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Merged
pgleeson merged 25 commits into from
Jun 13, 2025
Merged

Tests with netpyne format #12

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cbf7c32
Cleaning up
pgleeson May 2, 2024
d8ec8bf
Add index file for HH
pgleeson May 2, 2024
dcfbe46
index file for 2 cells
pgleeson May 2, 2024
0d71eda
init file too...
pgleeson May 2, 2024
aae1543
Test ion fix
pgleeson May 3, 2024
0236f67
Regenerated
pgleeson May 31, 2024
9617d75
Merge branch 'master' into development
pgleeson May 31, 2024
57deff5
Regenerated...
pgleeson Jul 31, 2024
5a64e52
Switche tables install
pgleeson Jul 31, 2024
458e041
Regenerated
pgleeson Aug 19, 2024
95511e6
Tweak
pgleeson Aug 19, 2024
23a97f2
Merge branch 'master' into development
pgleeson Aug 19, 2024
62b4e45
Regenerated
pgleeson Dec 16, 2024
b5603b3
Regenerated
pgleeson Dec 19, 2024
390a2fa
Regenerated with latest netpyne
pgleeson Dec 20, 2024
d2241e8
Remove hard coded path
pgleeson Dec 20, 2024
59a5447
Fix regeneration script - prevent local path
pgleeson Dec 20, 2024
308fb1f
Update non-omv.yml
pgleeson Mar 10, 2025
746e4d8
Update omv-ci.yml
pgleeson Mar 10, 2025
2135ba6
Regenerated with latest nml libs
pgleeson Apr 11, 2025
6428732
Update README.md
pgleeson Jun 13, 2025
2159749
Test 3.12 not 3.8
pgleeson Jun 13, 2025
bcab02c
update setup tools
pgleeson Jun 13, 2025
c271968
Remove pin on numpy; add cron job
pgleeson Jun 13, 2025
2b6a816
Ensure latest numpy
pgleeson Jun 13, 2025
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7 changes: 4 additions & 3 deletions .github/workflows/non-omv.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@ jobs:
strategy:
fail-fast: false
matrix:
python-version: [ 3.9, "3.10" ]
python-version: [ 3.9, "3.12" ]
runs-on: [ ubuntu-latest, macos-latest ]

steps:
Expand All @@ -33,15 +33,16 @@ jobs:
run: |
pip install git+https://github.com/OpenSourceBrain/osb-model-validation
pip install scipy sympy matplotlib cython pandas tables

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


- name: Regenerate and test
run: |
omv install neuron
omv install netpyne
omv install pyNeuroML

pip list

export NEURON_HOME=$pythonLocation

omv list -V
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13 changes: 10 additions & 3 deletions .github/workflows/omv-ci.yml
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@@ -1,6 +1,8 @@
name: Continuous builds

on:
schedule:
- cron: "1 1 10 */1 *" # Run once a month to test...
push:
branches: [ master, development, experimental ]
pull_request:
Expand All @@ -9,11 +11,11 @@ on:
jobs:
build:

runs-on: ubuntu-latest
runs-on: ubuntu-22.04 # for eden...
strategy:
fail-fast: false
matrix:
python-version: [ 3.8, 3.9, "3.10" ]
python-version: [ 3.9, "3.10", "3.12" ]
engine: [ NetPyNE, jNeuroML, jNeuroML_NEURON, jNeuroML_NetPyNE, jNeuroML_EDEN, jNeuroML_validate ]

steps:
Expand All @@ -23,12 +25,17 @@ jobs:
with:
python-version: ${{ matrix.python-version }}


- name: Ensure setuptools is up-to-date
run: |
pip install --upgrade setuptools

- name: Install OMV
run: |
pip install git+https://github.com/OpenSourceBrain/osb-model-validation

pip install scipy sympy matplotlib cython pandas tables

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

- name: Run OMV tests on engine ${{ matrix.engine }}
run: |
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49 changes: 0 additions & 49 deletions .travis.yml
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This file was deleted.

6 changes: 3 additions & 3 deletions NetPyNE/ACnet/AMPA_syn.mod
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Expand Up @@ -3,9 +3,9 @@ TITLE Mod file for component: Component(id=AMPA_syn type=expTwoSynapse)
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 NetPyNE/ACnet/AMPA_syn_inh.mod
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Expand Up @@ -3,9 +3,9 @@ TITLE Mod file for component: Component(id=AMPA_syn_inh type=expTwoSynapse)
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 NetPyNE/ACnet/BackgroundRandomIClamps.mod
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Expand Up @@ -3,9 +3,9 @@ TITLE Mod file for component: Component(id=BackgroundRandomIClamps type=pulseGen
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 NetPyNE/ACnet/Ca_conc.mod
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Expand Up @@ -3,9 +3,9 @@ TITLE Mod file for component: Component(id=Ca_conc type=fixedFactorConcentration
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 NetPyNE/ACnet/Ca_pyr.mod
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Expand Up @@ -3,9 +3,9 @@ TITLE Mod file for component: Component(id=Ca_pyr type=ionChannelHH)
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 NetPyNE/ACnet/GABA_syn.mod
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Expand Up @@ -3,9 +3,9 @@ TITLE Mod file for component: Component(id=GABA_syn type=expTwoSynapse)
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 NetPyNE/ACnet/GABA_syn_inh.mod
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Original file line number Diff line number Diff line change
Expand Up @@ -3,9 +3,9 @@ TITLE Mod file for component: Component(id=GABA_syn_inh type=expTwoSynapse)
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 NetPyNE/ACnet/Kahp_pyr.mod
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Expand Up @@ -3,9 +3,9 @@ TITLE Mod file for component: Component(id=Kahp_pyr type=ionChannelHH)
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 NetPyNE/ACnet/Kdr_bask.mod
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Expand Up @@ -3,9 +3,9 @@ TITLE Mod file for component: Component(id=Kdr_bask type=ionChannelHH)
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 NetPyNE/ACnet/Kdr_pyr.mod
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Original file line number Diff line number Diff line change
Expand Up @@ -3,9 +3,9 @@ TITLE Mod file for component: Component(id=Kdr_pyr type=ionChannelHH)
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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8 changes: 4 additions & 4 deletions NetPyNE/ACnet/LEMS_MediumNet_netpyne.py
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Expand Up @@ -37,9 +37,9 @@


This NETPYNE 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 NetPyNE script for: network_ACnet2
Expand Down Expand Up @@ -69,7 +69,7 @@ def __init__(self, tstop=500.0, dt=0.01, seed=123456789, save_json=False, abs_to
self.report_file.write('SimulationFile=%s\n'%__file__)
self.report_file.write('PythonVersion=%s\n'%sys.version.replace('\n',' '))
self.report_file.write('NeuronVersion=%s\n'%h.nrnversion())
self.report_file.write('NeuroMLExportVersion=1.10.1\n')
self.report_file.write('NeuroMLExportVersion=1.11.0\n')
self.report_file.close()


Expand Down
6 changes: 3 additions & 3 deletions NetPyNE/ACnet/LeakConductance_bask.mod
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Expand Up @@ -3,9 +3,9 @@ TITLE Mod file for component: Component(id=LeakConductance_bask type=ionChannelP
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 NetPyNE/ACnet/LeakConductance_pyr.mod
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Original file line number Diff line number Diff line change
Expand Up @@ -3,9 +3,9 @@ TITLE Mod file for component: Component(id=LeakConductance_pyr type=ionChannelPa
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 NetPyNE/ACnet/Na_bask.mod
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Original file line number Diff line number Diff line change
Expand Up @@ -3,9 +3,9 @@ TITLE Mod file for component: Component(id=Na_bask type=ionChannelHH)
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 NetPyNE/ACnet/Na_pyr.mod
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Original file line number Diff line number Diff line change
Expand Up @@ -3,9 +3,9 @@ TITLE Mod file for component: Component(id=Na_pyr type=ionChannelHH)
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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8 changes: 4 additions & 4 deletions NetPyNE/GapJunctions/LEMS_GJ_netpyne.py
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Expand Up @@ -11,9 +11,9 @@


This NETPYNE 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 NetPyNE script for: net1
Expand Down Expand Up @@ -43,7 +43,7 @@ def __init__(self, tstop=700.0, dt=0.01, seed=123456789, save_json=False, abs_to
self.report_file.write('SimulationFile=%s\n'%__file__)
self.report_file.write('PythonVersion=%s\n'%sys.version.replace('\n',' '))
self.report_file.write('NeuronVersion=%s\n'%h.nrnversion())
self.report_file.write('NeuroMLExportVersion=1.10.1\n')
self.report_file.write('NeuroMLExportVersion=1.11.0\n')
self.report_file.close()


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6 changes: 3 additions & 3 deletions NetPyNE/GapJunctions/gj1.mod
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Expand Up @@ -3,9 +3,9 @@ TITLE Mod file for component: Component(id=gj1 type=gapJunction)
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 NetPyNE/GapJunctions/iaf.mod
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Expand Up @@ -3,9 +3,9 @@ TITLE Mod file for component: Component(id=iaf type=iafCell)
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 NetPyNE/GapJunctions/pulseGen1.mod
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Expand Up @@ -3,9 +3,9 @@ TITLE Mod file for component: Component(id=pulseGen1 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 NetPyNE/GapJunctions/pulseGen2.mod
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Expand Up @@ -3,9 +3,9 @@ TITLE Mod file for component: Component(id=pulseGen2 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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