From 7232a8221f46ea66db9b9a4a2c3f27725043d3a9 Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Tue, 29 Jul 2025 11:06:22 +0100 Subject: [PATCH 1/6] Regenerated --- examples/LEMS_SimExample3.xml | 2 +- examples/LEMS_SimExample4.xml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/examples/LEMS_SimExample3.xml b/examples/LEMS_SimExample3.xml index 242674a..0944b9b 100644 --- a/examples/LEMS_SimExample3.xml +++ b/examples/LEMS_SimExample3.xml @@ -2,7 +2,7 @@ diff --git a/examples/LEMS_SimExample4.xml b/examples/LEMS_SimExample4.xml index dac6b77..0fab7a1 100644 --- a/examples/LEMS_SimExample4.xml +++ b/examples/LEMS_SimExample4.xml @@ -2,7 +2,7 @@ From cad6d5103517730ece5d082d15efb86766ac6980 Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Thu, 21 Aug 2025 12:11:03 +0100 Subject: [PATCH 2/6] Regenerated --- examples/Example6.py | 1 - examples/LEMS_SimExample3.xml | 2 +- examples/LEMS_SimExample4.xml | 2 +- 3 files changed, 2 insertions(+), 3 deletions(-) diff --git a/examples/Example6.py b/examples/Example6.py index 62274c6..fc350f7 100644 --- a/examples/Example6.py +++ b/examples/Example6.py @@ -114,7 +114,6 @@ def generate(ref="Example6_PyNN", add_inputs=True): d = {} d[ref] = Population(id=pop_id, size='int(%s*N_scaling)'%N_full[l][t], component=cell.id, properties={'color':color, 'type':t}) - # Instead of exec, set the attribute directly using locals() d[ref].random_layout = RandomLayout(region=r.id) net.populations.append(d[ref]) pop_dict['%s'% (pop_id)] = d[ref] diff --git a/examples/LEMS_SimExample3.xml b/examples/LEMS_SimExample3.xml index 0944b9b..a646cb5 100644 --- a/examples/LEMS_SimExample3.xml +++ b/examples/LEMS_SimExample3.xml @@ -2,7 +2,7 @@ diff --git a/examples/LEMS_SimExample4.xml b/examples/LEMS_SimExample4.xml index 0fab7a1..12c5be3 100644 --- a/examples/LEMS_SimExample4.xml +++ b/examples/LEMS_SimExample4.xml @@ -2,7 +2,7 @@ From aa506c208746dbf02c99e5ee21c31c7ef21b0481 Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Tue, 25 Nov 2025 19:51:40 +0000 Subject: [PATCH 3/6] Add Python 3.14 to CI workflow matrix --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index b43b1b8..de6aa4a 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -13,7 +13,7 @@ jobs: strategy: fail-fast: false matrix: - python-version: ["3.10", "3.11", "3.12", "3.13"] + python-version: ["3.10", "3.11", "3.12", "3.13", "3.14"] env: JNML_HOME: "/home/runner/work/NeuroMLlite/NeuroMLlite/jNeuroML" HDF5_DISABLE_VERSION_CHECK: 1 From fb59a178b5f567b589aa94771afc0b6c505e8dd3 Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Tue, 6 Jan 2026 14:25:36 +0000 Subject: [PATCH 4/6] Limit neuron =8.2.2" # Specify version of neuron - 8.2.1 fails + pip install "NEURON>=8.2.2,<9.0.0" # Specify version of neuron - 8.2.1 fails #pip install -r requirements-dev.txt pip install . cd - @@ -105,6 +105,7 @@ jobs: #export HDF5_DISABLE_VERSION_CHECK=1 if [[ ${{ matrix.python-version }} != 2.7 ]]; then omv install PyNEST; fi #pip install h5py + omv list -V # list installed engines - name: Run pytest From 92817c9f5e61edecd2639dce22bc528554c377c7 Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Tue, 6 Jan 2026 17:44:02 +0000 Subject: [PATCH 5/6] Remove py 3.14 for now, tables not supported... --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 6a93919..9b47ec9 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -13,7 +13,7 @@ jobs: strategy: fail-fast: false matrix: - python-version: ["3.10", "3.11", "3.12", "3.13", "3.14"] + python-version: ["3.10", "3.11", "3.12", "3.13"] env: JNML_HOME: "/home/runner/work/NeuroMLlite/NeuroMLlite/jNeuroML" HDF5_DISABLE_VERSION_CHECK: 1 From c437961ad783184735d63a87c3a0276779b1f134 Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Tue, 6 Jan 2026 17:44:44 +0000 Subject: [PATCH 6/6] Issue with numpy 2.4 and quantities, see https://github.com/OpenSourceBrain/osb-model-validation/issues/150 --- .github/workflows/ci.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 9b47ec9..026dcb1 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -34,6 +34,8 @@ jobs: run: | pip install . pip install .[dev] + pip install "numpy<2.4" # Issue with numpy 2.4 and quantities, see https://github.com/OpenSourceBrain/osb-model-validation/issues/150 + - name: Lint with flake8