=None, tau_tol=0.03, **kwargs):
"""
Function calling simulation of the model.
This is typically called by the run function in GillesPy2 model objects
and will inherit those parameters which are passed with the model
as the arguments this run function.
:param model: The model on which the solver will operate. (Deprecated)
:type model: gillespy2.Model
:param t: Simulation run time.
:type t: int or float
:param number_of_trajectories: Number of trajectories to simulate. By default number_of_trajectories = 1.
:type number_of_trajectories: int
:param increment: Save point increment for recording data.
:type increment: float
:param seed: The random seed for the simulation. Optional, defaults to None.
:type seed: int
:param debug: Set to True to provide additional debug information about the simulation.
:type debug: bool
:param profile: Set to True to provide information about step size (tau) taken at each step.
:type profile: bool
:param live_output: The type of output to be displayed by solver. Can be "progress", "text", or "graph".
:type live_output: str
:param live_output_options: Contains options for live_output. By default {"interval":1}. "interval"
specifies seconds between displaying. "clear_output" specifies if display should be refreshed with each
display.
:type live_output_options: dict
:param timeout: If set, if simulation takes longer than timeout, will exit.
:type timeout: int
:param resume: Result of a previously run simulation, to be resumed.
:type resume: gillespy2.Results
:param tau_tol: Tolerance level for Tau leaping algorithm. Larger tolerance values will
result in larger tau steps. Default value is 0.03.
:type tau_tol: float
:returns: A result object containing the results of the simulation.
:rtype: gillespy2.Results
"""
from gillespy2 import log
if self is None:
# Post deprecation block
# raise SimulationError("TauLeapingSolver must be instantiated to run the simulation")
# Pre deprecation block
log.warning(
"""
`gillespy2.Model.run(solver=TauLeapingSolver)` is deprecated.
You should use `gillespy2.Model.run(solver=TauLeapingSolver(model=gillespy2.Model))
Future releases of GillesPy2 may not support this feature.
"""
)
self = TauLeapingSolver(model=model, debug=debug, profile=profile)
if model is not None:
log.warning('model = gillespy2.model is deprecated. Future releases '
'of GillesPy2 may not support this feature.')
if self.model is None:
if model is None:
raise SimulationError("A model is required to run the simulation.")
self.model = copy.deepcopy(model)
self.model.compile_prep()
self.validate_model(self.model, model)
self.validate_sbml_features(model=self.model)
self.validate_tspan(increment=increment, t=t)
if increment is None:
increment = self.model.tspan[-1] - self.model.tspan[-2]
if t is None:
t = self.model.tspan[-1]
self.stop_event = Event()
self.pause_event = Event()
if timeout is not None and timeout <= 0:
timeout = None
if len(kwargs) > 0:
for key in kwargs:
log.warning('Unsupported keyword argument to {0} solver: {1}'.format(self.name, key))
# create numpy array for timeline
if resume is not None:
# start where we last left off if resuming a simulatio
lastT = resume['time'][-1]
step = lastT - resume['time'][-2]
timeline = np.arange(lastT, t+step, step)
else:
timeline = np.linspace(0, t, int(round(t / increment + 1)))
species = list(self.model._listOfSpecies.keys())
trajectory_base, tmpSpecies = nputils.numpy_trajectory_base_initialization(self.model, number_of_trajectories,
timeline, species, resume=resume)
# total_time and curr_state are list of len 1 so that __run receives reference
if resume is not None:
total_time = [resume['time'][-1]]
else:
total_time = [0]
curr_state = [None]
live_grapher = [None]
sim_thread = Thread(target=self.___run, args=(curr_state, total_time, timeline, trajectory_base, tmpSpecies,
live_grapher,), kwargs={'t': t,
'number_of_trajectories':
number_of_trajectories,
'increment': increment, 'seed': seed,
'debug': debug, 'resume': resume,
'timeout': timeout, 'tau_tol': tau_tol
})
try:
time = 0
sim_thread.start()
if live_output is not None:
import gillespy2.core.liveGraphing
live_output_options['type'] = live_output
gillespy2.core.liveGraphing.valid_graph_params(
live_output_options)
if resume is not None:
resumeTest = True # If resuming, relay this information to live_grapher
else:
resumeTest = False
live_grapher[
0] = gillespy2.core.liveGraphing.LiveDisplayer(self.model,
timeline,
number_of_trajectories,
live_output_options,
resume=resumeTest)
display_timer = gillespy2.core.liveGraphing.RepeatTimer(
live_output_options['interval'],
live_grapher[0].display, args=(curr_state,
total_time,
trajectory_base,
live_output
)
)
display_timer.start()
if timeout is not None:
while sim_thread.is_alive():
sim_thread.join(.1)
time += .1
if time >= timeout:
break
else:
while sim_thread.is_alive():
sim_thread.join(.1)
if live_grapher[0] is not None:
display_timer.cancel()
self.stop_event.set()
while self.result is None:
pass
except KeyboardInterrupt:
if live_output:
display_timer.pause = True
display_timer.cancel()
self.pause_event.set()
while self.result is None:
pass
if hasattr(self, 'has_raised_exception'):
raise SimulationError(
f"Error encountered while running simulation:\nReturn code: {int(self.rc)}.\n"
) from self.has_raised_exception
return Results.build_from_solver_results(self, live_output_options)
def run(self=None, model=None, t=None, number_of_trajectories=1, increment=None, integrator='lsoda',
integrator_options={}, live_output=None, live_output_options={}, timeout=None, resume=None, **kwargs):
"""
:param model: The model on which the solver will operate. (Deprecated)
:type model: gillespy2.Model
:param t: End time of simulation.
:type t: int or float
:param number_of_trajectories: Number of trajectories to simulate. By default number_of_trajectories = 1.
This is deterministic and will always have same results.
:type number_of_trajectories: int
:param increment: Time step increment for plotting.
:type increment: float
:param integrator: integrator to be used from scipy.integrate.ode. Options include 'vode', 'zvode', 'lsoda',
'dopri5', and 'dop853'. For more details,
see https://docs.scipy.org/doc/scipy/reference/generated/scipy.integrate.ode.html
:type integrator: str
:param integrator_options: a dictionary containing options to the scipy integrator. for a list of options,
see https://docs.scipy.org/doc/scipy/reference/generated/scipy.integrate.ode.html.
Example use: {max_step : 0, rtol : .01}
:type integrator_options: dict
:param live_output: The type of output to be displayed by solver. Can be "progress", "text", or "graph".
:type live_output: str
:param live_output_options: dictionary contains options for live_output. By default {"interval":1}.
"interval" specifies seconds between displaying.
"clear_output" specifies if display should be refreshed with each display.
:type live_output_options: dict
:param timeout: If set, if simulation takes longer than timeout, will exit.
:type timeout: int
:param resume: Result of a previously run simulation, to be resumed.
:type resume: gillespy2.Results
:returns: A result object containing the results of the simulation.
:rtype: gillespy2.Results
"""
from gillespy2 import log
if self is None:
# Post deprecation block
# raise SimulationError("ODESolver must be instantiated to run the simulation")
# Pre deprecation block
log.warning(
"""
`gillespy2.Model.run(solver=ODESolver)` is deprecated.
You should use `gillespy2.Model.run(solver=ODESolver(model=gillespy2.Model))
Future releases of GillesPy2 may not support this feature.
"""
)
self = ODESolver(model=model)
if model is not None:
log.warning('model = gillespy2.model is deprecated. Future releases '
'of GillesPy2 may not support this feature.')
if self.model is None:
if model is None:
raise SimulationError("A model is required to run the simulation.")
self.model = copy.deepcopy(model)
self.model.compile_prep()
self.validate_model(self.model, model)
self.validate_sbml_features(model=self.model)
self.validate_tspan(increment=increment, t=t)
if increment is None:
increment = self.model.tspan[-1] - self.model.tspan[-2]
if t is None:
t = self.model.tspan[-1]
self.stop_event = Event()
self.pause_event = Event()
if timeout is not None and timeout <= 0:
timeout = None
if len(kwargs) > 0:
for key in kwargs:
log.warning('Unsupported keyword argument to {0} solver: {1}'.format(self.name, key))
if number_of_trajectories > 1:
log.warning("Generating duplicate trajectories for model with ODE Solver. "
"Consider running with only 1 trajectory.")
if resume is not None:
# start where we last left off if resuming a simulation
lastT = resume['time'][-1]
step = lastT - resume['time'][-2]
timeline = np.arange(lastT, t+step, step)
else:
timeline = np.linspace(0, t, int(round(t / increment + 1)))
species = list(self.model._listOfSpecies.keys())
trajectory_base, tmpSpecies = nputils.numpy_trajectory_base_initialization(self.model, number_of_trajectories,
timeline, species, resume=resume)
# curr_time and curr_state are list of len 1 so that __run receives reference
if resume is not None:
curr_time = [resume['time'][-1]]
else:
curr_time = [0] # Current Simulation Time
curr_state = [None]
live_grapher = [None]
sim_thread = Thread(target=self.___run, args=(curr_state, curr_time, timeline, trajectory_base,
tmpSpecies, live_grapher,), kwargs={'t': t,
'number_of_trajectories':
number_of_trajectories,
'increment': increment,
'resume': resume,
'integrator': integrator,
'integrator_options':
integrator_options, })
try:
time = 0
sim_thread.start()
if live_output is not None:
import gillespy2.core.liveGraphing
live_output_options['type'] = live_output
gillespy2.core.liveGraphing.valid_graph_params(live_output_options)
if resume is not None:
resumeTest = True # If resuming, relay this information to live_grapher
else:
resumeTest = False
live_grapher[0] = gillespy2.core.liveGraphing.LiveDisplayer(self.model, timeline, number_of_trajectories,
live_output_options, resume=resumeTest)
display_timer = gillespy2.core.liveGraphing.RepeatTimer(live_output_options['interval'],
live_grapher[0].display,
args=(curr_state, curr_time, trajectory_base,live_output))
display_timer.start()
if timeout is not None:
while sim_thread.is_alive():
sim_thread.join(.1)
time += .1
if time >= timeout:
break
else:
while sim_thread.is_alive():
sim_thread.join(.1)
if live_grapher[0] is not None:
display_timer.cancel()
self.stop_event.set()
while self.result is None:
pass
except KeyboardInterrupt:
if live_output:
display_timer.pause = True
display_timer.cancel()
self.pause_event.set()
while self.result is None:
pass
if hasattr(self, 'has_raised_exception'):
raise SimulationError(
f"Error encountered while running simulation:\nReturn code: {int(self.rc)}.\n"
) from self.has_raised_exception
return Results.build_from_solver_results(self, live_output_options)
def run(self, solver=None, **solver_args):
"""
Function calling simulation of the model. There are a number of
parameters to be set here.
Return
----------
If show_labels is False, returns a numpy array of arrays of species population data. If show_labels is True and
number_of_trajectories is 1, returns a results object that inherits UserDict and supports plotting functions.
If show_labels is False and number_of_trajectories is greater than 1, returns an ensemble_results object that
inherits UserList and contains results objects and supports ensemble graphing.
Attributes
----------
number_of_trajectories : int
The number of times to sample the chemical master equation. Each
trajectory will be returned at the end of the simulation.
Optional, defaults to 1.
seed : int
The random seed for the simulation. Optional, defaults to None.
solver : gillespy.GillesPySolver
The solver by which to simulate the model. This solver object may
be initialized separately to specify an algorithm. Optional,
defaults to ssa solver.
show_labels: bool (True)
If true, simulation returns a list of trajectories, where each list entry is a dictionary containing key value pairs of species : trajectory. If false, returns a numpy array with shape [traj_no, time, species]
switch_tol: float
Tolerance for Continuous/Stochastic representation of species, based on coefficient of variance for each step.
tau_tol: float
Relative error tolerance value for calculating tau step between 0.0 and 1.0
integrator: String
integrator to be used form scipy.integrate.ode. Options include 'vode', 'zvode', 'lsoda', 'dopri5', and 'dop835'. For more details, see https://docs.scipy.org/doc/scipy/reference/generated/scipy.integrate.ode.html
integrator_options: dictionary
contains options to the scipy integrator. for a list of options, see https://docs.scipy.org/doc/scipy/reference/generated/scipy.integrate.ode.html.
Example use: {max_step : 0, rtol : .01}
"""
if solver is not None:
if ((isinstance(solver, type)
and issubclass(solver, GillesPySolver))) or issubclass(
type(solver), GillesPySolver):
solver_results = solver.run(model=self,
t=self.tspan[-1],
increment=self.tspan[-1] -
self.tspan[-2],
**solver_args)
else:
raise SimulationError(
"argument 'solver' to run() must be a subclass of GillesPySolver"
)
else:
from gillespy2.solvers.auto import SSASolver
solver = SSASolver
solver_results = SSASolver.run(model=self,
t=self.tspan[-1],
increment=self.tspan[-1] -
self.tspan[-2],
**solver_args)
if isinstance(solver_results[0], (np.ndarray)):
return solver_results
if len(solver_results) is 1:
return Results(data=solver_results[0],
model=self,
solver_name=solver.name)
if len(solver_results) > 1:
results_list = []
for i in range(0, solver_args.get('number_of_trajectories')):
results_list.append(
Results(data=solver_results[i],
model=self,
solver_name=solver.name))
return EnsembleResults(results_list)
else:
raise ValueError(
"number_of_trajectories must be non-negative and non-zero")