Improved Neuron testing...

.github/workflows/non-omv-ci.yml

@@ -10,20 +10,27 @@ on:
 jobs:
   build:
 
-    runs-on: ubuntu-latest
+    name: Build for Python ${{ matrix.python-version }} on ${{ matrix.runs-on }}
+    runs-on: ${{ matrix.runs-on }}
     strategy:
       fail-fast: false
       matrix:
-        python-version: [ 3.7, 3.9 ]
+        python-version: [ "3.9", "3.10" ]
+        runs-on: [ubuntu-latest, macos-latest]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Set up Python  ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version:  ${{ matrix.python-version }}
 
+    - name: Install HDF5 for pytables on macos-latest
+      if: ${{ matrix.runs-on == 'macos-latest' }}
+      run: |
+        brew install hdf5
+
     - name: Run scripts
       run: |
         pip install pyneuroml

.github/workflows/omv-ci.yml

@@ -9,30 +9,37 @@ on:
 
 jobs:
   build:
-
-    runs-on: ubuntu-latest
+  
+    runs-on: ${{ matrix.runs-on }}
     strategy:
       fail-fast: false
       matrix:
-        python-version: [ 3.8, 3.9 ]
+        python-version: [ 3.9, "3.10" ]
         engine: 
           - jNeuroML_validate
           # - "NEURON:7.8.2"  # slightly different spike times...
           - "NEURON:8.0.0"
           - "NEURON:8.0.2"
           - "NEURON:8.1"
+          - "NEURON:8.2.0"
           - jNeuroML
           - jNeuroML_NEURON
           - jNeuroML_NetPyNE
+        runs-on: [ubuntu-latest, macos-latest]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Set up Python  ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version:  ${{ matrix.python-version }}
 
+    - name: Install HDF5 for pytables on macos-latest
+      if: ${{ matrix.runs-on == 'macos-latest' }}
+      run: |
+        brew install hdf5
+
     - name: Install OMV
       run: |
         pip install git+https://github.com/OpenSourceBrain/osb-model-validation
@@ -42,9 +49,14 @@ jobs:
     - name: Compile some mod files
       if: ${{ contains( matrix.engine, 'NEURON' ) }}
       run: |
-        omv install NEURON
+        omv install ${{ matrix.engine }}
         cd NEURON/test
         nrnivmodl ../channels
+        ls -alt
+
+    - name: Pip version info
+      run: |
+        pip list 
 
     - name: Run OMV tests on engine ${{ matrix.engine }}
       run: |

.gitignore

@@ -21,3 +21,5 @@ x86_64
 NET_*.net.nml
 *.channel.nml
 arm64
+/NeuroML2/.ipynb_checkpoints
+/NeuroML2/__pycache__

NeuroML2/CellBuilder.py

@@ -11,7 +11,9 @@
 
 from typing import List
 from neuroml import (Cell, Morphology, MembraneProperties, IntracellularProperties, BiophysicalProperties, Segment, SegmentGroup, Point3DWithDiam, SegmentParent, Member, InitMembPotential, Resistivity, SpecificCapacitance, NeuroMLDocument, IncludeType, ChannelDensity) # type: ignore  # noqa
-from pyneuroml.pynml import print_function  # type: ignore
+
+def print_function(string):
+    print('CellBuilder: %s'%string)
 
 
 neuro_lex_ids = {

NeuroML2/LEMS_pyr_single_comp.xml

@@ -1,19 +1,19 @@
 <Lems>
-    
+
     <!-- 
 
-        This LEMS file has been automatically generated using PyNeuroML v0.7.2 (libNeuroML v0.4.1)
+        This LEMS file has been automatically generated using PyNeuroML v1.1.13 (libNeuroML v0.5.8)
 
      -->
-    
+
     <!-- Specify which component to run -->
     <Target component="pyr_single_comp"/>
 
     <!-- Include core NeuroML2 ComponentType definitions -->
     <Include file="Cells.xml"/>
     <Include file="Networks.xml"/>
     <Include file="Simulation.xml"/>
-    
+
     <Include file="pyr_soma.net.nml"/>
     <Include file="pyr_soma_cell.nml"/>
     <Include file="kfast.channel.nml"/>
@@ -22,41 +22,40 @@
     <Include file="nat.channel.nml"/>
     <Include file="nap.channel.nml"/>
     <Include file="IKM.channel.nml"/>
-   
+
     <Simulation id="pyr_single_comp" length="700ms" step="0.005ms" target="single_pyr_cell_network" seed="123">  <!-- Note seed: ensures same random numbers used every run -->
-
         <OutputFile id="output0" fileName="pyr_single_comp.dat">
-            <OutputColumn id="pop0_0_v" quantity="pop0[0]/v"/> 
+            <OutputColumn id="pop0_0_v" quantity="pop0[0]/v"/>
         </OutputFile>
-        
+
         <OutputFile id="na_m" fileName="pyr_single_comp.na_m.dat">
-            <OutputColumn id="pop0_0_na_m" quantity="pop0[0]/pyr_b_prop/membraneProperties/nat_channels/nat/m/q"/> 
+            <OutputColumn id="pop0_0_na_m" quantity="pop0[0]/pyr_b_prop/membraneProperties/nat_channels/nat/m/q"/>
         </OutputFile>
-        
+
         <OutputFile id="na_h" fileName="pyr_single_comp.na_h.dat">
-            <OutputColumn id="pop0_0_na_h" quantity="pop0[0]/pyr_b_prop/membraneProperties/nat_channels/nat/h/q"/> 
+            <OutputColumn id="pop0_0_na_h" quantity="pop0[0]/pyr_b_prop/membraneProperties/nat_channels/nat/h/q"/>
         </OutputFile>
-        
+
         <OutputFile id="kfast_n" fileName="pyr_single_comp.kfast_n.dat">
-            <OutputColumn id="pop0_0_kfast_n" quantity="pop0[0]/pyr_b_prop/membraneProperties/kfast_channels/kfast/n/q"/> 
+            <OutputColumn id="pop0_0_kfast_n" quantity="pop0[0]/pyr_b_prop/membraneProperties/kfast_channels/kfast/n/q"/>
         </OutputFile>
-        
+
         <OutputFile id="nap_m" fileName="pyr_single_comp.nap_m.dat">
-            <OutputColumn id="pop0_0_nap_m" quantity="pop0[0]/pyr_b_prop/membraneProperties/nap_channels/nap/m/q"/> 
+            <OutputColumn id="pop0_0_nap_m" quantity="pop0[0]/pyr_b_prop/membraneProperties/nap_channels/nap/m/q"/>
         </OutputFile>
-        
+
         <OutputFile id="kslow_a" fileName="pyr_single_comp.kslow_a.dat">
-            <OutputColumn id="pop0_0_kslow_a" quantity="pop0[0]/pyr_b_prop/membraneProperties/kslow_channels/kslow/a/q"/> 
+            <OutputColumn id="pop0_0_kslow_a" quantity="pop0[0]/pyr_b_prop/membraneProperties/kslow_channels/kslow/a/q"/>
         </OutputFile>
-        
+
         <OutputFile id="kslow_b" fileName="pyr_single_comp.kslow_b.dat">
-            <OutputColumn id="pop0_0_kslow_b" quantity="pop0[0]/pyr_b_prop/membraneProperties/kslow_channels/kslow/b/q"/> 
+            <OutputColumn id="pop0_0_kslow_b" quantity="pop0[0]/pyr_b_prop/membraneProperties/kslow_channels/kslow/b/q"/>
         </OutputFile>
-        
+
         <OutputFile id="ikm_m" fileName="pyr_single_comp.ikm_m.dat">
-            <OutputColumn id="pop0_0_ikm_m" quantity="pop0[0]/pyr_b_prop/membraneProperties/km_channels/km/m/q"/> 
+            <OutputColumn id="pop0_0_ikm_m" quantity="pop0[0]/pyr_b_prop/membraneProperties/km_channels/km/m/q"/>
         </OutputFile>
-        
+
     </Simulation>
 
 </Lems>