From da5d04694ea3bd6fd337035d720c0acf41e7b6ca Mon Sep 17 00:00:00 2001 From: pgleeson Date: Mon, 16 Jun 2025 12:48:54 +0100 Subject: [PATCH 1/5] Another fix for source_ids/channel_ids --- PyNN/NeuroMLTest_PyNN0.9.py | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/PyNN/NeuroMLTest_PyNN0.9.py b/PyNN/NeuroMLTest_PyNN0.9.py index 87c8d9e..f55f01a 100644 --- a/PyNN/NeuroMLTest_PyNN0.9.py +++ b/PyNN/NeuroMLTest_PyNN0.9.py @@ -100,11 +100,18 @@ def get_source_id(spiketrain): elif 'channel_id' in spiketrain.annotations: # See https://github.com/NeuralEnsemble/PyNN/pull/762 return spiketrain.annotations['channel_id'] + 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'] + + for pop in [pop_IF_curr_alpha, pop_IF_curr_exp, pop_IF_cond_exp, pop_IF_cond_alpha,pop_EIF_cond_exp_isfa_ista, pop_HH_cond_exp, pop_post1,pop_post2]: data = pop.get_data('v', gather=False) analogsignal = data.segments[0].analogsignals[0] name = analogsignal.name - source_ids = analogsignal.annotations['source_ids'] + source_ids = get_source_ids_as(analogsignal) print('Saving data recorded for %s in pop %s, global ids: %s'%(name, pop.label, source_ids)) for i in range(len(source_ids)): glob_id = source_ids[i] From aa5dacb6360642a2c78e091032ff8c2fcd177dab Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Mon, 4 Aug 2025 18:32:56 +0100 Subject: [PATCH 2/5] Regenerated --- NeuroML2/ConnectionsTest.net.nml | 22 +++++++++++----------- NeuroML2/Inputs.net.nml | 2 +- NeuroML2/LEMS_Sim_Inputs.xml | 2 +- NeuroML2/LEMS_Sim_PyNN_NeuroML2_Export.xml | 2 +- NeuroML2/PyNN_NeuroML2_Export.net.nml | 2 +- 5 files changed, 15 insertions(+), 15 deletions(-) diff --git a/NeuroML2/ConnectionsTest.net.nml b/NeuroML2/ConnectionsTest.net.nml index 285088b..58de2ca 100644 --- a/NeuroML2/ConnectionsTest.net.nml +++ b/NeuroML2/ConnectionsTest.net.nml @@ -3,7 +3,7 @@ This NeuroML 2 file has been generated from: PyNN v0.11.0 libNeuroML v0.6.8 - pyNeuroML v1.3.19 + pyNeuroML v1.3.22 @@ -17,38 +17,38 @@ - + - + - + - + - + - + - + - + - + - + diff --git a/NeuroML2/Inputs.net.nml b/NeuroML2/Inputs.net.nml index d3069dd..ddf4e4b 100644 --- a/NeuroML2/Inputs.net.nml +++ b/NeuroML2/Inputs.net.nml @@ -3,7 +3,7 @@ This NeuroML 2 file has been generated from: PyNN v0.11.0 libNeuroML v0.6.8 - pyNeuroML v1.3.19 + pyNeuroML v1.3.22 diff --git a/NeuroML2/LEMS_Sim_Inputs.xml b/NeuroML2/LEMS_Sim_Inputs.xml index 24f72d3..e3a7efb 100644 --- a/NeuroML2/LEMS_Sim_Inputs.xml +++ b/NeuroML2/LEMS_Sim_Inputs.xml @@ -4,7 +4,7 @@ This LEMS file has been generated from: PyNN v0.11.0 libNeuroML v0.6.8 - pyNeuroML v1.3.19 + pyNeuroML v1.3.22 --> diff --git a/NeuroML2/LEMS_Sim_PyNN_NeuroML2_Export.xml b/NeuroML2/LEMS_Sim_PyNN_NeuroML2_Export.xml index ca0d527..c3eda93 100644 --- a/NeuroML2/LEMS_Sim_PyNN_NeuroML2_Export.xml +++ b/NeuroML2/LEMS_Sim_PyNN_NeuroML2_Export.xml @@ -4,7 +4,7 @@ This LEMS file has been generated from: PyNN v0.11.0 libNeuroML v0.6.8 - pyNeuroML v1.3.19 + pyNeuroML v1.3.22 --> diff --git a/NeuroML2/PyNN_NeuroML2_Export.net.nml b/NeuroML2/PyNN_NeuroML2_Export.net.nml index c59bb93..67a3add 100644 --- a/NeuroML2/PyNN_NeuroML2_Export.net.nml +++ b/NeuroML2/PyNN_NeuroML2_Export.net.nml @@ -3,7 +3,7 @@ This NeuroML 2 file has been generated from: PyNN v0.11.0 libNeuroML v0.6.8 - pyNeuroML v1.3.19 + pyNeuroML v1.3.22 From b271d89548ea1796a627e7d03c2ef234d5bbe467 Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Mon, 4 Aug 2025 18:50:54 +0100 Subject: [PATCH 3/5] Updates jnml/pynml handling --- .github/workflows/omv-ci.yml | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/.github/workflows/omv-ci.yml b/.github/workflows/omv-ci.yml index 819b86f..5d3e91c 100644 --- a/.github/workflows/omv-ci.yml +++ b/.github/workflows/omv-ci.yml @@ -40,11 +40,9 @@ jobs: - name: Regenerate run: | - export JNML_HOME=/home/runner/jnml/jNeuroMLJar - export PATH=$JNML_HOME:$PATH - omv install PyNN # required for regeneration... - omv install pyNeuroML # required for regeneration... - omv install jNeuroML + omv install pyNeuroML # required for regeneration (installs jnml too)... + + which pynml which jnml ./regenerate.sh From 439f07eee02338e173a441b6af98b49e1ca2ae3c Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Mon, 4 Aug 2025 18:55:17 +0100 Subject: [PATCH 4/5] Install pynn too --- .github/workflows/omv-ci.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/omv-ci.yml b/.github/workflows/omv-ci.yml index 5d3e91c..b6640b7 100644 --- a/.github/workflows/omv-ci.yml +++ b/.github/workflows/omv-ci.yml @@ -41,6 +41,7 @@ jobs: - name: Regenerate run: | omv install pyNeuroML # required for regeneration (installs jnml too)... + omv install PyNN # required for regeneration... which pynml which jnml From 4c96895a6e605379778efe2068dd940c3c18e305 Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Fri, 20 Mar 2026 14:12:13 +0000 Subject: [PATCH 5/5] add pip list --- .github/workflows/omv-ci.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/omv-ci.yml b/.github/workflows/omv-ci.yml index ae7ff74..5f8330f 100644 --- a/.github/workflows/omv-ci.yml +++ b/.github/workflows/omv-ci.yml @@ -33,6 +33,8 @@ jobs: pip install matplotlib "cython<3.1.0" # let omv handle other deps... + pip list + - name: Run OMV tests on engine ${{ matrix.engine }} run: |