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import pytest
from testutils import compare_data, tol
@pytest.fixture
def empty_regions_model(neuron_instance):
"""A model with an empty region"""
h, rxd, data, save_path = neuron_instance
sec = h.Section()
sec.L = 100
sec.diam = 1
sec.nseg = 100
cells = []
cyt = rxd.Region(cells, name="cyt", nrn_region="i")
mem = rxd.Region(cells, name="mem", geometry=rxd.membrane)
ecs = rxd.Extracellular(-5, -5, -5, 5, 5, 5, dx=5)
k = rxd.Species(
[ecs, cyt],
name="k",
d=0,
charge=1,
initial=lambda nd: 140 if hasattr(nd, "x") else 3,
)
model = (sec, cyt, mem, ecs, k)
yield (neuron_instance, model)
def test_empty_region_no_rate(empty_regions_model):
"""Test a rate that should do nothing with an empty region"""
neuron_instance, model = empty_regions_model
h, rxd, data, save_path = neuron_instance
sec, cyt, mem, ecs, k = model
kcyt = k[cyt]
react = rxd.Rate(kcyt, -10 * kcyt)
h.finitialize(-70)
h.continuerun(10)
if not save_path:
max_err = compare_data(data)
assert max_err < tol
def test_empty_region_ecs_rate(empty_regions_model):
"""Test a rate that should change the ECS with an empty region"""
neuron_instance, model = empty_regions_model
h, rxd, data, save_path = neuron_instance
sec, cyt, mem, ecs, k = model
react = rxd.Rate(k, -10 * k)
h.finitialize(-70)
h.continuerun(10)
if not save_path:
max_err = compare_data(data)
assert max_err < tol
def test_empty_region_no_reaction(empty_regions_model):
"""Test a reaction that should change the ECS with an empty region"""
neuron_instance, model = empty_regions_model
h, rxd, data, save_path = neuron_instance
sec, cyt, mem, ecs, k = model
react = rxd.Reaction(2 * k, k, 10, regions=[cyt])
h.finitialize(-70)
h.continuerun(10)
if not save_path:
max_err = compare_data(data)
assert max_err < tol
def test_empty_region_ecs_reaction(empty_regions_model):
"""Test a reaction that should change the ECS with an empty region"""
neuron_instance, model = empty_regions_model
h, rxd, data, save_path = neuron_instance
sec, cyt, mem, ecs, k = model
react = rxd.Reaction(2 * k, k, 10)
h.finitialize(-70)
h.continuerun(10)
if not save_path:
max_err = compare_data(data)
assert max_err < tol
def test_empty_region_multicompartment_reaction(empty_regions_model):
"""Test a reaction that should change the ECS with an empty region"""
neuron_instance, model = empty_regions_model
h, rxd, data, save_path = neuron_instance
sec, cyt, mem, ecs, k = model
kcyt, kecs = k[cyt], k[ecs]
react = rxd.MultiCompartmentReaction(
kcyt, kecs, 1e5, 0, membrane=mem, membrane_flux=False
)
h.finitialize(-70)
h.continuerun(10)
if not save_path:
max_err = compare_data(data)
assert max_err < tol
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