def test_model_add__multiple_components__in_order(self):
import gillespy2
s1 = gillespy2.Species(name="s1", initial_value=29)
k1 = gillespy2.Parameter(name="k1", expression=29)
r1 = gillespy2.Reaction(name="r1", reactants={"s1": 1}, rate="k1")
rr1 = gillespy2.RateRule(name="rr1", variable="k1", formula="29")
ar1 = gillespy2.AssignmentRule(name="ar1", variable="s1", formula="29")
ea = gillespy2.EventAssignment(name="ea",
variable="k1",
expression="29")
et = gillespy2.EventTrigger(expression="t > 29")
e1 = gillespy2.Event(name="e1", trigger=et, assignments=[ea])
divide = gillespy2.FunctionDefinition(name="divide",
function="x / y",
args=["x", "y"])
tspan = gillespy2.TimeSpan(range(100))
model = gillespy2.Model(name="Test Model")
model.add([s1, k1, r1, rr1, ar1, e1, divide, tspan])
self.assertIn("ar1", model.listOfAssignmentRules)
self.assertIn("e1", model.listOfEvents)
self.assertIn("divide", model.listOfFunctionDefinitions)
self.assertIn("k1", model.listOfParameters)
self.assertIn("rr1", model.listOfRateRules)
self.assertIn("r1", model.listOfReactions)
self.assertIn("s1", model.listOfSpecies)
self.assertEqual(tspan, model.tspan)
def test_add_assignment_rule(self):
model = Example()
species = gillespy2.Species('test_species4', initial_value=1)
rule = gillespy2.AssignmentRule(name='ar1', variable=species.name, formula='2')
model.add_species([species])
model.add_assignment_rule([rule])
results = model.run()
self.assertEquals(results[species.name][0], 2)
self.assertEquals(results[species.name][-1], 2)
self.assertEqual(results[0].solver_name,'TauHybridSolver')
def setUpClass(cls):
cls.solvers = [
SSACSolver,
ODESolver,
NumPySSASolver,
TauLeapingSolver,
TauHybridSolver,
ODECSolver,
TauLeapingCSolver,
TauHybridCSolver,
]
cls.sbml_features = {
"AssignmentRule": lambda model, variable:
model.add_assignment_rule(gillespy2.AssignmentRule(variable=variable, formula="1/(t+1)")),
"RateRule": lambda model, variable:
model.add_rate_rule(gillespy2.RateRule(variable=variable, formula="2*t")),
"Event": lambda model, variable:
model.add_event(gillespy2.Event(
trigger=gillespy2.EventTrigger(expression="t>1"),
assignments=[gillespy2.EventAssignment(variable=variable, expression="100")]
)),
"FunctionDefinition": lambda model, variable:
model.add_function_definition(
gillespy2.FunctionDefinition(name="fn", function="variable", args=["variable"])),
}
# List of supported SBML features for each solver.
# When a feature is implemented for a particular solver, add the feature to its list.
cls.solver_supported_sbml_features = {
NumPySSASolver: [],
TauLeapingSolver: [],
ODESolver: [],
TauHybridSolver: [
"AssignmentRule",
"RateRule",
"Event",
"FunctionDefinition",
],
SSACSolver: [],
ODECSolver: [],
TauLeapingCSolver: [],
TauHybridCSolver: [
"RateRule",
"Event",
],
}
cls.model = create_decay()
cls.results = {}
cls.labeled_results = {}
cls.labeled_results_more_trajectories = {}
def __get_rules(sbml_model, gillespy_model, errors):
for i in range(sbml_model.getNumRules()):
rule = sbml_model.getRule(i)
rule_name = rule.getId()
rule_variable = rule.getVariable()
rule_string = __get_math(rule.getMath())
if rule_variable in gillespy_model.listOfParameters:
# Treat Non-Constant Parameters as Species
value = gillespy_model.listOfParameters[rule_variable].expression
species = gillespy2.Species(name=rule_variable,
initial_value=value,
allow_negative_populations=True,
mode='continuous')
gillespy_model.delete_parameter(rule_variable)
gillespy_model.add_species([species])
t = []
if rule.isAssignment():
assign_value = eval(rule_string, {**eval_globals, **init_state})
postponed_evals[rule_variable] = rule_string
gillespy_rule = gillespy2.AssignmentRule(name=rule_name,
variable=rule_variable,
formula=rule_string)
gillespy_model.add_assignment_rule(gillespy_rule)
init_state[gillespy_rule.variable] = eval(gillespy_rule.formula, {
**init_state,
**eval_globals
})
if rule.isRate():
gillespy_rule = gillespy2.RateRule(name=rule_name,
variable=rule_variable,
formula=rule_string)
gillespy_model.add_rate_rule(gillespy_rule)
if rule.isAlgebraic():
t.append('algebraic')
if len(t) > 0:
t[0] = t[0].capitalize()
msg = ", ".join(t)
msg += " rule"
else:
msg = "Rule"
errors.append([
"{0} '{1}' found on line '{2}' with equation '{3}'. gillespy does not support SBML Algebraic Rules"
.format(msg, rule.getId(), rule.getLine(),
libsbml.formulaToString(rule.getMath())), -5
])