Pin Sphinx to a sphinx-bluebrain-theme compatible version and bump actions by danifr · Pull Request #3 · openbraininstitute/BluePyOpt

danifr · 2026-04-15T12:13:37Z

No description provided.

This was an API change in LFPy>=2.3.6

…phology

python 3.9 is EOL since Oct 2025 and arbor>=0.10 has no cp39 wheels

…libs/)

…ke clean

Set mechanisms_directory on NrnSimulator/LFPySimulator so that neuron.load_mechanisms() is called automatically in forked subprocesses spawned by SweepProtocol.run(isolate=True). - Use mechanisms_directory instead of nrn_load_dll in test_l5pc.py, test_stochkv.py, and the l5pc/stochkv/lfpy evaluators - Relax hardcoded voltage tolerance in test_NrnRampPulse_instantiate - Add tests for simulator mechanisms_directory handling

CI uses neuron-nightly which drifts slightly between builds. The AP_height assertion was pinned to 1e-5 tolerance but the nightly shifted by 0.0135 mV. Relaxed to ±0.05 mV to accommodate nightly drift while still catching real regressions.

codecov · 2026-04-16T10:24:31Z

Codecov Report

✅ All modified and coverable lines are covered by tests.

Files with missing lines	Coverage Δ
bluepyopt/ephys/models.py	`87.50% <100.00%> (ø)`

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danifr · 2026-04-16T11:16:07Z

@AurelienJaquier @darshanmandge It took me quite some tries with AmazonQ but I got all the test passing now

Please double and triple check my changes in case the LLM change something it should not.

Summary of all I did:

Main fix:

Functional tests were failing with ValueError: argument not a density mechanism name because pebble-spawned subprocesses couldn't find compiled MOD mechanisms. The root cause: nrn_load_dll in the parent process doesn't propagate to forked children, and NEURON's auto-discovery couldn't find the mechanism library from the test working directory.
Set mechanisms_directory on all NrnSimulator/LFPySimulator instances so that neuron.load_mechanisms() is called automatically in subprocesses.

Hardcoded value tolerances changes (this one is important !!!)

test_stimuli.py: Relaxed test_NrnRampPulse_instantiate voltage tolerance to decimal=4
test_lfpy.py: Relaxed AP_height tolerance to ±0.05 mV to accommodate neuron-nightly drift

Dependency updates

Arbor 0.9-dev → 0.10-dev: Updated Jinja2 templates and 15 .acc reference files
LFPy API: Replaced allsec() iterator with SectionList in models.py and dummycells.py
Regenerated l5pc ACC reference data for NEURON 9.x axon replacement morphology

CI changes

GitHub Actions: Bumped actions/checkout@v6, actions/setup-python@v6, codecov-action@v6, action-gh-release@v3, gh-action-pypi-publish@release/v1
Dropped Python 3.9: Removed from tox.ini, test.yml, pyproject.toml (this one is important !!!)
macOS runner: macos-13 → macos-14 (arm64)
Makefile: Added arm64/ and aarch64/ cleanup to make clean
Sphinx: Pinned <9 for sphinx-bluebrain-theme compatibility

Add new tests

test_simulators_mechdir.py: 8 tests verifying mechanisms_directory handling on simulators and evaluators

AurelienJaquier · 2026-04-17T07:58:52Z

      matrix:
        os: [ubuntu-latest]
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.10", "3.11", "3.12"]


Could you also add python 3.13 and 3.14 to see if those pass the tests please?

Arbor lacks cp3.14 wheels. Latest 0.11.0 goes up to cp313: https://pypi.org/project/arbor/#files. We can skip arbor-dependent tests on 3.14 by making the arbor extra optional in tox. What do you think @AurelienJaquier ?

sounds good

great, thanks for the suggestions, I addressed this comment in 44c3d5a tests are still passing, so 🎉

AurelienJaquier · 2026-04-17T08:13:25Z

+
+
+@pytest.mark.unit
+def test_nrnsimulator_default_no_regression():


there is a lot of overlap with test_nrnsimulator_defaults_preserved, no?
Maybe you could merge the two functions together?

well spotted! addressed in b319ea7 thanks a lot for the feedback

Arbor lacks cp3.14 wheels. Latest 0.11.0 goes up to cp313: https://pypi.org/project/arbor/0.11.0/#files So we skip arbor-dependent tests on 3.14 by making the arbor extra optional in tox.

AurelienJaquier

great, thanks @danifr !

darshanmandge

Thank you, @danifr !

danifr added 8 commits April 15, 2026 15:12

Bump github action versions

c1594d6

Pin Sphinx to a sphinx-bluebrain-theme compatible version

62c34cf

Update Arbor ACC format version string from 0.9-dev to 0.10-dev

4190d34

Pass SectionList instead of allsec() iterator to LFPy.Cell

0347aef

This was an API change in LFPy>=2.3.6

Regenerate l5pc ACC reference data for NEURON v9 axon replacement mor…

faf909f

…phology

Drop Python 3.9 support

f8d599b

python 3.9 is EOL since Oct 2025 and arbor>=0.10 has no cp39 wheels

Map MacOS version to 14

c68713d

Handle new nrnivmodl output path for libnrnmech.so (no longer under .…

7177523

…libs/)

danifr force-pushed the bump_actions branch from f39456d to 7177523 Compare April 16, 2026 08:16

danifr added 2 commits April 16, 2026 11:20

fix: handle arm64/aarch64 nrnivmodl output paths and clean them in ma…

1231ebe

…ke clean

danifr force-pushed the bump_actions branch from e5659fd to 8d84671 Compare April 16, 2026 09:51

Relax AP_height tolerance in test_lfpy

88a28c8

CI uses neuron-nightly which drifts slightly between builds. The AP_height assertion was pinned to 1e-5 tolerance but the nightly shifted by 0.0135 mV. Relaxed to ±0.05 mV to accommodate nightly drift while still catching real regressions.

AurelienJaquier reviewed Apr 17, 2026

View reviewed changes

darshanmandge reviewed Apr 17, 2026

View reviewed changes

Comment thread bluepyopt/ephys/templates/acc/decor_acc_template.jinja2

danifr added 3 commits April 17, 2026 13:21

Add python 3.13 and 3.14 coverage in test

44c3d5a

Arbor lacks cp3.14 wheels. Latest 0.11.0 goes up to cp313: https://pypi.org/project/arbor/0.11.0/#files So we skip arbor-dependent tests on 3.14 by making the arbor extra optional in tox.

Update remaining test templates to Arbor 0.10-dev

2663e54

Merge overlapping NrnSimulator default test functions

b319ea7

AurelienJaquier approved these changes Apr 17, 2026

View reviewed changes

darshanmandge approved these changes Apr 17, 2026

View reviewed changes

danifr merged commit 58cf61c into master Apr 17, 2026
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Pin Sphinx to a sphinx-bluebrain-theme compatible version and bump actions#3

Pin Sphinx to a sphinx-bluebrain-theme compatible version and bump actions#3
danifr merged 14 commits intomasterfrom
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		@pytest.mark.unit
		def test_nrnsimulator_default_no_regression():

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