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Update GitHub Actions and restore includes for jNeuroML_NEURON #4

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Merged
pgleeson merged 3 commits into from
Jul 27, 2026
Merged

Update GitHub Actions and restore includes for jNeuroML_NEURON #4

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2ba8d78
Update GHA
pgleeson Jul 27, 2026
8bbd32e
Test on jNeuroML_NEURON
pgleeson Jul 27, 2026
a55a2c1
Put back includes
pgleeson Jul 27, 2026
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8 changes: 4 additions & 4 deletions .github/workflows/omv-ci.yml
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Expand Up @@ -17,16 +17,16 @@ 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

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 }}

Expand All @@ -41,5 +41,5 @@ jobs:

- name: OMV final version info
run: |
omv list -V # list installed engines
omv list -V # list installed engines
env
31 changes: 31 additions & 0 deletions NeuroML2/ACnet2/.test.jnmlnrn.omt
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@@ -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



9 changes: 9 additions & 0 deletions NeuroML2/ACnet2/.test.mep
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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]
63 changes: 63 additions & 0 deletions NeuroML2/ACnet2/LEMS_ACnet2_LowDt.xml
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<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>