AssertionError: Cell keyword argument morphology not recognized as neuron.h.SectionList

[to-br]

In version 9.0.0 of neuron, upon creating a cell using an instance of neuron.h.SectionList as morphology argument, the keyword was not recognized. This led to an assertion error: "AssertionError: Could not recognize Cell keyword argument morphology as neuron.h.SectionList instance".

Steps to reproduce the behavior
import neuron
h = neuron.h
import LFPy
print(neuron.version)

soma = h.Section(name='soma')
soma.L = 20
soma.diam = 20
soma.insert('hh')

secs = h.SectionList()
secs.append(soma)

print("Type of SectionList:", type(secs))

cell_params = dict(
v_init=-65,
tstop=10,
dt=0.1,
)

cell = LFPy.Cell(morphology=secs,**cell_params)

Output:
AssertionError: Could not recognize Cell keyword argument morphology as neuron.h.SectionList instance

Possible solution:
In cell.py replace
assert isinstance(self.morphology, type(neuron.h.SectionList)),
("Could not recognize Cell keyword argument morphology as " +
"neuron.h.SectionList instance")
with
if not hasattr(self.morphology, "wholetree"):
raise TypeError ("Could not recognize Cell keyword argument morphology as " +
"neuron.h.SectionList instance")

Setup:

• OS: Ubuntu 22.04
• Python version: Python 3.12.3
• NEURON version: 9.0.0
• LFPy version: 2.2.4 (installed via pip)

[torbjone]

Thank you for posting! But can you make this request at LFPy / LFPy instead of LFPy / ElectricBrainSignals, since this seems to be a LFPy-related problem?