From da5d04694ea3bd6fd337035d720c0acf41e7b6ca Mon Sep 17 00:00:00 2001 From: pgleeson Date: Mon, 16 Jun 2025 12:48:54 +0100 Subject: [PATCH 1/9] 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 2/9] 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 3/9] 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 4/9] 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 5/9] 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: | From 48be7d75744ff6eaccb77c8418669b6b8c63370f Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Mon, 18 May 2026 17:51:18 +0100 Subject: [PATCH 6/9] Remove old travis file --- .travis.yml | 53 ----------------------------------------------------- 1 file changed, 53 deletions(-) delete mode 100644 .travis.yml diff --git a/.travis.yml b/.travis.yml deleted file mode 100644 index 320ab91..0000000 --- a/.travis.yml +++ /dev/null @@ -1,53 +0,0 @@ -# Framework for running automated tests on OSB using Travis-CI, see https://github.com/OpenSourceBrain/osb-model-validation - -dist: bionic # bionic + py3.6 required for building Nest using omv... - -addons: - apt: - packages: - # Requirements for Brian & NEST - - python-numpy - - python-scipy - - python-matplotlib - - python-sympy - - python-tables - - python-tornado - - libreadline6-dev - - libncurses5-dev - - libgsl0-dev - - cython - - -language: python -python: - - 2.7 - - 3.6 # bionic + py3.6 required for building Nest using omv... - -env: - - OMV_ENGINE=jNeuroML - - OMV_ENGINE=jNeuroML_NEURON - - OMV_ENGINE=jNeuroML_PyNN_NEURON - - OMV_ENGINE=jNeuroML_validate - - OMV_ENGINE=PyNN_NEURON - - OMV_ENGINE=PyNN_Nest - - OMV_ENGINE=PyNN_Brian1 - - OMV_ENGINE=PyNN_NeuroML - -install: - - pip install git+https://github.com/OpenSourceBrain/osb-model-validation - - pip install tables scipy # Why is this needed? Doesn't seem to get installed correctly on travis with addons above... - - # Need to pre install NEURON for PyNN_NEURON so nrnivmodl can be run on generated mods - - if [[ ${OMV_ENGINE} == "PyNN_NEURON" ]]; then - omv install NEURON; - cd PyNN; - /home/travis/neuron/nrn/x86_64/bin/nrnivmodl; - cd ..; - omv list-engines; - fi; - -script: - - omv all -V --ignore-non-py3 # will ignore Brian1 tests when run on py3 - - omv list -V - - pip freeze - - env From c7e6083c0bc8613585251fac55dfc649ed26f0ec Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Mon, 18 May 2026 18:13:00 +0100 Subject: [PATCH 7/9] Test older numpy version... --- .github/workflows/omv-ci.yml | 1 + NeuroML2/ConnectionsTest.net.nml | 20 ++++++++++---------- 2 files changed, 11 insertions(+), 10 deletions(-) diff --git a/.github/workflows/omv-ci.yml b/.github/workflows/omv-ci.yml index 5f8330f..d3d8fe2 100644 --- a/.github/workflows/omv-ci.yml +++ b/.github/workflows/omv-ci.yml @@ -32,6 +32,7 @@ jobs: run: | pip install matplotlib "cython<3.1.0" # let omv handle other deps... + pip install 'numpy<=1.23.0' # to test against older numpy versions... pip list diff --git a/NeuroML2/ConnectionsTest.net.nml b/NeuroML2/ConnectionsTest.net.nml index 58de2ca..fbf1dab 100644 --- a/NeuroML2/ConnectionsTest.net.nml +++ b/NeuroML2/ConnectionsTest.net.nml @@ -17,38 +17,38 @@ - + - + - + - + - + - + - + - + - + - + From 2b19bf8eb476dea515638bcb1c59888487af2273 Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Mon, 18 May 2026 18:16:27 +0100 Subject: [PATCH 8/9] numpy==2.2.6 --- .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 d3d8fe2..c1594eb 100644 --- a/.github/workflows/omv-ci.yml +++ b/.github/workflows/omv-ci.yml @@ -32,7 +32,7 @@ jobs: run: | pip install matplotlib "cython<3.1.0" # let omv handle other deps... - pip install 'numpy<=1.23.0' # to test against older numpy versions... + pip install 'numpy==2.2.6' # to test against older numpy versions... pip list From fa0d6e923e0e16cba9a46d3bf75c0b41527ddba0 Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Mon, 18 May 2026 18:22:35 +0100 Subject: [PATCH 9/9] Modify Python version matrix and update comments Updated Python version matrix to remove 3.10 and added a TODO comment for numpy installation. --- .github/workflows/omv-ci.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/omv-ci.yml b/.github/workflows/omv-ci.yml index c1594eb..9e717ed 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: [ "3.10", "3.12", "3.13" ] # Brian no longer supported on py3.9! + python-version: [ "3.12", "3.13" ] # Brian no longer supported on py3.10! engine: [ jNeuroML, jNeuroML_NEURON, jNeuroML_PyNN_NEURON, jNeuroML_validate, PyNN_NEURON, PyNN_Nest, PyNN_NeuroML, PyNN_Brian2] steps: @@ -32,7 +32,7 @@ jobs: run: | pip install matplotlib "cython<3.1.0" # let omv handle other deps... - pip install 'numpy==2.2.6' # to test against older numpy versions... + pip install 'numpy==2.2.6' # to test against older numpy versions... TODO: remove when pynn v0.12 used! pip list