From 9babd125c15d1073c4c03f03154607b6b540c70c Mon Sep 17 00:00:00 2001 From: pgleeson Date: Mon, 10 Feb 2025 17:47:38 +0000 Subject: [PATCH 1/8] Regenerated --- NeuroML2/ConnectionsTest.net.nml | 24 ++++++++++----------- NeuroML2/Inputs.net.nml | 4 ++-- NeuroML2/LEMS_Sim_Inputs.xml | 4 ++-- NeuroML2/LEMS_Sim_PyNN_NeuroML2_Export.xml | 4 ++-- NeuroML2/Positions.net.nml.h5 | Bin 23784 -> 23823 bytes NeuroML2/PyNN_NeuroML2_Export.net.nml | 4 ++-- 6 files changed, 20 insertions(+), 20 deletions(-) diff --git a/NeuroML2/ConnectionsTest.net.nml b/NeuroML2/ConnectionsTest.net.nml index 2dbb8a2..a4b8c65 100644 --- a/NeuroML2/ConnectionsTest.net.nml +++ b/NeuroML2/ConnectionsTest.net.nml @@ -2,8 +2,8 @@ This NeuroML 2 file has been generated from: PyNN v0.11.0 - libNeuroML v0.6.3 - pyNeuroML v1.3.7 + libNeuroML v0.6.5 + pyNeuroML v1.3.14 @@ -17,38 +17,38 @@ - + - + - + - + - + - + - + - + - + - + diff --git a/NeuroML2/Inputs.net.nml b/NeuroML2/Inputs.net.nml index d65583f..e28f14a 100644 --- a/NeuroML2/Inputs.net.nml +++ b/NeuroML2/Inputs.net.nml @@ -2,8 +2,8 @@ This NeuroML 2 file has been generated from: PyNN v0.11.0 - libNeuroML v0.6.3 - pyNeuroML v1.3.7 + libNeuroML v0.6.5 + pyNeuroML v1.3.14 diff --git a/NeuroML2/LEMS_Sim_Inputs.xml b/NeuroML2/LEMS_Sim_Inputs.xml index 343bd85..6d1f271 100644 --- a/NeuroML2/LEMS_Sim_Inputs.xml +++ b/NeuroML2/LEMS_Sim_Inputs.xml @@ -3,8 +3,8 @@ diff --git a/NeuroML2/LEMS_Sim_PyNN_NeuroML2_Export.xml b/NeuroML2/LEMS_Sim_PyNN_NeuroML2_Export.xml index 0c08f73..315794f 100644 --- a/NeuroML2/LEMS_Sim_PyNN_NeuroML2_Export.xml +++ b/NeuroML2/LEMS_Sim_PyNN_NeuroML2_Export.xml @@ -3,8 +3,8 @@ diff --git a/NeuroML2/Positions.net.nml.h5 b/NeuroML2/Positions.net.nml.h5 index 94dde7dc71c56543c8124e3718532e65ee5087ec..06e82cb2e37dd7abc19073157b238280ca2b999d 100644 GIT binary patch delta 8697 zcmVu^s`vvk5E<3jw9G6*sj3 z0X35W3K#-0G_&M5;{ktoUhUL*G*w^w0B}QwOJquhC?%PT%;O!DN)a+P$Pkh#6`?W@ z8Ol7=HG~XNnTc@kRff`lh>~xFk}?yae&-zh-oM_p-oM{>J)dP+=bpXKv!DI!=bVt3 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From b673a82a90c07413ae5a9171a7e5ed7704805b93 Mon Sep 17 00:00:00 2001 From: pgleeson Date: Fri, 11 Apr 2025 12:12:24 +0100 Subject: [PATCH 2/8] Regenerated with latest nml libs --- NeuroML2/ConnectionsTest.net.nml | 24 ++++++++++----------- NeuroML2/Inputs.net.nml | 4 ++-- NeuroML2/LEMS_Sim_Inputs.xml | 4 ++-- NeuroML2/LEMS_Sim_PyNN_NeuroML2_Export.xml | 4 ++-- NeuroML2/Positions.net.nml.h5 | Bin 23823 -> 23816 bytes NeuroML2/PyNN_NeuroML2_Export.net.nml | 4 ++-- PyNN/LEMS_2007One_pynn.py | 6 +++--- PyNN/RS.mod | 6 +++--- PyNN/RS_Iext.mod | 6 +++--- PyNN/RS_Iext_inputdefinition.py | 6 +++--- PyNN/RS_celldefinition.py | 6 +++--- 11 files changed, 35 insertions(+), 35 deletions(-) diff --git a/NeuroML2/ConnectionsTest.net.nml b/NeuroML2/ConnectionsTest.net.nml index a4b8c65..2fa82f4 100644 --- a/NeuroML2/ConnectionsTest.net.nml +++ b/NeuroML2/ConnectionsTest.net.nml @@ -2,8 +2,8 @@ This NeuroML 2 file has been generated from: PyNN v0.11.0 - libNeuroML v0.6.5 - pyNeuroML v1.3.14 + libNeuroML v0.6.6 + pyNeuroML v1.3.17 @@ -17,38 +17,38 @@ - + - + - + - + - + - + - + - + - + - + diff --git a/NeuroML2/Inputs.net.nml b/NeuroML2/Inputs.net.nml index e28f14a..e56da3d 100644 --- a/NeuroML2/Inputs.net.nml +++ b/NeuroML2/Inputs.net.nml @@ -2,8 +2,8 @@ This NeuroML 2 file has been generated from: PyNN v0.11.0 - libNeuroML v0.6.5 - pyNeuroML v1.3.14 + libNeuroML v0.6.6 + pyNeuroML v1.3.17 diff --git a/NeuroML2/LEMS_Sim_Inputs.xml b/NeuroML2/LEMS_Sim_Inputs.xml index 6d1f271..9aa2706 100644 --- a/NeuroML2/LEMS_Sim_Inputs.xml +++ b/NeuroML2/LEMS_Sim_Inputs.xml @@ -3,8 +3,8 @@ diff --git a/NeuroML2/LEMS_Sim_PyNN_NeuroML2_Export.xml b/NeuroML2/LEMS_Sim_PyNN_NeuroML2_Export.xml index 315794f..dafb1b3 100644 --- a/NeuroML2/LEMS_Sim_PyNN_NeuroML2_Export.xml +++ b/NeuroML2/LEMS_Sim_PyNN_NeuroML2_Export.xml @@ -3,8 +3,8 @@ diff --git a/NeuroML2/Positions.net.nml.h5 b/NeuroML2/Positions.net.nml.h5 index 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zpEVsYyWl%gYkpI>;Jaux}g)*H~iE8lTi&MlmA==1RCi~OY0JRZ~y=R diff --git a/NeuroML2/PyNN_NeuroML2_Export.net.nml b/NeuroML2/PyNN_NeuroML2_Export.net.nml index 5f79045..3b03fe0 100644 --- a/NeuroML2/PyNN_NeuroML2_Export.net.nml +++ b/NeuroML2/PyNN_NeuroML2_Export.net.nml @@ -2,8 +2,8 @@ This NeuroML 2 file has been generated from: PyNN v0.11.0 - libNeuroML v0.6.5 - pyNeuroML v1.3.14 + libNeuroML v0.6.6 + pyNeuroML v1.3.17 diff --git a/PyNN/LEMS_2007One_pynn.py b/PyNN/LEMS_2007One_pynn.py index d48ba1d..c2507ab 100644 --- a/PyNN/LEMS_2007One_pynn.py +++ b/PyNN/LEMS_2007One_pynn.py @@ -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 diff --git a/PyNN/RS.mod b/PyNN/RS.mod index 7ac284b..5767bc6 100644 --- a/PyNN/RS.mod +++ b/PyNN/RS.mod @@ -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 diff --git a/PyNN/RS_Iext.mod b/PyNN/RS_Iext.mod index 677626d..0aad522 100644 --- a/PyNN/RS_Iext.mod +++ b/PyNN/RS_Iext.mod @@ -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 diff --git a/PyNN/RS_Iext_inputdefinition.py b/PyNN/RS_Iext_inputdefinition.py index 4aedd92..4ccdb17 100644 --- a/PyNN/RS_Iext_inputdefinition.py +++ b/PyNN/RS_Iext_inputdefinition.py @@ -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 diff --git a/PyNN/RS_celldefinition.py b/PyNN/RS_celldefinition.py index 7f6a681..2cdeda3 100644 --- a/PyNN/RS_celldefinition.py +++ b/PyNN/RS_celldefinition.py @@ -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 From 49dcb1a53f2f2d761ab96e1ca6a70ab1edaacafc Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Fri, 13 Jun 2025 14:51:45 +0100 Subject: [PATCH 3/8] Update omv-ci.yml --- .github/workflows/omv-ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/omv-ci.yml b/.github/workflows/omv-ci.yml index 568be2a..a8bee4e 100644 --- a/.github/workflows/omv-ci.yml +++ b/.github/workflows/omv-ci.yml @@ -13,7 +13,7 @@ jobs: strategy: fail-fast: false matrix: - python-version: [ "3.9", "3.10" ] # Brian no longer supported on py3.8 + python-version: [ "3.9", "3.10", "3.12" ] # Brian no longer supported on py3.8 engine: [ jNeuroML, jNeuroML_NEURON, jNeuroML_PyNN_NEURON, jNeuroML_validate, PyNN_NEURON, PyNN_Nest, PyNN_NeuroML, PyNN_Brian2] steps: From 729a4b7b5fa9de2014233f0fa6f593545566e280 Mon Sep 17 00:00:00 2001 From: pgleeson Date: Fri, 13 Jun 2025 14:56:07 +0100 Subject: [PATCH 4/8] numpy 2 & "cython<3.1.0" --- .github/workflows/omv-ci.yml | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/.github/workflows/omv-ci.yml b/.github/workflows/omv-ci.yml index ae9ddd6..3dc0289 100644 --- a/.github/workflows/omv-ci.yml +++ b/.github/workflows/omv-ci.yml @@ -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 }} From 46fb5283e3c855fd306521483fed2d9ca57fb27c Mon Sep 17 00:00:00 2001 From: pgleeson Date: Fri, 13 Jun 2025 14:59:56 +0100 Subject: [PATCH 5/8] More test options --- .github/workflows/omv-ci.yml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/.github/workflows/omv-ci.yml b/.github/workflows/omv-ci.yml index 3dc0289..a0d2abe 100644 --- a/.github/workflows/omv-ci.yml +++ b/.github/workflows/omv-ci.yml @@ -13,8 +13,11 @@ jobs: strategy: fail-fast: false matrix: - python-version: [ "3.9", "3.10", "3.12" ] # Brian no longer supported on py3.8 + python-version: [ "3.9","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] + exclude: + - python-version: "3.9" + - engine: "PyNN_Brian2" steps: - uses: actions/checkout@v4 From 5da295961336ee06828f5a5857f6dca47fb562a7 Mon Sep 17 00:00:00 2001 From: pgleeson Date: Mon, 16 Jun 2025 11:44:11 +0100 Subject: [PATCH 6/8] Rem py 3.9 --- .github/workflows/omv-ci.yml | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/.github/workflows/omv-ci.yml b/.github/workflows/omv-ci.yml index a0d2abe..819b86f 100644 --- a/.github/workflows/omv-ci.yml +++ b/.github/workflows/omv-ci.yml @@ -13,11 +13,8 @@ jobs: strategy: fail-fast: false matrix: - python-version: [ "3.9","3.10", "3.12", "3.13" ] # Brian no longer supported on py3.9! + 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] - exclude: - - python-version: "3.9" - - engine: "PyNN_Brian2" steps: - uses: actions/checkout@v4 From dbeb158248cd14a3fb78f450695f9aff10fc023f Mon Sep 17 00:00:00 2001 From: pgleeson Date: Mon, 16 Jun 2025 11:44:30 +0100 Subject: [PATCH 7/8] Regenerated with latest nml --- NeuroML2/ConnectionsTest.net.nml | 24 ++++++++++----------- NeuroML2/Inputs.net.nml | 4 ++-- NeuroML2/LEMS_Sim_Inputs.xml | 4 ++-- NeuroML2/LEMS_Sim_PyNN_NeuroML2_Export.xml | 4 ++-- NeuroML2/Positions.net.nml.h5 | Bin 23816 -> 23830 bytes NeuroML2/PyNN_NeuroML2_Export.net.nml | 4 ++-- 6 files changed, 20 insertions(+), 20 deletions(-) diff --git a/NeuroML2/ConnectionsTest.net.nml b/NeuroML2/ConnectionsTest.net.nml index 2fa82f4..285088b 100644 --- a/NeuroML2/ConnectionsTest.net.nml +++ b/NeuroML2/ConnectionsTest.net.nml @@ -2,8 +2,8 @@ This NeuroML 2 file has been generated from: PyNN v0.11.0 - libNeuroML v0.6.6 - pyNeuroML v1.3.17 + libNeuroML v0.6.8 + pyNeuroML v1.3.19 @@ -17,38 +17,38 @@ - + - + - + - + - + - + - + - + - + - + diff --git a/NeuroML2/Inputs.net.nml b/NeuroML2/Inputs.net.nml index e56da3d..d3069dd 100644 --- a/NeuroML2/Inputs.net.nml +++ b/NeuroML2/Inputs.net.nml @@ -2,8 +2,8 @@ This NeuroML 2 file has been generated from: PyNN v0.11.0 - libNeuroML v0.6.6 - pyNeuroML v1.3.17 + libNeuroML v0.6.8 + pyNeuroML v1.3.19 diff --git a/NeuroML2/LEMS_Sim_Inputs.xml b/NeuroML2/LEMS_Sim_Inputs.xml index 9aa2706..24f72d3 100644 --- a/NeuroML2/LEMS_Sim_Inputs.xml +++ b/NeuroML2/LEMS_Sim_Inputs.xml @@ -3,8 +3,8 @@ diff --git a/NeuroML2/LEMS_Sim_PyNN_NeuroML2_Export.xml b/NeuroML2/LEMS_Sim_PyNN_NeuroML2_Export.xml index dafb1b3..ca0d527 100644 --- a/NeuroML2/LEMS_Sim_PyNN_NeuroML2_Export.xml +++ b/NeuroML2/LEMS_Sim_PyNN_NeuroML2_Export.xml @@ -3,8 +3,8 @@ diff --git a/NeuroML2/Positions.net.nml.h5 b/NeuroML2/Positions.net.nml.h5 index 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+0100 Subject: [PATCH 8/8] Check for source_ids/channel_ids --- PyNN/InputsTest.py | 11 +++++++++-- 1 file changed, 9 insertions(+), 2 deletions(-) diff --git a/PyNN/InputsTest.py b/PyNN/InputsTest.py index 799db30..6d7cc6b 100644 --- a/PyNN/InputsTest.py +++ b/PyNN/InputsTest.py @@ -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 = [] @@ -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)