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import os.path as osp
import numpy
import pytest
import gc
from .testutils import collect_data
def pytest_addoption(parser):
parser.addoption("--mpi", action="store_true", default=False, help="use MPI")
parser.addoption("--save", action="store", default=None, help="save the test data")
@pytest.fixture(scope="session")
def neuron_import(request):
"""Provides an instance of neuron h and rxd for tests"""
# to use NEURON with MPI, mpi4py must be imported first.
if request.config.getoption("--mpi"):
from mpi4py import MPI # noqa: F401
save_path = request.config.getoption("--save")
# we may not be not running in the test path so we have to load the mechanisms
import neuron
neuron.load_mechanisms(osp.abspath(osp.dirname(__file__)))
from neuron import h, rxd
return h, rxd, save_path
@pytest.fixture
def neuron_nosave_instance(neuron_import):
"""Sets/Resets the rxd test environment."""
h, rxd, save_path = neuron_import
h.load_file("stdrun.hoc")
h.load_file("import3d.hoc")
h.nrnunit_use_legacy(True)
# pytest fixtures at the function scope that require neuron_instance will go
# out of scope after neuron_instance. So species, sections, etc. will go
# out of scope after neuron_instance is torn down.
# Here we assert that no section left alive. If the assertion fails it is
# due to a problem with the previous test, not the test which failed.
gc.collect()
for sec in h.allsec():
assert False
cvode = h.CVode()
cvode.active(False)
cvode.atol(1e-3)
h.dt = 0.025
h.stoprun = False
yield (h, rxd, save_path)
# With Python 3.11 on macOS there seemed to be problems related to garbage
# collection happening during the following teardown
gc.disable()
for r in rxd.rxd._all_reactions[:]:
if r():
rxd.rxd._unregister_reaction(r)
for s in rxd.species._all_species:
if s():
s().__del__()
gc.enable()
rxd.region._all_regions = []
rxd.region._region_count = 0
rxd.region._c_region_lookup = None
rxd.species._species_counts = 0
rxd.section1d._purge_cptrs()
rxd.initializer.has_initialized = False
rxd.rxd.free_conc_ptrs()
rxd.rxd.free_curr_ptrs()
rxd.rxd.rxd_include_node_flux1D(0, None, None, None)
rxd.species._has_1d = False
rxd.species._has_3d = False
rxd.rxd._zero_volume_indices = numpy.ndarray(0, dtype=numpy.int_)
rxd.set_solve_type(dimension=1)
@pytest.fixture
def neuron_instance(neuron_nosave_instance):
"""Sets/Resets the rxd test environment.
Provides 'data', a dictionary used to store voltages and rxd node
values for comparisons with the 'correct_data'.
"""
h, rxd, save_path = neuron_nosave_instance
data = {"record_count": 0, "data": []}
def gather():
return collect_data(h, rxd, data, save_path)
cvode = h.CVode()
cvode.extra_scatter_gather(0, gather)
yield (h, rxd, data, save_path)
cvode.extra_scatter_gather_remove(gather)
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