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import pytest
from testutils import compare_data, tol
@pytest.fixture
def ics_include_flux(neuron_instance):
"""A model using node.include_flux for the 3d intracellular space.
node.include_flux can take either a; integer, Python function or NEURON
pointer. All three are tested here for 3d intracellular rxd.
"""
h, rxd, data, save_path = neuron_instance
sec = h.Section(name="sec")
sec.L = 1
sec.nseg = 11
sec.diam = 2
rxd.set_solve_type(dimension=3)
cyt = rxd.Region(h.allsec(), name="cyt", nrn_region="i")
ip3 = rxd.Species(
cyt, name="ip3", initial=lambda nd: 1000 if nd.segment == sec(0.3) else 0
)
def callbackfun():
return 1000
for nd in ip3.nodes(sec(0.1)):
nd.include_flux(1000)
for nd in ip3.nodes(sec(0.5)):
nd.include_flux(callbackfun)
for nd in ip3.nodes(sec(0.9)):
nd.include_flux(sec(0.3)._ref_ip3i)
model = (sec, cyt, ip3, callbackfun)
yield (neuron_instance, model)
def test_include_flux3d(ics_include_flux):
"""Test ics_include_flux with fixed step methods"""
neuron_instance, model = ics_include_flux
h, rxd, data, save_path = neuron_instance
h.finitialize(-70)
h.continuerun(10)
if not save_path:
max_err = compare_data(data)
assert max_err < tol
def test_include_flux3d_cvode(ics_include_flux):
"""Test ics_include_flux with variable step methods"""
neuron_instance, model = ics_include_flux
h, rxd, data, save_path = neuron_instance
h.CVode().active(True)
h.finitialize(-70)
h.continuerun(10)
if not save_path:
max_err = compare_data(data)
assert max_err < tol
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