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fix arbor tests with latest arbor version #498

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merged 11 commits into from
Aug 23, 2024
Merged

fix arbor tests with latest arbor version #498

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3c887d7
fix arbor tests with latest arbor version
Aug 20, 2024
c1befc6
lint fix
Aug 20, 2024
0b06f73
Merge branch 'master' into arbor-v0.10
AurelienJaquier Aug 20, 2024
68f315b
drop support for python 3.8
Aug 20, 2024
0373e39
Merge branch 'arbor-v0.10' of https://github.com/BlueBrain/BluePyOpt …
Aug 20, 2024
f400cbb
fix arbor-related functional tests
Aug 20, 2024
86e2c14
update codecov action version to v4
Aug 20, 2024
5ad7f4d
add test for load_component using iexpr
Aug 21, 2024
5778cd5
fix iexpr test
Aug 21, 2024
f9ac053
arbor-related code improvement
Aug 22, 2024
d1758ba
add load_component test
Aug 23, 2024
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4 changes: 2 additions & 2 deletions .github/workflows/test.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@ jobs:
strategy:
matrix:
os: [ubuntu-latest]
python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
python-version: ["3.9", "3.10", "3.11", "3.12"]
include:
- os: macos-12
python-version: "3.10"
Expand All @@ -34,7 +34,7 @@ jobs:
run: tox

- name: "Upload coverage to Codecov"
uses: codecov/codecov-action@v2
uses: codecov/codecov-action@v4
with:
token: ${{ secrets.CODECOV_TOKEN }}
fail_ci_if_error: false
2 changes: 1 addition & 1 deletion README.rst
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Expand Up @@ -85,7 +85,7 @@ News
Requirements
============

* `Python 3.8+ <https://www.python.org/downloads/release/python-380/>`_
* `Python 3.9+ <https://www.python.org/downloads/release/python-390/>`_
* `Pip <https://pip.pypa.io>`_ (installed by default in newer versions of Python)
* `Neuron 7.4+ <http://neuron.yale.edu/>`_ (compiled with Python support)
* `eFEL eFeature Extraction Library <https://github.com/BlueBrain/eFEL>`_ (automatically installed by pip)
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2 changes: 2 additions & 0 deletions bluepyopt/ephys/morphologies.py
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Expand Up @@ -307,6 +307,8 @@ def load(morpho_filename, replace_axon):
morpho = arbor.load_component(morpho_filename).component
elif morpho_suffix == '.swc':
morpho = arbor.load_swc_arbor(morpho_filename)
# turn loaded_morphology into morphology type
morpho = morpho.morphology
elif morpho_suffix == '.asc':
morpho = arbor.load_asc(morpho_filename).morphology
else:
Expand Down
11 changes: 9 additions & 2 deletions bluepyopt/ephys/protocols.py
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Expand Up @@ -602,7 +602,12 @@ def instantiate_iclamp_stimuli(self, decor, use_labels=False):
for i, stim in enumerate(self.stimuli):
if not isinstance(stim, stimuli.SynapticStimulus):
if hasattr(stim, 'envelope'):
arb_iclamp = arbor.iclamp(stim.envelope())
envelope = stim.envelope()
envelope = [
(t * arbor.units.ms, curr * arbor.units.nA)
for (t, curr) in envelope
]
arb_iclamp = arbor.iclamp(envelope)
else:
raise ValueError('Stimulus must provide envelope method '
' or be of type NrnNetStimStimulus to be'
Expand Down Expand Up @@ -648,7 +653,9 @@ def instantiate_recordings(self, cell_model, use_labels=False):

cell_model.probe('voltage',
arb_loc.ref if use_labels else arb_loc.loc,
frequency=10) # could be a parameter
f"probe-{i}",
# frequency could be a parameter
frequency=10 * arbor.units.kHz)

return cell_model

Expand Down
6 changes: 4 additions & 2 deletions bluepyopt/ephys/simulators.py
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Expand Up @@ -372,9 +372,11 @@ def run(self, arb_cell_model, tstop=None, dt=None):
dt = dt if dt is not None else self.dt

if dt is not None:
return arb_cell_model.run(tfinal=tstop, dt=dt)
return arb_cell_model.run(
tfinal=tstop * arbor.units.ms, dt=dt * arbor.units.ms
)
else:
return arb_cell_model.run(tfinal=tstop)
return arb_cell_model.run(tfinal=tstop * arbor.units.ms)


class ArbSimulatorException(Exception):
Expand Down
8 changes: 4 additions & 4 deletions bluepyopt/ephys/templates/acc/decor_acc_template.jinja2
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As said before using Arbor to write these might be an easier option.

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Is there a function that can write these kind of files?

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Yes, there's versions for full cable cells or just parts thereof.
https://docs.arbor-sim.org/en/latest/fileformat/cable_cell.html#parsable-arbor-components-and-meta-data
In Python, you'd construct a cable cell (or the parts you're interested in) and call arbor.write_component(thing, filename)
https://docs.arbor-sim.org/en/latest/python/cable_cell_format.html#reading-and-writing-arbor-components

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That would basically mean to turn this template into code at the end of the ACC exporter by instantiating Arbor objects that are then serialized again. Could be an option - I guess it comes down to how much control you need over the export vs. learning the s-expression syntax. The original design of BluePyOpt was to make model exporting configurable (overridable by the user) through templates, hence I chose this option.

In my view, most of the complexity in the ACC exporter comes from converting BluePyOpt's frontend representation to one suitable for Arbor. That last step of dumping the decor is less complicated, but requires some understanding of the format.

I don't want to take any particular side, though. Would only suggest that if you plan to make major changes to the ACC exporter, maybe a good idea would be to do that in a separate PR.

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Yes, I'd support splitting this. One straight port that can be verified and a lateral move to another scheme.

The original design of BluePyOpt was to make model exporting configurable (overridable by the user) through templates, hence I chose this option.

This is why I as an outsider should have an opinion here :D

Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
(arbor-component
(meta-data (version "0.1-dev"))
(meta-data (version "0.9-dev"))
(decor
{%- for mech, params in global_mechs.items() %}
{%- if mech is not none %}
Expand All @@ -10,7 +10,7 @@
{%- endif %}
{%- else %}
{%- for param in params %}
(default ({{ param.name }} {{ param.value }}))
(default ({{ param.name }} {{ param.value }} (scalar 1.0)))
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I won't check all of those in detail, but this is correct for a fixed value.
If the tests are green, I'd assume all are correct.

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The tests are green

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I'd recommend to additionally check the major examples' notebooks qualitatively by inspection (not everything is run as part of the test suite).

{%- endfor %}
{%- endif %}
{%- endfor %}
Expand All @@ -27,13 +27,13 @@
{%- endif %}
{%- else %}
{%- for param in params %}
(paint {{loc.ref}} ({{ param.name }} {{ param.value }}))
(paint {{loc.ref}} ({{ param.name }} {{ param.value }} (scalar 1.0)))
{%- endfor %}
{%- endif %}
{%- endfor %}

{%- for synapse_name, mech_params in pprocess_mechs[loc].items() %}
(place {{loc.ref}} (synapse (mechanism "{{ mech_params.mech }}" {%- for param in mech_params.params %} ("{{ param.name }}" {{ param.value }}){%- endfor %})) "{{ synapse_name }}")
(place {{loc.ref}} (synapse (mechanism "{{ mech_params.mech }}" {%- for param in mech_params.params %} ("{{ param.name }}" {{ param.value }} (scalar 1.0)){%- endfor %})) "{{ synapse_name }}")
{%- endfor %}

{%- endfor %}))
2 changes: 1 addition & 1 deletion bluepyopt/ephys/templates/acc/label_dict_acc_template.jinja2
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@@ -1,5 +1,5 @@
(arbor-component
(meta-data (version "0.1-dev"))
(meta-data (version "0.9-dev"))
(label-dict
{%- for loc, label in label_dict.items() %}
{{ label.defn }}
Expand Down
6 changes: 5 additions & 1 deletion bluepyopt/tests/test_ephys/test_create_acc.py
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Expand Up @@ -537,7 +537,7 @@ def run_short_sim(cable_cell):
arb_cell_model.properties.catalogue.extend(arbor.bbp_catalogue(), "BBP::")

# Run a very short simulation to test mechanism instantiation
arb_cell_model.run(tfinal=0.1)
arb_cell_model.run(tfinal=0.1 * arbor.units.ms)


@pytest.mark.unit
Expand Down Expand Up @@ -665,6 +665,10 @@ def check_acc_dir(test_dir, ref_dir):
with open(ref_dir_file / file) as f:
ref_file = f.read()
assert ref_file == test_file
# check that load_component is not raising any error here
fpath = pathlib.Path(test_dir) / file
if fpath.suffix == "acc":
arbor.load_component(fpath).component


@pytest.mark.unit
Expand Down
34 changes: 33 additions & 1 deletion bluepyopt/tests/test_ephys/test_parameterscalers.py
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@@ -1,7 +1,9 @@
"""Test ephys.parameterscalers"""

import json

import pathlib
import tempfile
import arbor

import pytest

Expand Down Expand Up @@ -143,3 +145,33 @@ def test_parameterscalers_iexpr_generator_unsupported_attr():
'unsupported attribute tau.'):
iexpr = value_scaler.acc_scale_iexpr(
value=value, constant_formatter=lambda v: '%.9g' % v)


@pytest.mark.unit
def test_parameterscalers_iexpr():
"""ephys.parameterscalers: Test iexpr"""
# iexpr from bluepyopt/tests/test_ephys/test_parameterscalers.py
iexpr = '(sub (scalar 0.62109375) ' \
'(mul (log (pi) ) ' \
'(exp (div (distance (region "soma")) ' \
'(scalar 0.421875) ) ) ) )'

# modified decor as in
# bluepyopt/tests/test_ephys/testdata/acc/simplecell/simple_cell_decor.acc
simple_cell_decor_with_iexpr = \
'(arbor-component\n' \
' (meta-data (version "0.9-dev"))\n' \
' (decor\n' \
' (paint (region "soma") ' \
'(membrane-capacitance 0.01 (scalar 1.0)))\n' \
' (paint (region "soma") ' \
'(scaled-mechanism (density (mechanism "default::hh" ' \
'("gnabar" 0.10299326453483033) ("gkbar" 0.027124836082684685))) ' \
f'("gkbar" {iexpr})))))'

with tempfile.TemporaryDirectory() as test_dir:
decor_filename = pathlib.Path(test_dir).joinpath("decor.acc")
with open(decor_filename, "w") as f:
f.write(simple_cell_decor_with_iexpr)
# check that load_component is not raising any error here
arbor.load_component(decor_filename).component
12 changes: 6 additions & 6 deletions bluepyopt/tests/test_ephys/testdata/acc/CCell/CCell_decor.acc
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@@ -1,10 +1,10 @@
(arbor-component
(meta-data (version "0.1-dev"))
(meta-data (version "0.9-dev"))
(decor
(default (gSKv3_1bar_SKv3_1 65))
(paint (region "soma") (gSKv3_1bar_SKv3_1 65))
(paint (region "soma") (gSKv3_1bar_SKv3_1 65))
(default (gSKv3_1bar_SKv3_1 65 (scalar 1.0)))
(paint (region "soma") (gSKv3_1bar_SKv3_1 65 (scalar 1.0)))
(paint (region "soma") (gSKv3_1bar_SKv3_1 65 (scalar 1.0)))
(paint (region "dend") (density (mechanism "BBP::Ih")))
(paint (region "apic") (gSKv3_1bar_SKv3_1 65))
(paint (region "apic") (gSKv3_1bar_SKv3_1 65))
(paint (region "apic") (gSKv3_1bar_SKv3_1 65 (scalar 1.0)))
(paint (region "apic") (gSKv3_1bar_SKv3_1 65 (scalar 1.0)))
(paint (region "apic") (density (mechanism "BBP::Ih")))))
2 changes: 1 addition & 1 deletion bluepyopt/tests/test_ephys/testdata/acc/CCell/CCell_label_dict.acc
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@@ -1,5 +1,5 @@
(arbor-component
(meta-data (version "0.1-dev"))
(meta-data (version "0.9-dev"))
(label-dict
(region-def "all" (all))
(region-def "apic" (tag 4))
Expand Down
2 changes: 1 addition & 1 deletion bluepyopt/tests/test_ephys/testdata/acc/CCell/simple_axon_replacement.acc
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@@ -1,6 +1,6 @@
(arbor-component
(meta-data
(version "0.1-dev"))
(version "0.9-dev"))
(morphology
(branch 0 -1
(segment 0
Expand Down
6 changes: 3 additions & 3 deletions bluepyopt/tests/test_ephys/testdata/acc/expsyn/simple_cell_decor.acc
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@@ -1,6 +1,6 @@
(arbor-component
(meta-data (version "0.1-dev"))
(meta-data (version "0.9-dev"))
(decor
(paint (region "soma") (membrane-capacitance 0.01))
(paint (region "soma") (membrane-capacitance 0.01 (scalar 1.0)))
(paint (region "soma") (density (mechanism "default::pas")))
(place (locset "somacenter") (synapse (mechanism "default::expsyn" ("tau" 10))) "expsyn")))
(place (locset "somacenter") (synapse (mechanism "default::expsyn" ("tau" 10 (scalar 1.0)))) "expsyn")))
2 changes: 1 addition & 1 deletion bluepyopt/tests/test_ephys/testdata/acc/expsyn/simple_cell_label_dict.acc
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@@ -1,5 +1,5 @@
(arbor-component
(meta-data (version "0.1-dev"))
(meta-data (version "0.9-dev"))
(label-dict
(region-def "all" (all))
(region-def "soma" (tag 1))
Expand Down
2 changes: 1 addition & 1 deletion bluepyopt/tests/test_ephys/testdata/acc/l5pc/C060114A7_axon_replacement.acc
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@@ -1,6 +1,6 @@
(arbor-component
(meta-data
(version "0.1-dev"))
(version "0.9-dev"))
(morphology
(branch 0 -1
(segment 0
Expand Down
2 changes: 1 addition & 1 deletion bluepyopt/tests/test_ephys/testdata/acc/l5pc/C060114A7_modified.acc
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@@ -1,6 +1,6 @@
(arbor-component
(meta-data
(version "0.1-dev"))
(version "0.9-dev"))
(morphology
(branch 0 -1
(segment 0
Expand Down
26 changes: 13 additions & 13 deletions bluepyopt/tests/test_ephys/testdata/acc/l5pc/l5pc_decor.acc
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@@ -1,22 +1,22 @@
(arbor-component
(meta-data (version "0.1-dev"))
(meta-data (version "0.9-dev"))
(decor
(default (membrane-potential -65))
(default (temperature-kelvin 307.14999999999998))
(default (membrane-capacitance 0.01))
(default (axial-resistivity 100))
(default (membrane-potential -65 (scalar 1.0)))
(default (temperature-kelvin 307.14999999999998 (scalar 1.0)))
(default (membrane-capacitance 0.01 (scalar 1.0)))
(default (axial-resistivity 100 (scalar 1.0)))
(paint (region "all") (density (mechanism "default::pas/e=-75" ("g" 3.0000000000000001e-05))))
(paint (region "soma") (ion-reversal-potential "na" 50))
(paint (region "soma") (ion-reversal-potential "k" -85))
(paint (region "soma") (ion-reversal-potential "na" 50 (scalar 1.0)))
(paint (region "soma") (ion-reversal-potential "k" -85 (scalar 1.0)))
(paint (region "soma") (density (mechanism "BBP::NaTs2_t" ("gNaTs2_tbar" 0.98395500000000002))))
(paint (region "soma") (density (mechanism "BBP::SKv3_1" ("gSKv3_1bar" 0.30347200000000002))))
(paint (region "soma") (density (mechanism "BBP::SK_E2" ("gSK_E2bar" 0.0084069999999999995))))
(paint (region "soma") (density (mechanism "BBP::Ca_HVA" ("gCa_HVAbar" 0.00099400000000000009))))
(paint (region "soma") (density (mechanism "BBP::Ca_LVAst" ("gCa_LVAstbar" 0.00033300000000000002))))
(paint (region "soma") (density (mechanism "BBP::CaDynamics_E2" ("gamma" 0.00060899999999999995) ("decay" 210.48528400000001))))
(paint (region "soma") (density (mechanism "BBP::Ih" ("gIhbar" 8.0000000000000007e-05))))
(paint (region "axon") (ion-reversal-potential "na" 50))
(paint (region "axon") (ion-reversal-potential "k" -85))
(paint (region "axon") (ion-reversal-potential "na" 50 (scalar 1.0)))
(paint (region "axon") (ion-reversal-potential "k" -85 (scalar 1.0)))
(paint (region "axon") (density (mechanism "BBP::NaTa_t" ("gNaTa_tbar" 3.1379679999999999))))
(paint (region "axon") (density (mechanism "BBP::Nap_Et2" ("gNap_Et2bar" 0.0068269999999999997))))
(paint (region "axon") (density (mechanism "BBP::K_Pst" ("gK_Pstbar" 0.97353800000000001))))
Expand All @@ -26,11 +26,11 @@
(paint (region "axon") (density (mechanism "BBP::Ca_HVA" ("gCa_HVAbar" 0.00098999999999999999))))
(paint (region "axon") (density (mechanism "BBP::Ca_LVAst" ("gCa_LVAstbar" 0.0087519999999999994))))
(paint (region "axon") (density (mechanism "BBP::CaDynamics_E2" ("gamma" 0.0029099999999999998) ("decay" 287.19873100000001))))
(paint (region "dend") (membrane-capacitance 0.02))
(paint (region "dend") (membrane-capacitance 0.02 (scalar 1.0)))
(paint (region "dend") (density (mechanism "BBP::Ih" ("gIhbar" 8.0000000000000007e-05))))
(paint (region "apic") (ion-reversal-potential "na" 50))
(paint (region "apic") (ion-reversal-potential "k" -85))
(paint (region "apic") (membrane-capacitance 0.02))
(paint (region "apic") (ion-reversal-potential "na" 50 (scalar 1.0)))
(paint (region "apic") (ion-reversal-potential "k" -85 (scalar 1.0)))
(paint (region "apic") (membrane-capacitance 0.02 (scalar 1.0)))
(paint (region "apic") (density (mechanism "BBP::NaTs2_t" ("gNaTs2_tbar" 0.026145000000000002))))
(paint (region "apic") (density (mechanism "BBP::SKv3_1" ("gSKv3_1bar" 0.0042259999999999997))))
(paint (region "apic") (density (mechanism "BBP::Im" ("gImbar" 0.00014300000000000001))))
Expand Down
2 changes: 1 addition & 1 deletion bluepyopt/tests/test_ephys/testdata/acc/l5pc/l5pc_label_dict.acc
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@@ -1,5 +1,5 @@
(arbor-component
(meta-data (version "0.1-dev"))
(meta-data (version "0.9-dev"))
(label-dict
(region-def "all" (all))
(region-def "soma" (tag 1))
Expand Down
26 changes: 13 additions & 13 deletions bluepyopt/tests/test_ephys/testdata/acc/l5pc_py37/l5pc_decor.acc
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@@ -1,22 +1,22 @@
(arbor-component
(meta-data (version "0.1-dev"))
(meta-data (version "0.9-dev"))
(decor
(default (membrane-potential -65))
(default (temperature-kelvin 307.14999999999998))
(default (membrane-capacitance 0.01))
(default (axial-resistivity 100))
(default (membrane-potential -65 (scalar 1.0)))
(default (temperature-kelvin 307.14999999999998 (scalar 1.0)))
(default (membrane-capacitance 0.01 (scalar 1.0)))
(default (axial-resistivity 100 (scalar 1.0)))
(paint (region "all") (density (mechanism "default::pas/e=-75" ("g" 3.0000000000000001e-05))))
(paint (region "soma") (ion-reversal-potential "na" 50))
(paint (region "soma") (ion-reversal-potential "k" -85))
(paint (region "soma") (ion-reversal-potential "na" 50 (scalar 1.0)))
(paint (region "soma") (ion-reversal-potential "k" -85 (scalar 1.0)))
(paint (region "soma") (density (mechanism "BBP::NaTs2_t" ("gNaTs2_tbar" 0.98395500000000002))))
(paint (region "soma") (density (mechanism "BBP::SKv3_1" ("gSKv3_1bar" 0.30347200000000002))))
(paint (region "soma") (density (mechanism "BBP::SK_E2" ("gSK_E2bar" 0.0084069999999999995))))
(paint (region "soma") (density (mechanism "BBP::Ca_HVA" ("gCa_HVAbar" 0.00099400000000000009))))
(paint (region "soma") (density (mechanism "BBP::Ca_LVAst" ("gCa_LVAstbar" 0.00033300000000000002))))
(paint (region "soma") (density (mechanism "BBP::CaDynamics_E2" ("gamma" 0.00060899999999999995) ("decay" 210.48528400000001))))
(paint (region "soma") (density (mechanism "BBP::Ih" ("gIhbar" 8.0000000000000007e-05))))
(paint (region "axon") (ion-reversal-potential "na" 50))
(paint (region "axon") (ion-reversal-potential "k" -85))
(paint (region "axon") (ion-reversal-potential "na" 50 (scalar 1.0)))
(paint (region "axon") (ion-reversal-potential "k" -85 (scalar 1.0)))
(paint (region "axon") (density (mechanism "BBP::NaTa_t" ("gNaTa_tbar" 3.1379679999999999))))
(paint (region "axon") (density (mechanism "BBP::Nap_Et2" ("gNap_Et2bar" 0.0068269999999999997))))
(paint (region "axon") (density (mechanism "BBP::K_Pst" ("gK_Pstbar" 0.97353800000000001))))
Expand All @@ -26,11 +26,11 @@
(paint (region "axon") (density (mechanism "BBP::Ca_HVA" ("gCa_HVAbar" 0.00098999999999999999))))
(paint (region "axon") (density (mechanism "BBP::Ca_LVAst" ("gCa_LVAstbar" 0.0087519999999999994))))
(paint (region "axon") (density (mechanism "BBP::CaDynamics_E2" ("gamma" 0.0029099999999999998) ("decay" 287.19873100000001))))
(paint (region "dend") (membrane-capacitance 0.02))
(paint (region "dend") (membrane-capacitance 0.02 (scalar 1.0)))
(paint (region "dend") (density (mechanism "BBP::Ih" ("gIhbar" 8.0000000000000007e-05))))
(paint (region "apic") (ion-reversal-potential "na" 50))
(paint (region "apic") (ion-reversal-potential "k" -85))
(paint (region "apic") (membrane-capacitance 0.02))
(paint (region "apic") (ion-reversal-potential "na" 50 (scalar 1.0)))
(paint (region "apic") (ion-reversal-potential "k" -85 (scalar 1.0)))
(paint (region "apic") (membrane-capacitance 0.02 (scalar 1.0)))
(paint (region "apic") (density (mechanism "BBP::NaTs2_t" ("gNaTs2_tbar" 0.026145000000000002))))
(paint (region "apic") (density (mechanism "BBP::SKv3_1" ("gSKv3_1bar" 0.0042259999999999997))))
(paint (region "apic") (density (mechanism "BBP::Im" ("gImbar" 0.00014300000000000001))))
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2 changes: 1 addition & 1 deletion bluepyopt/tests/test_ephys/testdata/acc/simplecell/simple_axon_replacement.acc
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@@ -1,6 +1,6 @@
(arbor-component
(meta-data
(version "0.1-dev"))
(version "0.9-dev"))
(morphology
(branch 0 -1
(segment 0
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4 changes: 2 additions & 2 deletions bluepyopt/tests/test_ephys/testdata/acc/simplecell/simple_cell_decor.acc
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(arbor-component
(meta-data (version "0.1-dev"))
(meta-data (version "0.9-dev"))
(decor
(paint (region "soma") (membrane-capacitance 0.01))
(paint (region "soma") (membrane-capacitance 0.01 (scalar 1.0)))
(paint (region "soma") (density (mechanism "default::hh" ("gnabar" 0.10299326453483033) ("gkbar" 0.027124836082684685))))))
2 changes: 1 addition & 1 deletion bluepyopt/tests/test_ephys/testdata/acc/simplecell/simple_cell_label_dict.acc
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@@ -1,5 +1,5 @@
(arbor-component
(meta-data (version "0.1-dev"))
(meta-data (version "0.9-dev"))
(label-dict
(region-def "all" (all))
(region-def "soma" (tag 1))
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2 changes: 1 addition & 1 deletion bluepyopt/tests/test_ephys/testdata/acc/simplecell/simple_modified.acc
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@@ -1,6 +1,6 @@
(arbor-component
(meta-data
(version "0.1-dev"))
(version "0.9-dev"))
(morphology
(branch 0 -1
(segment 0
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