From 2ba8d78248e0261601dc4bd8876ad78f0e6466f9 Mon Sep 17 00:00:00 2001
From: Padraig Gleeson <p.gleeson@gmail.com>
Date: Mon, 27 Jul 2026 11:55:49 +0100
Subject: [PATCH 1/3] Update GHA

---
 .github/workflows/omv-ci.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/omv-ci.yml b/.github/workflows/omv-ci.yml
index 33b85df..4b3cebe 100644
--- a/.github/workflows/omv-ci.yml
+++ b/.github/workflows/omv-ci.yml
@@ -23,10 +23,10 @@ jobs:
             engine: Brian2
 
     steps:
-    - uses: actions/checkout@v6
+    - uses: actions/checkout@v7
     
     - name: Set up Python  ${{ matrix.python-version }}
-      uses: actions/setup-python@v6
+      uses: actions/setup-python@v7
       with:
         python-version:  ${{ matrix.python-version }}
         

From 8bbd32eda762e45a70b3b063dfde56d5ca7ca655 Mon Sep 17 00:00:00 2001
From: Padraig Gleeson <p.gleeson@gmail.com>
Date: Mon, 27 Jul 2026 12:06:24 +0100
Subject: [PATCH 2/3] Test on jNeuroML_NEURON

---
 .github/workflows/omv-ci.yml          |  4 +-
 NeuroML2/ACnet2/.test.jnmlnrn.omt     | 31 +++++++++++++
 NeuroML2/ACnet2/.test.mep             |  9 ++++
 NeuroML2/ACnet2/LEMS_ACnet2_LowDt.xml | 63 +++++++++++++++++++++++++++
 NeuroML2/ACnet2/MediumNet.net.nml     | 31 -------------
 5 files changed, 105 insertions(+), 33 deletions(-)
 create mode 100644 NeuroML2/ACnet2/.test.jnmlnrn.omt
 create mode 100644 NeuroML2/ACnet2/.test.mep
 create mode 100644 NeuroML2/ACnet2/LEMS_ACnet2_LowDt.xml

diff --git a/.github/workflows/omv-ci.yml b/.github/workflows/omv-ci.yml
index 4b3cebe..c2ba2d5 100644
--- a/.github/workflows/omv-ci.yml
+++ b/.github/workflows/omv-ci.yml
@@ -17,7 +17,7 @@ jobs:
       fail-fast: false
       matrix:
         python-version: [ "3.10", "3.12", "3.13" ]
-        engine: [ jNeuroML_validate, Brian2 ]
+        engine: [ jNeuroML_validate, Brian2, jNeuroML_NEURON ]
         exclude:
           - python-version: "3.10"
             engine: Brian2
@@ -41,5 +41,5 @@ jobs:
         
     - name: OMV final version info
       run: |
-        omv list -V # list installed engines
+        omv list -V # list installed engines 
         env
diff --git a/NeuroML2/ACnet2/.test.jnmlnrn.omt b/NeuroML2/ACnet2/.test.jnmlnrn.omt
new file mode 100644
index 0000000..2686e50
--- /dev/null
+++ b/NeuroML2/ACnet2/.test.jnmlnrn.omt
@@ -0,0 +1,31 @@
+# Script for running automated tests on OSB, see https://github.com/OpenSourceBrain/osb-model-validation 
+
+target: LEMS_ACnet2_LowDt.xml
+engine: jNeuroML_NEURON
+mep: .test.mep
+experiments:
+  Current clamp pyramidal:
+    observables:
+      spike times:
+        file:
+          path: pyramidal_soma_0.dat
+          columns: [0,1]
+          scaling: [1000, 1000]
+        spike detection:
+          method: threshold
+          threshold: 0
+        tolerance: 0
+  Current clamp basket:
+    observables:
+      spike times:
+        file:
+          path: basket_soma_0.dat
+          columns: [0,1]
+          scaling: [1000, 1000]
+        spike detection:
+          method: threshold
+          threshold: 0
+        tolerance: 0
+
+
+        
diff --git a/NeuroML2/ACnet2/.test.mep b/NeuroML2/ACnet2/.test.mep
new file mode 100644
index 0000000..016f0f7
--- /dev/null
+++ b/NeuroML2/ACnet2/.test.mep
@@ -0,0 +1,9 @@
+system: Testing a single compartment cell
+
+experiments:
+  Current clamp pyramidal:
+    expected:
+        spike times: [102.48500000000001, 120.757, 148.52499999999998, 255.994, 330.37300000000005, 407.452, 483.889, 560.274]
+  Current clamp basket:
+    expected:
+        spike times: [109.946, 128.452, 146.958, 165.465, 183.971, 202.477, 220.983, 239.489, 257.99499999999995, 276.502, 295.008, 313.514, 332.02, 350.526, 369.03200000000004, 387.53900000000004, 406.045, 424.551, 443.05699999999996, 461.563, 480.069, 498.576, 517.082, 535.588, 554.0939999999999, 572.6, 591.106]
diff --git a/NeuroML2/ACnet2/LEMS_ACnet2_LowDt.xml b/NeuroML2/ACnet2/LEMS_ACnet2_LowDt.xml
new file mode 100644
index 0000000..9fb0916
--- /dev/null
+++ b/NeuroML2/ACnet2/LEMS_ACnet2_LowDt.xml
@@ -0,0 +1,63 @@
+<Lems xmlns="http://www.neuroml.org/lems/0.7.2" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/lems/0.7.2  https://raw.github.com/LEMS/LEMS/development/Schemas/LEMS/LEMS_v0.7.2.xsd">
+
+    <Target component="sim1" reportFile="simulator.props" timesFile="time.dat"/>
+
+        <!--Include standard NeuroML 2 ComponentType definitions-->
+
+    <Include file="Cells.xml"/>
+    <Include file="Networks.xml"/>
+    <Include file="Simulation.xml"/>
+
+    
+
+        <!--Include the generated NeuroML 2 files-->
+
+
+        <!--   Channel/synapse files-->
+    <Include file="Ca_conc.nml"/>
+    <Include file="Ca_pyr.channel.nml"/>
+    <Include file="Kahp_pyr.channel.nml"/>
+    <Include file="Kdr_bask.channel.nml"/>
+    <Include file="Kdr_pyr.channel.nml"/>
+    <Include file="LeakConductance_bask.channel.nml"/>
+    <Include file="LeakConductance_pyr.channel.nml"/>
+    <Include file="Na_bask.channel.nml"/>
+    <Include file="Na_pyr.channel.nml"/>
+        <!--   Cell files-->
+    <Include file="bask_soma.cell.nml"/>
+    <Include file="pyr_4_sym_soma.cell.nml"/>
+        <!--   Network file-->
+    <Include file="ACnet2.net.nml"/>
+    
+
+        <!--Note: this could be: Simulation id="sim1" ... , but Component type="Simulation" ... 
+        is used to allow validation of this file according to the LEMS schema specified above...-->
+    <Component type="Simulation" id="sim1" length="700.0ms" step="0.001ms" target="network_ACnet2">
+        
+        <Display id="basket_soma_v" title="ACnet2: TestSoma, basket_soma, VOLTAGE" xmin="-70.0" xmax="770.0" ymin="-104.0" ymax="64.0" timeScale="1ms">
+            <Line id="VOLTAGE-basket_soma_0" timeScale="1ms" quantity="basket_soma/0/bask_soma/v" scale="1 mV" color="#000000"/>
+        </Display>
+    
+        <Display id="pyramidal_soma_v" title="ACnet2: TestSoma, pyramidal_soma, VOLTAGE" xmin="-70.0" xmax="770.0" ymin="-104.0" ymax="64.0" timeScale="1ms">
+            <Line id="VOLTAGE-pyramidal_soma_0" timeScale="1ms" quantity="pyramidal_soma/0/pyr_4_sym_soma/v" scale="1 mV" color="#000000"/>
+        </Display>
+    
+        <Display id="GraphWin_12" title="ACnet2: TestSoma, pyramidal_soma, Ca_conc:CONC:ca" xmin="-70.0" xmax="770.0" ymin="-1E-5" ymax="9E-5" timeScale="1ms">
+            <Line id="Ca_conc_CONC_ca-pyramidal_soma_0" timeScale="1ms" quantity="pyramidal_soma/0/pyr_4_sym_soma/caConc" scale="1 mol_per_cm3" color="#000000"/>
+        </Display>
+    
+        <OutputFile id="basket_soma_v_OF" fileName="basket_soma_0.dat">
+            <OutputColumn id="v" quantity="basket_soma/0/bask_soma/v"/>
+        </OutputFile>
+    
+        <OutputFile id="pyramidal_soma_v_OF" fileName="pyramidal_soma_0.dat">
+            <OutputColumn id="v" quantity="pyramidal_soma/0/pyr_4_sym_soma/v"/>
+        </OutputFile>
+    
+        <OutputFile id="pyramidals_ca_2_OF" fileName="pyramidal_soma_0.Ca_conc_CONC_ca.dat">
+            <OutputColumn id="caConc" quantity="pyramidal_soma/0/pyr_4_sym_soma/caConc"/>
+        </OutputFile>
+    </Component>
+
+
+</Lems>
\ No newline at end of file
diff --git a/NeuroML2/ACnet2/MediumNet.net.nml b/NeuroML2/ACnet2/MediumNet.net.nml
index ae6ad9d..3b2eceb 100644
--- a/NeuroML2/ACnet2/MediumNet.net.nml
+++ b/NeuroML2/ACnet2/MediumNet.net.nml
@@ -1,37 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <neuroml xmlns="http://www.neuroml.org/schema/neuroml2" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2  https://raw.githubusercontent.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2beta4.xsd" id="network_ACnet2">
 
-    <notes>
-
-Network structure (NeuroML 2beta4) for project: ACnet2 saved with neuroConstruct v1.7.1 on: 16:08:20, 22-Oct-14
-
-Cell Group: pyramidals_48 contains 48 cells
-Cell Group: baskets_12 contains 12 cells
-
-Network connection: SmallNet_bask_bask contains 60 individual synaptic connections
-Network connection: SmallNet_bask_pyr contains 336 individual synaptic connections
-Network connection: SmallNet_pyr_pyr contains 336 individual synaptic connections
-Network connection: SmallNet_pyr_bask contains 252 individual synaptic connections
-
-
-    </notes>
-
-
-    <include href="AMPA_syn.synapse.nml"/>
-    <include href="AMPA_syn_inh.synapse.nml"/>
-    <include href="bask.cell.nml"/>
-    <include href="Ca_conc.nml"/>
-    <include href="Ca_pyr.channel.nml"/>
-    <include href="GABA_syn.synapse.nml"/>
-    <include href="GABA_syn_inh.synapse.nml"/>
-    <include href="Kahp_pyr.channel.nml"/>
-    <include href="Kdr_bask.channel.nml"/>
-    <include href="Kdr_pyr.channel.nml"/>
-    <include href="LeakConductance_bask.channel.nml"/>
-    <include href="LeakConductance_pyr.channel.nml"/>
-    <include href="Na_bask.channel.nml"/>
-    <include href="Na_pyr.channel.nml"/>
-    <include href="pyr_4_sym.cell.nml"/>
 
     <pulseGenerator id="BackgroundRandomIClamps" delay="0.0s" duration="100.0s" amplitude="6.0E-10A"/>
 

From a55a2c102e3e6dd5608a2e123d14b8aec188ca43 Mon Sep 17 00:00:00 2001
From: Padraig Gleeson <p.gleeson@gmail.com>
Date: Mon, 27 Jul 2026 12:10:47 +0100
Subject: [PATCH 3/3] Put back includes

---
 NeuroML2/ACnet2/MediumNet.net.nml | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)

diff --git a/NeuroML2/ACnet2/MediumNet.net.nml b/NeuroML2/ACnet2/MediumNet.net.nml
index 3b2eceb..ae6ad9d 100644
--- a/NeuroML2/ACnet2/MediumNet.net.nml
+++ b/NeuroML2/ACnet2/MediumNet.net.nml
@@ -1,6 +1,37 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <neuroml xmlns="http://www.neuroml.org/schema/neuroml2" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2  https://raw.githubusercontent.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2beta4.xsd" id="network_ACnet2">
 
+    <notes>
+
+Network structure (NeuroML 2beta4) for project: ACnet2 saved with neuroConstruct v1.7.1 on: 16:08:20, 22-Oct-14
+
+Cell Group: pyramidals_48 contains 48 cells
+Cell Group: baskets_12 contains 12 cells
+
+Network connection: SmallNet_bask_bask contains 60 individual synaptic connections
+Network connection: SmallNet_bask_pyr contains 336 individual synaptic connections
+Network connection: SmallNet_pyr_pyr contains 336 individual synaptic connections
+Network connection: SmallNet_pyr_bask contains 252 individual synaptic connections
+
+
+    </notes>
+
+
+    <include href="AMPA_syn.synapse.nml"/>
+    <include href="AMPA_syn_inh.synapse.nml"/>
+    <include href="bask.cell.nml"/>
+    <include href="Ca_conc.nml"/>
+    <include href="Ca_pyr.channel.nml"/>
+    <include href="GABA_syn.synapse.nml"/>
+    <include href="GABA_syn_inh.synapse.nml"/>
+    <include href="Kahp_pyr.channel.nml"/>
+    <include href="Kdr_bask.channel.nml"/>
+    <include href="Kdr_pyr.channel.nml"/>
+    <include href="LeakConductance_bask.channel.nml"/>
+    <include href="LeakConductance_pyr.channel.nml"/>
+    <include href="Na_bask.channel.nml"/>
+    <include href="Na_pyr.channel.nml"/>
+    <include href="pyr_4_sym.cell.nml"/>
 
     <pulseGenerator id="BackgroundRandomIClamps" delay="0.0s" duration="100.0s" amplitude="6.0E-10A"/>