Switch to NMODL-Glia (#33)

* switched to pyproject.toml

* define public api

* black

* bump glia

* fix workflow file

* fix workflow file pt 2

* fix main workflow deps

* drop 3.8

* run some tests separately to avoid segfault

see neuronsimulator/nrn#2641

* fix parallel spike assertions

* bump numpy dep for faster 3.11 tests

.github/workflows/black.yml

@@ -8,8 +8,8 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v1
+    - uses: actions/checkout@v3
     - name: Black Check
-      uses: jpetrucciani/black-check
+      uses: jpetrucciani/black-check@master
       with:
-        path: 'patch'
+        path: 'arborize'

.github/workflows/main.yml

@@ -8,19 +8,19 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        py: ["3.8", "3.9", "3.10"]
+        py: ["3.9", "3.10", "3.11"]
     steps:
-    - uses: actions/checkout
+    - uses: actions/checkout@v3
     - name: Set up Python ${{ matrix.py }}
-      uses: actions/setup-python
+      uses: actions/setup-python@v3
       with:
         python-version: ${{ matrix.py }}
     - name: Install apt dependencies
       run: |
         sudo apt-get update
         sudo apt-get install openmpi-bin libopenmpi-dev
     - name: Cache pip
-      uses: actions/cache
+      uses: actions/cache@v3
       with:
         path: ~/.cache/pip
         key: ${{ runner.os }}-pip-${{ hashFiles('requirements.txt') }}
@@ -30,12 +30,14 @@ jobs:
     - name: Install dependencies & self
       run: |
         python -m pip install --upgrade pip
-        pip install wheel
+        pip install . --no-deps
         pip install -r requirements.txt --prefer-binary
         pip install bsb==4.0.0a57
         pip install -e .
     - name: Run tests & coverage
       run: |
         coverage run --parallel-mode -m unittest
         mpiexec -n 2 coverage run --parallel-mode -m unittest
+        NRN_SEGFAULT=1 coverage run --parallel-mode -m unittest
+        NRN_SEGFAULT=1 mpiexec -n 2 coverage run --parallel-mode -m unittest
         bash <(curl -s https://codecov.io/bash)

arborize/__init__.py

@@ -1,5 +1,10 @@
-from .builders import *
-from .schematics import *
+"""
+Write descriptions for NEURON cell models in an Arbor-like manner for both the Arbor and
+NEURON brain simulation engines.
+"""
+
+from .builders import neuron_build
+from .schematics import file_schematic, bsb_schematic
 from .definitions import (
     CableType,
     CableProperties,
@@ -11,4 +16,17 @@
 )
 from .schematic import Schematic
 
-__version__ = "4.0.0b0"
+__version__ = "4.0.0b1"
+__all__ = [
+    "CableProperties",
+    "CableType",
+    "Ion",
+    "Mechanism",
+    "ModelDefinition",
+    "Schematic",
+    "bsb_schematic",
+    "define_model",
+    "file_schematic",
+    "is_mech_id",
+    "neuron_build",
+]

arborize/_util.py

@@ -20,5 +20,5 @@ def get_location_name(pts: Iterable["Point"]) -> str:
 def get_arclengths(pts: Iterable["Point"]) -> npt.NDArray[float]:
     coords = np.array([pt.coords for pt in pts])
     rel_dist = np.diff(coords, axis=0, prepend=[coords[0, :]])
-    arcsums = np.cumsum(np.sum(rel_dist ** 2, axis=1) ** 0.5)
+    arcsums = np.cumsum(np.sum(rel_dist**2, axis=1) ** 0.5)
     return arcsums / arcsums[-1]

arborize/builders/_neuron.py

@@ -124,6 +124,13 @@ def insert_transmitter(
     def get_random_location(self):
         return random.choice([*self._locations.keys()])
 
+    def record(self):
+        soma = [s for s in self._sections if "soma" in s.labels]
+        if not soma:
+            raise RuntimeError("No soma to record from")
+        else:
+            return soma[0].record()
+
     def __getattr__(self, item):
         if item in self._cable_types:
             return [s for s in self._sections if item in s.labels]

arborize/schematics/__init__.py

@@ -1,2 +1,2 @@
 from ._bsb import bsb_schematic
-from ._file import file_schematic
+from ._file import file_schematic

docs/source/conf.py

@@ -49,7 +49,7 @@
     "scipy",
     "six",
     "plotly",
-    "morphio"
+    "morphio",
 ]
 
 # -- General configuration ---------------------------------------------------
@@ -78,4 +78,4 @@
 # -- Options for HTML output -------------------------------------------------
 
 html_theme = "furo"
-html_static_path = ["_static"]
+html_static_path = ["_static"]

pyproject.toml

@@ -0,0 +1,21 @@
+[build-system]
+requires = ["flit_core >=3.2,<4"]
+build-backend = "flit_core.buildapi"
+
+[project]
+name = "arborize"
+authors = [{name = "Robin De Schepper", email = "robingilbert.deschepper@unipv.it"}]
+readme = "README.md"
+license = {file = "LICENSE"}
+classifiers = ["License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)"]
+dynamic = ["version", "description"]
+dependencies = ["numpy", "errr>=1.2.0", "morphio>=3.3.6"]
+requires-python = ">=3.9"
+
+[project.optional-dependencies]
+neuron = ["nrn-patch>=4.0.0b3", "nmodl-glia[neuron]>=4.0.0b6"]
+arbor = ["arbor>=0.8"]
+dev = ["sphinx", "sphinx_rtd_theme"]
+
+[project.urls]
+Home = "https://github.com/dbbs-lab/arborize"

requirements.txt

@@ -1,5 +1,6 @@
-nrn-patch==4.0.0a4
-nrn-glia==4.0.0a4
-numpy==1.22.0
+nrn-patch==4.0.0b3
+nmodl-glia==4.0.0b6
+numpy==1.26.0
 errr==1.2.0
-mpi4py
+coverage~=7.0
+mpi4py==3.1.5

tests/test_neuron_models.py

@@ -1,3 +1,4 @@
+import os
 import unittest
 
 from ._shared import SchematicsFixture
@@ -10,6 +11,10 @@
 import numpy as np
 
 
+@unittest.skipIf(
+    "NRN_SEGFAULT" in os.environ,
+    "These tests are skipped to test the other tests below separately. See https://github.com/neuronsimulator/nrn/issues/2641",
+)
 class TestModelBuilding(SchematicsFixture, unittest.TestCase):
     def test_mech_insert(self):
         cell = neuron_build(self.p75_pas)
@@ -49,60 +54,11 @@ def test_synapses(self):
 
         p.run(100)
 
-        self.assertEqual(list(r), list(r2), "Recording from same loc should be identical")
-        self.assertFalse(min(r) == max(r), "No synaptic currents detected")
-        self.assertTrue(min(r_nosyn) == max(r_nosyn), "Synaptic currents detected")
-
-    def test_transmitter_receiver(self):
-        if not p.parallel.id():
-            cell2 = neuron_build(self.p75_expsyn)
-            ais = cell2.filter_sections(["soma"])[0].locations[-1]
-            cell2.insert_transmitter(1, ais)
-            cell2.insert_synapse("ExpSyn", (0, 0)).stimulate(
-                start=0, number=5, interval=10, weight=1, delay=1
-            )
-
-        cell = neuron_build(self.p75_expsyn)
-        cell.insert_receiver(1, "ExpSyn", (0, 0), weight=0.04, delay=1)
-        r = p.record(cell.get_segment((0, 0), 0.5))
-        spt, spid = p.parallel.spike_record()
-        p.parallel._warn_new_gids = False
-
-        p.run(100)
-
-        arr = np.array(p.parallel.py_allgather([*r])).T
-        self.assertEqual(2, len(spid), "Expected 2 spikes")
-        self.assertTrue(np.allclose(np.diff(arr, axis=1), 0), "diff across nodes")
-        self.assertNotEqual(min(r), max(r), "no current detected")
-
-    def test_double_transmitter_receiver(self):
-        # Tests that NEURON still only transmits spikes from 1 detector per Section
-        if not p.parallel.id():
-            cell2 = neuron_build(self.p75_expsyn)
-            ais = cell2.filter_sections(["soma"])[0].locations[-1]
-            cell2.insert_transmitter(2, ais)
-            # Arborize doesn't let you place 2 transmitters on the same section,
-            # so bypass the security measure with some magic.
-            la = cell2.get_location(ais)
-            tm = p.ParallelCon(cell2.get_segment(ais, 0.5), 3)
-            cell2.insert_synapse("ExpSyn", (0, 0)).stimulate(
-                start=0, number=5, interval=10, weight=1, delay=1
-            )
-
-        cell = neuron_build(self.p75_expsyn)
-        cell.insert_receiver(2, "ExpSyn", (0, 0), weight=0.04, delay=1)
-        cell.insert_receiver(3, "ExpSyn", (0, 0), weight=0.04, delay=50)
-        spt, spid = p.parallel.spike_record()
-        p.parallel._warn_new_gids = False
-
-        p.run(100)
-
-        # If you'd insert more than 1 threshold detectors into the same Section,
-        # only 1 of them would actually detect thresholds, go figure. If this assert fails
-        # NEURON finally fixed that! :tada:
         self.assertEqual(
-            2, len(spid), "NEURON stopped silently not doing what it should! Yay?"
+            list(r), list(r2), "Recording from same loc should be identical"
         )
+        self.assertFalse(min(r) == max(r), "No synaptic currents detected")
+        self.assertTrue(min(r_nosyn) == max(r_nosyn), "Synaptic currents detected")
 
     def test_cable_building(self):
         self.cell010.definition = define_model(
@@ -163,6 +119,68 @@ def test_cable_building(self):
         self.assertEqual(130, na["nao"][0])
 
 
+@unittest.skipIf(
+    "NRN_SEGFAULT" not in os.environ,
+    "Run these tests separately. See https://github.com/neuronsimulator/nrn/issues/2641",
+)
+class TestTransmission(SchematicsFixture, unittest.TestCase):
+    def test_transmitter_receiver(self):
+        if not p.parallel.id():
+            cell2 = neuron_build(self.p75_expsyn)
+            ais = cell2.filter_sections(["soma"])[0].locations[-1]
+            cell2.insert_transmitter(1, ais)
+            cell2.insert_synapse("ExpSyn", (0, 0)).stimulate(
+                start=0, number=5, interval=10, weight=1, delay=1
+            )
+
+        cell = neuron_build(self.p75_expsyn)
+        cell.insert_receiver(1, "ExpSyn", (0, 0), weight=0.04, delay=1)
+        r = p.record(cell.get_segment((0, 0), 0.5))
+        spt, spid = p.parallel.spike_record()
+        p.parallel._warn_new_gids = False
+
+        p.run(100)
+
+        arr = np.array(p.parallel.py_allgather([*r])).T
+
+        if not p.parallel.id():
+            self.assertEqual(2, len(spid), "Expected 2 spikes")
+        self.assertTrue(np.allclose(np.diff(arr, axis=1), 0), "diff across nodes")
+        self.assertNotEqual(min(r), max(r), "no current detected")
+
+    def test_double_transmitter_receiver(self):
+        # We insert 2 transmitters that SHOULD each cause a spike in their receiver. But
+        # NEURON is broken and transmits spikes only through 1 detector per Section.
+        # If this test starts failing, NEURON fixed the issue, and we can simplify our
+        # logic.
+        if not p.parallel.id():
+            cell2 = neuron_build(self.p75_expsyn)
+            ais = cell2.filter_sections(["soma"])[0].locations[-1]
+            cell2.insert_transmitter(2, ais)
+            # Arborize doesn't let you place 2 transmitters on the same section for this reason,
+            # so bypass the security measure by manually inserting another PCon.
+            p.ParallelCon(cell2.get_segment(ais, 0.5), 3)
+            cell2.insert_synapse("ExpSyn", (0, 0)).stimulate(
+                start=0, number=5, interval=10, weight=1, delay=1
+            )
+
+        cell = neuron_build(self.p75_expsyn)
+        cell.insert_receiver(2, "ExpSyn", (0, 0), weight=0.08, delay=1)
+        cell.insert_receiver(3, "ExpSyn", (0, 0), weight=0.08, delay=50)
+        r = cell.record()
+        spt, spid = p.parallel.spike_record()
+        p.parallel._warn_new_gids = False
+
+        p.run(100, v_init=-65)
+
+        if not p.parallel.id():
+            # If you'd insert more than 1 threshold detectors into the same Section,
+            # only 1 of them would actually detect thresholds, go figure. If this assert
+            # fails NEURON finally fixed that! :tada:
+            self.assertEqual(1, len(spid))
+        self.assertTrue(np.any(np.array(r) != -65))
+
+
 tagsGrC = {
     16: ["axon", "axon_hillock"],
     17: ["axon", "axon_initial_segment"],