def test_variable(self):
from libcellml import Component, Variable
# VariablePtr variable(size_t index)
c = Component()
v = Variable()
name = 'green'
v.setName(name)
self.assertIsNone(c.variable(0))
self.assertIsNone(c.variable(1))
self.assertIsNone(c.variable(-1))
c.addVariable(v)
self.assertIsNone(c.variable(1))
self.assertIsNone(c.variable(-1))
self.assertIsNotNone(c.variable(0))
self.assertEqual(c.variable(0).name(), name)
del [c, v, name]
# VariablePtr variable(const std::string &name)
c = Component()
v = Variable()
name = 'green'
v.setName(name)
self.assertIsNone(c.variable(name))
c.addVariable(v)
self.assertIsNone(c.variable('red'))
self.assertIsNotNone(c.variable(name))
self.assertEqual(c.variable(name).name(), name)
ms = Units('ms')
ms.addUnit('second', 'milli')
mM = Units('mM')
mM.addUnit('mole', 'milli')
model.addUnits(ms)
model.addUnits(mV)
model.addUnits(mM)
model.addUnits(microA_per_cm2)
model.addUnits(mS_per_cm2)
# 2.g
# Set the units on each of the variables.
# Call the validator again, and expect there to be no errors.
k_channel_equations.variable('E_K').setUnits(mV)
k_channel_equations.variable('i_K').setUnits(microA_per_cm2)
k_channel_equations.variable('g_K').setUnits(mS_per_cm2)
k_channel_equations.variable('V').setUnits(mV)
k_channel_equations.variable('t').setUnits(ms)
k_channel_equations.variable('n').setUnits('dimensionless')
validator.validateModel(model)
print_issues(validator)
# end 2
print('------------------------------------------------------------')
print(' STEP 3: Create the n_gate and n_gate_equations components ')
print('------------------------------------------------------------')
t.setName("t")
t.setUnits("ms")
environment.addVariable(t)
# 4.c Add the new component to the model and validate
model.addComponent(environment)
validator.validateModel(model)
print_errors_to_terminal(validator)
print("-----------------------------------------------")
print(" STEP 5: Connecting variables and components")
print("-----------------------------------------------")
# 5.a Connecting the equivalent variables between all the components
Variable.addEquivalence(environment.variable("t"), sodium_channel.variable("t"))
Variable.addEquivalence(sodium_channel.variable("t"), mGate.variable("t"))
Variable.addEquivalence(sodium_channel.variable("t"), hGate.variable("t"))
environment.variable("t").setInterfaceType("public")
sodium_channel.variable("t").setInterfaceType("public_and_private")
mGate.variable("t").setInterfaceType("public")
hGate.variable("t").setInterfaceType("public")
Variable.addEquivalence(environment.variable("V"), sodium_channel.variable("V"))
Variable.addEquivalence(sodium_channel.variable("V"), mGate.variable("V"))
Variable.addEquivalence(sodium_channel.variable("V"), hGate.variable("V"))
environment.variable("V").setInterfaceType("public")
sodium_channel.variable("V").setInterfaceType("public_and_private")
mGate.variable("V").setInterfaceType("public")
hGate.variable("V").setInterfaceType("public")
per_ms = Units('per_ms')
# 5.b
# Add Unit items to the units you created to define them.
ms.addUnit('second', 'milli')
per_ms.addUnit('second', 'milli', -1)
# 5.c
# Add the Units to the model (not the component) so that other components can make
# use of them too.
model.addUnits(ms)
model.addUnits(per_ms)
# 5.d
# Use the setUnits function to associate them with the appropriate variables.
gateEquations.variable('t').setUnits(ms)
gateEquations.variable('alpha_X').setUnits(per_ms)
gateEquations.variable('beta_X').setUnits(per_ms)
gateEquations.variable('X').setUnits('dimensionless')
# 5.e
# Validate again, and expect no errors.
validator.validateModel(model)
print_issues(validator)
# end 5
print('----------------------------------------------------------')
print(' STEP 6: Analyse the model ')
print('----------------------------------------------------------')
t.setUnits("ms")
environment.addVariable(t)
# 5.c Add the new component to the model and validate
validator.validateModel(model)
print_errors_to_terminal(validator)
print("\n-----------------------------------------------")
print(" STEP 6: Connect the equivalent variables")
print("-----------------------------------------------")
# 6.a Connecting the membrane to its sibling environment, and the channels to their
# parent membrane component.
Variable.addEquivalence(membrane.variable("t"), sodium_channel.variable("t"))
Variable.addEquivalence(membrane.variable("t"), potassium_channel.variable("t"))
Variable.addEquivalence(environment.variable("t"), membrane.variable("t"))
Variable.addEquivalence(membrane.variable("V"), sodium_channel.variable("V"))
Variable.addEquivalence(membrane.variable("V"), potassium_channel.variable("V"))
Variable.addEquivalence(membrane.variable("V"), leakage_current.variable("V"))
Variable.addEquivalence(environment.variable("V"), membrane.variable("V"))
# 6.b Setting the interface types for those which haven't been inherited already
environment.variable("t").setInterfaceType("public")
membrane.variable("t").setInterfaceType("public_and_private")
environment.variable("V").setInterfaceType("public")
membrane.variable("V").setInterfaceType("public_and_private")
validator.validateModel(model)
print_errors_to_terminal(validator)
print("\n-----------------------------------------------")
