Pin Sphinx to a sphinx-bluebrain-theme compatible version and bump actions

.github/workflows/build.yml

@@ -22,15 +22,15 @@ jobs:
       contents: write
       id-token: write  # needed for pypi publication
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v6
 
       - name: Set up Python 3.12
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v6
         with:
           python-version: "3.12"
 
       - name: Bump version and push tag
-        uses: anothrNick/github-tag-action@1.64.0
+        uses: anothrNick/github-tag-action@v1
         if: ${{ !startsWith(github.ref, 'refs/tags/') }}
         id: tag
         env:
@@ -51,11 +51,11 @@ jobs:
         run: echo "TAG_NAME=${{ github.ref_name }}" >> $GITHUB_ENV
 
       - name: Release
-        uses: softprops/action-gh-release@v1
+        uses: softprops/action-gh-release@v3
         with:
           tag_name: ${{ env.TAG_NAME }}
           name: ${{ env.TAG_NAME }}
           generate_release_notes: true
 
       - name: Publish package to PyPI
-        uses: pypa/gh-action-pypi-publish@release/v1.12
+        uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/keep-alive.yml

@@ -13,7 +13,7 @@ jobs:
     name: Keep workflow alive
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v6
         with:
           ref: master
 

.github/workflows/test.yml

@@ -12,16 +12,18 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest]
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.10", "3.11", "3.12", "3.13", "3.14"]
         include:
-          - os: macos-13
+          - os: macos-14
             python-version: "3.12"
+          - python-version: "3.14"
+            continue-on-error: true
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v6
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v6
       with:
         python-version: ${{ matrix.python-version }}
 
@@ -34,7 +36,7 @@ jobs:
       run: tox
 
     - name: "Upload coverage to Codecov"
-      uses: codecov/codecov-action@v5
+      uses: codecov/codecov-action@v6
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         fail_ci_if_error: false

Makefile

@@ -78,8 +78,14 @@ clean:
 	rm -rf examples/l5pc/l5pc_validate_neuron_arbor_somatic.ipynb
 	rm -rf examples/l5pc/l5pc_validate_neuron_arbor_somatic.py
 	rm -rf examples/l5pc/x86_64
+	rm -rf examples/l5pc/arm64
+	rm -rf examples/l5pc/aarch64
 	rm -rf examples/stochkv/x86_64
+	rm -rf examples/stochkv/arm64
+	rm -rf examples/stochkv/aarch64
 	rm -rf x86_64
+	rm -rf arm64
+	rm -rf aarch64
 	rm -rf .coverage
 	rm -rf coverage.xml
 	rm -rf channels

bluepyopt/ephys/models.py

@@ -775,8 +775,11 @@ def instantiate(self, sim=None):
 
         self.morphology.instantiate(sim=sim, icell=self.icell)
 
+        morph_sl = sim.neuron.h.SectionList()
+        for sec in sim.neuron.h.allsec():
+            morph_sl.append(sec=sec)
         self.lfpy_cell = Cell(
-            morphology=sim.neuron.h.allsec(),
+            morphology=morph_sl,
             dt=self.dt,
             v_init=self.v_init,
             pt3d=True,

bluepyopt/ephys/templates/acc/decor_acc_template.jinja2

@@ -1,5 +1,5 @@
 (arbor-component
-  (meta-data (version "0.9-dev"))
+  (meta-data (version "0.10-dev"))
   (decor
     {%- for mech, params in global_mechs.items() %}
     {%- if mech is not none %}

bluepyopt/ephys/templates/acc/label_dict_acc_template.jinja2

@@ -1,5 +1,5 @@
 (arbor-component
-  (meta-data (version "0.9-dev"))
+  (meta-data (version "0.10-dev"))
   (label-dict
   {%- for loc, label in label_dict.items() %}
     {{ label.defn }}

bluepyopt/tests/test_ephys/test_parameterscalers.py

@@ -160,7 +160,7 @@ def test_parameterscalers_iexpr():
     # 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' \
+        '  (meta-data (version "0.10-dev"))\n' \
         '  (decor\n' \
         '    (paint (region "soma") ' \
         '(membrane-capacitance 0.01 (scalar 1.0)))\n' \

bluepyopt/tests/test_ephys/test_simulators_mechdir.py

@@ -0,0 +1,103 @@
+"""Tests for NrnSimulator and LFPySimulator mechanisms_directory.
+
+Verifies that simulators correctly store mechanisms_directory and that
+evaluators set it, ensuring pebble subprocesses can reload mechanisms.
+
+**Validates: Requirements 1.1, 1.2, 2.1, 2.2, 3.1, 3.2, 3.5, 3.6**
+"""
+
+import os
+import sys
+
+import pytest
+
+import bluepyopt.ephys as ephys
+
+
+# -------------------------------------------------------------------
+# Bug condition tests: mechanisms_directory handling
+# -------------------------------------------------------------------
+
+@pytest.mark.unit
+def test_nrnsimulator_mechanisms_directory_set():
+    """NrnSimulator(mechanisms_directory=path) stores the attribute."""
+    for path in ["/tmp/mechs", "/some/other/path", "relative/path"]:
+        sim = ephys.simulators.NrnSimulator(
+            mechanisms_directory=path)
+        assert sim.mechanisms_directory == path
+
+
+@pytest.mark.unit
+def test_lfpysimulator_mechanisms_directory_set():
+    """LFPySimulator(mechanisms_directory=path) stores the attribute."""
+    for path in ["/tmp/mechs", "/some/other/path"]:
+        sim = ephys.simulators.LFPySimulator(
+            mechanisms_directory=path)
+        assert sim.mechanisms_directory == path
+
+
+@pytest.mark.unit
+def test_l5pc_evaluator_has_mechanisms_directory():
+    """l5pc_evaluator.create() sets mechanisms_directory on sim."""
+    l5pc_path = os.path.abspath(
+        os.path.join(
+            os.path.dirname(__file__),
+            "../../../examples/l5pc"))
+    sys.path.insert(0, l5pc_path)
+
+    import l5pc_evaluator  # noqa: E402
+
+    evaluator = l5pc_evaluator.create()
+    assert evaluator.sim.mechanisms_directory is not None
+
+
+@pytest.mark.unit
+def test_l5pc_lfpy_evaluator_has_mechanisms_directory():
+    """l5pc_lfpy_evaluator.create() sets mechanisms_directory."""
+    lfpy_path = os.path.abspath(
+        os.path.join(
+            os.path.dirname(__file__),
+            "../../../examples/l5pc_lfpy"))
+    sys.path.insert(0, lfpy_path)
+
+    import l5pc_lfpy_evaluator  # noqa: E402
+
+    feature_file = os.path.join(
+        lfpy_path, "extra_features.json")
+    evaluator = l5pc_lfpy_evaluator.create(
+        feature_file=feature_file)
+    assert evaluator.sim.mechanisms_directory is not None
+
+
+# -------------------------------------------------------------------
+# Preservation tests: NrnSimulator core behavior unchanged
+# -------------------------------------------------------------------
+
+@pytest.mark.unit
+def test_nrnsimulator_defaults_preserved():
+    """NrnSimulator() defaults are all correct, and custom args are stored."""
+    sim = ephys.simulators.NrnSimulator()
+    assert sim.cvode_active is True
+    assert isinstance(sim.dt, float)
+    assert sim.dt > 0
+    assert sim.mechanisms_directory is None
+    assert sim.cvode_minstep_value is None
+    assert sim.random123_globalindex is None
+
+
+@pytest.mark.unit
+def test_nrnsimulator_attributes_preserved():
+    """NrnSimulator preserves dt, cvode_active, mechanisms_directory."""
+    test_cases = [
+        (0.025, False, "/tmp/mechs"),
+        (0.001, True, None),
+        (0.1, False, "/another/path"),
+    ]
+    for dt_val, cv_val, md_val in test_cases:
+        sim = ephys.simulators.NrnSimulator(
+            dt=dt_val,
+            cvode_active=cv_val,
+            mechanisms_directory=md_val)
+        assert sim.dt == dt_val
+        assert sim.cvode_active == cv_val
+        assert sim.mechanisms_directory == md_val

bluepyopt/tests/test_ephys/test_stimuli.py

@@ -210,7 +210,7 @@ def test_NrnRampPulse_instantiate():
         voltage[
             numpy.where(
                 (ramp_delay + ramp_duration < time)
-                & (time <= total_duration))]), -57.994437612124869)
+                & (time <= total_duration))]), -57.994437612124869, decimal=4)
     recording.destroy(sim=nrn_sim)
     stim.destroy(sim=nrn_sim)
     dummy_cell.destroy(sim=nrn_sim)

bluepyopt/tests/test_ephys/testdata/acc/CCell/CCell_decor.acc

@@ -1,5 +1,5 @@
 (arbor-component
-  (meta-data (version "0.9-dev"))
+  (meta-data (version "0.10-dev"))
   (decor
     (default (gSKv3_1bar_SKv3_1 65 (scalar 1.0)))
     (paint (region "soma") (gSKv3_1bar_SKv3_1 65 (scalar 1.0)))

bluepyopt/tests/test_ephys/testdata/acc/CCell/CCell_label_dict.acc

@@ -1,5 +1,5 @@
 (arbor-component
-  (meta-data (version "0.9-dev"))
+  (meta-data (version "0.10-dev"))
   (label-dict 
     (region-def "all" (all)) 
     (region-def "apic" (tag 4)) 

bluepyopt/tests/test_ephys/testdata/acc/CCell/simple_axon_replacement.acc

@@ -1,6 +1,6 @@
 (arbor-component 
   (meta-data 
-    (version "0.9-dev"))
+    (version "0.10-dev"))
   (morphology 
     (branch 0 -1 
       (segment 0 

bluepyopt/tests/test_ephys/testdata/acc/expsyn/simple_cell_decor.acc

@@ -1,5 +1,5 @@
 (arbor-component
-  (meta-data (version "0.9-dev"))
+  (meta-data (version "0.10-dev"))
   (decor
     (paint (region "soma") (membrane-capacitance 0.01 (scalar 1.0)))
     (paint (region "soma") (density (mechanism "default::pas")))

bluepyopt/tests/test_ephys/testdata/acc/expsyn/simple_cell_label_dict.acc

@@ -1,5 +1,5 @@
 (arbor-component
-  (meta-data (version "0.9-dev"))
+  (meta-data (version "0.10-dev"))
   (label-dict
     (region-def "all" (all))
     (region-def "soma" (tag 1))

bluepyopt/tests/test_ephys/testdata/acc/l5pc/C060114A7_axon_replacement.acc

@@ -1,21 +1,21 @@
 (arbor-component 
   (meta-data 
-    (version "0.9-dev"))
+    (version "0.10-dev"))
   (morphology 
     (branch 0 -1 
       (segment 0 
-        (point 263.248016 5.356219 -3.380000 0.690000)
-        (point 262.996735 -9.641676 -3.380000 0.690000)
+        (point 263.685455 31.465240 -3.380000 0.690000)
+        (point 263.936737 46.463135 -3.380000 0.690000)
         2)
       (segment 1 
-        (point 262.996735 -9.641676 -3.380000 0.690000)
-        (point 262.745453 -24.639572 -3.380000 0.690000)
+        (point 263.936737 46.463135 -3.380000 0.690000)
+        (point 264.188019 61.461033 -3.380000 0.690000)
         2)
       (segment 2 
-        (point 262.745453 -24.639572 -3.380000 0.460000)
-        (point 262.494171 -39.637466 -3.380000 0.460000)
+        (point 264.188019 61.461033 -3.380000 0.460000)
+        (point 264.439301 76.458931 -3.380000 0.460000)
         2)
       (segment 3 
-        (point 262.494171 -39.637466 -3.380000 0.460000)
-        (point 262.242889 -54.635365 -3.380000 0.460000)
+        (point 264.439301 76.458931 -3.380000 0.460000)
+        (point 264.690582 91.456825 -3.380000 0.460000)
         2))))

bluepyopt/tests/test_ephys/testdata/acc/l5pc/C060114A7_modified.acc

@@ -1,6 +1,6 @@
 (arbor-component 
   (meta-data 
-    (version "0.9-dev"))
+    (version "0.10-dev"))
   (morphology 
     (branch 0 -1 
       (segment 0 
@@ -21685,18 +21685,18 @@
         4))
     (branch 197 -1 
       (segment 5371 
-        (point 263.248016 5.356219 -3.380000 0.690000)
-        (point 262.996735 -9.641676 -3.380000 0.690000)
+        (point 263.685455 31.465240 -3.380000 0.690000)
+        (point 263.936737 46.463135 -3.380000 0.690000)
         2)
       (segment 5372 
-        (point 262.996735 -9.641676 -3.380000 0.690000)
-        (point 262.745453 -24.639572 -3.380000 0.690000)
+        (point 263.936737 46.463135 -3.380000 0.690000)
+        (point 264.188019 61.461033 -3.380000 0.690000)
         2)
       (segment 5373 
-        (point 262.745453 -24.639572 -3.380000 0.460000)
-        (point 262.494171 -39.637466 -3.380000 0.460000)
+        (point 264.188019 61.461033 -3.380000 0.460000)
+        (point 264.439301 76.458931 -3.380000 0.460000)
         2)
       (segment 5374 
-        (point 262.494171 -39.637466 -3.380000 0.460000)
-        (point 262.242889 -54.635365 -3.380000 0.460000)
+        (point 264.439301 76.458931 -3.380000 0.460000)
+        (point 264.690582 91.456825 -3.380000 0.460000)
         2))))

bluepyopt/tests/test_ephys/testdata/acc/l5pc/l5pc.json

@@ -1,6 +1,6 @@
-{ 
+{
   "cell_model_name": "l5pc",
-  "produced_by": "Created by BluePyOpt(1.12.113) at 2022-11-06 18:21:20.822883", 
+  "produced_by": "Created by BluePyOpt(1.14.19.dev2) at 2026-04-16 09:46:59.248761",
   "morphology": {
      "original": "C060114A7.asc",
      "replace_axon": "C060114A7_axon_replacement.acc",

bluepyopt/tests/test_ephys/testdata/acc/l5pc/l5pc_decor.acc

@@ -1,5 +1,5 @@
 (arbor-component
-  (meta-data (version "0.9-dev"))
+  (meta-data (version "0.10-dev"))
   (decor
     (default (membrane-potential -65 (scalar 1.0)))
     (default (temperature-kelvin 307.14999999999998 (scalar 1.0)))

bluepyopt/tests/test_ephys/testdata/acc/l5pc/l5pc_label_dict.acc

@@ -1,5 +1,5 @@
 (arbor-component
-  (meta-data (version "0.9-dev"))
+  (meta-data (version "0.10-dev"))
   (label-dict
     (region-def "all" (all))
     (region-def "soma" (tag 1))

bluepyopt/tests/test_ephys/testdata/acc/l5pc_py37/l5pc_decor.acc

@@ -1,5 +1,5 @@
 (arbor-component
-  (meta-data (version "0.9-dev"))
+  (meta-data (version "0.10-dev"))
   (decor
     (default (membrane-potential -65 (scalar 1.0)))
     (default (temperature-kelvin 307.14999999999998 (scalar 1.0)))

bluepyopt/tests/test_ephys/testdata/acc/simplecell/simple_axon_replacement.acc

@@ -1,6 +1,6 @@
 (arbor-component 
   (meta-data 
-    (version "0.9-dev"))
+    (version "0.10-dev"))
   (morphology 
     (branch 0 -1 
       (segment 0 

bluepyopt/tests/test_ephys/testdata/acc/simplecell/simple_cell_decor.acc

@@ -1,5 +1,5 @@
 (arbor-component
-  (meta-data (version "0.9-dev"))
+  (meta-data (version "0.10-dev"))
   (decor
     (paint (region "soma") (membrane-capacitance 0.01 (scalar 1.0)))
     (paint (region "soma") (density (mechanism "default::hh" ("gnabar" 0.10299326453483033) ("gkbar" 0.027124836082684685))))))

bluepyopt/tests/test_ephys/testdata/acc/simplecell/simple_cell_label_dict.acc

@@ -1,5 +1,5 @@
 (arbor-component
-  (meta-data (version "0.9-dev"))
+  (meta-data (version "0.10-dev"))
   (label-dict
     (region-def "all" (all))
     (region-def "soma" (tag 1))