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Merged
pgleeson merged 9 commits into from
Jun 16, 2025
Merged

Check for source_ids/channel_ids #11

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9babd12
Regenerated
pgleeson Feb 10, 2025
b673a82
Regenerated with latest nml libs
pgleeson Apr 11, 2025
49dcb1a
Update omv-ci.yml
pgleeson Jun 13, 2025
167782e
Merge branch 'development' into experimental
pgleeson Jun 13, 2025
729a4b7
numpy 2 & "cython<3.1.0"
pgleeson Jun 13, 2025
46fb528
More test options
pgleeson Jun 13, 2025
5da2959
Rem py 3.9
pgleeson Jun 16, 2025
dbeb158
Regenerated with latest nml
pgleeson Jun 16, 2025
116f06d
Check for source_ids/channel_ids
pgleeson Jun 16, 2025
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9 changes: 4 additions & 5 deletions .github/workflows/omv-ci.yml
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Expand Up @@ -9,11 +9,11 @@ on:
jobs:
build:

runs-on: ubuntu-latest
runs-on: ubuntu-22.04
strategy:
fail-fast: false
matrix:
python-version: [ "3.9", "3.10", "3.11" ] # Brian no longer supported on py3.8
python-version: [ "3.10", "3.12", "3.13" ] # Brian no longer supported on py3.9!
engine: [ jNeuroML, jNeuroML_NEURON, jNeuroML_PyNN_NEURON, jNeuroML_validate, PyNN_NEURON, PyNN_Nest, PyNN_NeuroML, PyNN_Brian2]

steps:
Expand All @@ -30,9 +30,8 @@ jobs:

- name: Install additional packages
run: |
pip install scipy sympy matplotlib cython tables

# pip install 'numpy<=1.23.0' # see https://github.com/OpenSourceBrain/osb-model-validation/issues/91

pip install matplotlib "cython<3.1.0" # let omv handle other deps...


- name: Run OMV tests on engine ${{ matrix.engine }}
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24 changes: 12 additions & 12 deletions NeuroML2/ConnectionsTest.net.nml
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Expand Up @@ -2,8 +2,8 @@
<notes>
This NeuroML 2 file has been generated from:
PyNN v0.11.0
libNeuroML v0.6.3
pyNeuroML v1.3.7
libNeuroML v0.6.8
pyNeuroML v1.3.19
</notes>
<IF_cond_alpha id="IF_cond_alpha_pop_pre" cm="1.0" i_offset="0.9" tau_syn_E="2.0" tau_syn_I="5.0" v_init="-65.0" tau_m="20.0" tau_refrac="5.0" v_reset="-65.0" v_rest="-65.0" v_thresh="-50.0" e_rev_E="0.0" e_rev_I="-70.0"/>
<IF_cond_alpha id="IF_cond_alpha_pop_post" cm="1.0" i_offset="0.9" tau_syn_E="2.0" tau_syn_I="5.0" v_init="-65.0" tau_m="20.0" tau_refrac="5.0" v_reset="-65.0" v_rest="-65.0" v_thresh="-50.0" e_rev_E="0.0" e_rev_I="-70.0"/>
Expand All @@ -17,38 +17,38 @@
<property tag="radius" value="5"/>
<property tag="color" value="0 0.6 0"/>
<instance id="0">
<location x="-9.771402205615921" y="41.107735197887862" z="8.380479496098125"/>
<location x="67.968888080621582" y="-70.657158602734654" z="-18.315070185150397"/>
</instance>
<instance id="1">
<location x="11.787241779479075" y="-22.917415323944468" z="-69.969358778846896"/>
<location x="60.184476562654041" y="60.493279624680454" z="-4.759239011557659"/>
</instance>
<instance id="2">
<location x="24.148166862976762" y="-10.126267539995236" z="-6.507356698049249"/>
<location x="27.189024038368114" y="-73.036270319949594" z="-25.447207420452678"/>
</instance>
<instance id="3">
<location x="-14.878199498615952" y="49.650874267039804" z="18.835272881150388"/>
<location x="-24.852298939173203" y="-12.272599182378062" z="3.750079672379081"/>
</instance>
<instance id="4">
<location x="37.92567221050809" y="-22.437678624311431" z="-38.190180651135641"/>
<location x="24.133497816283622" y="10.517195276874403" z="-29.329915036014633"/>
</instance>
</population>
<population id="pop_post" component="IF_cond_alpha_pop_post" size="5" type="populationList">
<property tag="radius" value="5"/>
<property tag="color" value="0 0.2 0.6"/>
<instance id="0">
<location x="-30.357177121657621" y="148.821597074248928" z="41.550393258456353"/>
<location x="24.765200337632276" y="242.663676551724933" z="75.097696646567741"/>
</instance>
<instance id="1">
<location x="-75.487951984450333" y="241.449664932469261" z="4.06371645195327"/>
<location x="45.028559466580795" y="226.140823198868731" z="48.181218144946691"/>
</instance>
<instance id="2">
<location x="53.196249421914075" y="144.47758109254687" z="46.851975572138628"/>
<location x="52.54517028397283" y="161.954657204140887" z="-5.258407353297101"/>
</instance>
<instance id="3">
<location x="-20.844985362062317" y="188.239068673352108" z="-57.809991974759043"/>
<location x="-33.575509675391338" y="195.289896982416423" z="-19.682584593824927"/>
</instance>
<instance id="4">
<location x="41.000859853632619" y="279.306766456403295" z="35.048479751214437"/>
<location x="-14.798277951638838" y="173.216535964582647" z="93.772913738872958"/>
</instance>
</population>
<projection id="pop_pre__TO__pop_post" presynapticPopulation="pop_pre" postsynapticPopulation="pop_post" synapse="syn__pop_pre__TO__pop_post">
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4 changes: 2 additions & 2 deletions NeuroML2/Inputs.net.nml
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Expand Up @@ -2,8 +2,8 @@
<notes>
This NeuroML 2 file has been generated from:
PyNN v0.11.0
libNeuroML v0.6.3
pyNeuroML v1.3.7
libNeuroML v0.6.8
pyNeuroML v1.3.19
</notes>
<pulseGenerator id="DCSource_DCSource_0" delay="50.0ms" duration="350.0ms" amplitude="0.9nA"/>
<compoundInput id="ACSource_ACSource_1">
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4 changes: 2 additions & 2 deletions NeuroML2/LEMS_Sim_Inputs.xml
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Expand Up @@ -3,8 +3,8 @@
<!--
This LEMS file has been generated from:
PyNN v0.11.0
libNeuroML v0.6.3
pyNeuroML v1.3.7
libNeuroML v0.6.8
pyNeuroML v1.3.19
-->

<!-- Specify which component to run -->
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4 changes: 2 additions & 2 deletions NeuroML2/LEMS_Sim_PyNN_NeuroML2_Export.xml
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Expand Up @@ -3,8 +3,8 @@
<!--
This LEMS file has been generated from:
PyNN v0.11.0
libNeuroML v0.6.3
pyNeuroML v1.3.7
libNeuroML v0.6.8
pyNeuroML v1.3.19
-->

<!-- Specify which component to run -->
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Binary file modified NeuroML2/Positions.net.nml.h5
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4 changes: 2 additions & 2 deletions NeuroML2/PyNN_NeuroML2_Export.net.nml
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Expand Up @@ -2,8 +2,8 @@
<notes>
This NeuroML 2 file has been generated from:
PyNN v0.11.0
libNeuroML v0.6.3
pyNeuroML v1.3.7
libNeuroML v0.6.8
pyNeuroML v1.3.19
</notes>
<IF_curr_alpha id="IF_curr_alpha_pop_IF_curr_alpha" cm="1.0" i_offset="0.9" tau_syn_E="2.0" tau_syn_I="5.0" v_init="-65.0" tau_m="20.0" tau_refrac="10.0" v_reset="-62.0" v_rest="-65.0" v_thresh="-52.0"/>
<IF_curr_exp id="IF_curr_exp_pop_IF_curr_exp" cm="1.0" i_offset="1.0" tau_syn_E="2.0" tau_syn_I="5.0" v_init="-65.0" tau_m="20.0" tau_refrac="8.0" v_reset="-70.0" v_rest="-65.0" v_thresh="-50.0"/>
Expand Down
11 changes: 9 additions & 2 deletions PyNN/InputsTest.py
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Expand Up @@ -51,7 +51,14 @@
data = pop.get_data('v', gather=False)
analogsignal = data.segments[0].analogsignals[0]
name = analogsignal.name
source_ids = analogsignal.annotations['source_ids']

def get_source_ids_as(analogsignal):
if 'source_ids' in analogsignal.annotations:
return analogsignal.annotations['source_ids']
elif 'channel_ids' in analogsignal.annotations: # See https://github.com/NeuralEnsemble/PyNN/pull/762
return analogsignal.annotations['channel_ids']

source_ids = get_source_ids_as(analogsignal)
filename = "%s_%s.dat"%(pop.label,name)
print('Saving data recorded for %s in pop %s, global ids: %s to %s'%(name, pop.label, source_ids, filename))
times_vm_a = []
Expand Down Expand Up @@ -94,7 +101,7 @@ def get_source_id(spiketrain):
sim.end()

if '-gui' in sys.argv:
if simulator_name in ['neuron', 'nest', 'brian']:
if simulator_name in ['neuron', 'nest', 'brian2']:
import matplotlib.pyplot as plt

print("Plotting results of simulation in %s"%simulator_name)
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6 changes: 3 additions & 3 deletions PyNN/LEMS_2007One_pynn.py
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Expand Up @@ -9,9 +9,9 @@


This PyNN file has been generated by org.neuroml.export (see https://github.com/NeuroML/org.neuroml.export)
org.neuroml.export v1.10.1
org.neuroml.model v1.10.1
jLEMS v0.11.1
org.neuroml.export v1.11.0
org.neuroml.model v1.11.0
jLEMS v0.12.0

'''
# Main PyNN script for: net1
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6 changes: 3 additions & 3 deletions PyNN/RS.mod
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Expand Up @@ -3,9 +3,9 @@ TITLE Mod file for component: Component(id=RS type=izhikevich2007Cell)
COMMENT

This NEURON file has been generated by org.neuroml.export (see https://github.com/NeuroML/org.neuroml.export)
org.neuroml.export v1.10.1
org.neuroml.model v1.10.1
jLEMS v0.11.1
org.neuroml.export v1.11.0
org.neuroml.model v1.11.0
jLEMS v0.12.0

ENDCOMMENT

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6 changes: 3 additions & 3 deletions PyNN/RS_Iext.mod
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Expand Up @@ -3,9 +3,9 @@ TITLE Mod file for component: Component(id=RS_Iext type=pulseGenerator)
COMMENT

This NEURON file has been generated by org.neuroml.export (see https://github.com/NeuroML/org.neuroml.export)
org.neuroml.export v1.10.1
org.neuroml.model v1.10.1
jLEMS v0.11.1
org.neuroml.export v1.11.0
org.neuroml.model v1.11.0
jLEMS v0.12.0

ENDCOMMENT

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6 changes: 3 additions & 3 deletions PyNN/RS_Iext_inputdefinition.py
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Expand Up @@ -9,9 +9,9 @@
---------------------------------------------

This PyNN file has been generated by org.neuroml.export (see https://github.com/NeuroML/org.neuroml.export)
org.neuroml.export v1.10.1
org.neuroml.model v1.10.1
jLEMS v0.11.1
org.neuroml.export v1.11.0
org.neuroml.model v1.11.0
jLEMS v0.12.0

'''
# Input file for Component: RS_Iext
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6 changes: 3 additions & 3 deletions PyNN/RS_celldefinition.py
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Expand Up @@ -16,9 +16,9 @@
---------------------------------------------

This PyNN file has been generated by org.neuroml.export (see https://github.com/NeuroML/org.neuroml.export)
org.neuroml.export v1.10.1
org.neuroml.model v1.10.1
jLEMS v0.11.1
org.neuroml.export v1.11.0
org.neuroml.model v1.11.0
jLEMS v0.12.0

'''
# Cell file for Component: RS
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2 changes: 2 additions & 0 deletions README.md
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Expand Up @@ -9,3 +9,5 @@ See here: https://github.com/NeuroML/NeuroML2/issues/73 for current plans/update
See also: https://github.com/NeuralEnsemble/Networks_SIG/issues?q=is%3Aissue+is%3Aopen+label%3APyNN