From 4a08eb100cd1c6341c7029c095175b094b8442a1 Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Wed, 24 Jun 2026 14:31:20 +0100 Subject: [PATCH 01/12] Upgrade actions/checkout from v6 to v7 --- .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 82d694b..438d74d 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -19,7 +19,7 @@ jobs: HDF5_DISABLE_VERSION_CHECK: 1 steps: - - uses: actions/checkout@v6 + - uses: actions/checkout@v7 - name: Set up Python ${{ matrix.python-version }} uses: actions/setup-python@v6 with: From d63e75855b5adb7bf892110edcad44d7244f8572 Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Fri, 31 Jul 2026 10:27:45 +0100 Subject: [PATCH 02/12] Also test on test* branches --- .github/workflows/ci.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 438d74d..8ca7715 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -2,9 +2,9 @@ name: Continuous builds on: push: - branches: [ master, development, experimental, modelspec ] + branches: [ master, development, experimental, modelspec, test* ] pull_request: - branches: [ master, development, experimental, modelspec ] + branches: [ master, development, experimental, modelspec, test* ] jobs: build: From a3d24711de698091646537bdde1b5d019f7012b7 Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Fri, 31 Jul 2026 10:27:56 +0100 Subject: [PATCH 03/12] Add dependabot file --- .github/dependabot.yml | 14 ++++++++++++++ 1 file changed, 14 insertions(+) create mode 100644 .github/dependabot.yml diff --git a/.github/dependabot.yml b/.github/dependabot.yml new file mode 100644 index 0000000..28cb43e --- /dev/null +++ b/.github/dependabot.yml @@ -0,0 +1,14 @@ +# Source - https://stackoverflow.com/a/78380165 +# Posted by Stefan, modified by community. See post 'Timeline' for change history +# Retrieved 2026-04-14, License - CC BY-SA 4.0 + +# Set update schedule for GitHub Actions + +version: 2 +updates: + + - package-ecosystem: "github-actions" + directory: "/" + schedule: + # Check for updates to GitHub Actions every week + interval: "weekly" From 1d0eaf633dcee8727c95735cb38982cc2fd2c1ce Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Fri, 31 Jul 2026 10:35:14 +0100 Subject: [PATCH 04/12] Add test* to test branches --- .github/workflows/ci.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index f36109b..0c96292 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -2,9 +2,9 @@ name: Continuous builds on: push: - branches: [ master, development, experimental, modelspec ] + branches: [ master, development, experimental, modelspec, test* ] pull_request: - branches: [ master, development, experimental, modelspec ] + branches: [ master, development, experimental, modelspec, test* ] jobs: build: From e5fe0a695278944b617b13aba86ca1a5f5e03f27 Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Fri, 31 Jul 2026 10:35:21 +0100 Subject: [PATCH 05/12] Add dependabot --- .github/dependabot.yml | 14 ++++++++++++++ 1 file changed, 14 insertions(+) create mode 100644 .github/dependabot.yml diff --git a/.github/dependabot.yml b/.github/dependabot.yml new file mode 100644 index 0000000..28cb43e --- /dev/null +++ b/.github/dependabot.yml @@ -0,0 +1,14 @@ +# Source - https://stackoverflow.com/a/78380165 +# Posted by Stefan, modified by community. See post 'Timeline' for change history +# Retrieved 2026-04-14, License - CC BY-SA 4.0 + +# Set update schedule for GitHub Actions + +version: 2 +updates: + + - package-ecosystem: "github-actions" + directory: "/" + schedule: + # Check for updates to GitHub Actions every week + interval: "weekly" From 8ef0d50d02c7e89def0cd99a3396ad9243a2a48f Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Fri, 31 Jul 2026 10:35:54 +0100 Subject: [PATCH 06/12] Update GHA versions --- .github/workflows/ci.yml | 4 ++-- .github/workflows/python-publish.yml | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 0c96292..2fc4251 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -19,9 +19,9 @@ jobs: HDF5_DISABLE_VERSION_CHECK: 1 steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@v7 - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v5 + uses: actions/setup-python@v7 with: python-version: ${{ matrix.python-version }} diff --git a/.github/workflows/python-publish.yml b/.github/workflows/python-publish.yml index 85cc411..912b67a 100644 --- a/.github/workflows/python-publish.yml +++ b/.github/workflows/python-publish.yml @@ -18,9 +18,9 @@ jobs: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@v7 - name: Set up Python - uses: actions/setup-python@v5 + uses: actions/setup-python@v7 with: python-version: '3.x' - name: Install dependencies From f41a54211bcf4b9345fab7ed737b882bf954582e Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Fri, 31 Jul 2026 11:12:44 +0100 Subject: [PATCH 07/12] Latest ci.yml --- .github/workflows/ci.yml | 14 ++++++-------- 1 file changed, 6 insertions(+), 8 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 2fc4251..2695aef 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -13,7 +13,7 @@ jobs: strategy: fail-fast: false matrix: - python-version: ["3.8", "3.9", "3.10", "3.11"] + python-version: ["3.10", "3.11", "3.12", "3.13"] env: JNML_HOME: "/home/runner/work/NeuroMLlite/NeuroMLlite/jNeuroML" HDF5_DISABLE_VERSION_CHECK: 1 @@ -29,14 +29,12 @@ jobs: run: | python -m pip install --upgrade pip pip install flake8 + pip install setuptools==80 # needed for eden on Python 3.12... - name: Install NeuroMLlite and extra requirements run: | pip install . - pip install -r requirements-extra.txt - - #pip install 'numpy<=1.23.0' # temp fix, see https://github.com/OpenSourceBrain/osb-model-validation/issues/91 - + pip install .[dev] - name: Lint with flake8 run: | @@ -57,8 +55,7 @@ jobs: git clone https://github.com/NeuroML/pyNeuroML.git cd pyNeuroML git checkout $pynml_branch - pip install pandas==1.3.5 - pip install 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 - @@ -93,7 +90,7 @@ jobs: - name: Install some simulators for testing run: | - #pip install cython + pip install "cython<3.1.0" # for nest... omv install NEURON pip install NetPyNE # strange issues on py3.7 with omv install... omv install PyNN @@ -108,6 +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 79bca3676eedda49fc3fc79ab64965f5bdb5c5b1 Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Fri, 31 Jul 2026 11:40:52 +0100 Subject: [PATCH 08/12] Master not working with py3.13 yet --- .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 2695aef..d572e4b 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"] env: JNML_HOME: "/home/runner/work/NeuroMLlite/NeuroMLlite/jNeuroML" HDF5_DISABLE_VERSION_CHECK: 1 From 31a358851fbd5b3706a56cd5bc61621c1c6675e6 Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Fri, 31 Jul 2026 11:41:53 +0100 Subject: [PATCH 09/12] Test also 3.14 --- .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 d572e4b..9551b23 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"] + 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 8300fd91f7c773845958b86c59f59003d1a24e04 Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Fri, 31 Jul 2026 11:45:06 +0100 Subject: [PATCH 10/12] Ruff format --- neuromllite/GraphVizHandler.py | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/neuromllite/GraphVizHandler.py b/neuromllite/GraphVizHandler.py index 182bca4..dbfd6d2 100644 --- a/neuromllite/GraphVizHandler.py +++ b/neuromllite/GraphVizHandler.py @@ -545,7 +545,7 @@ def handle_population( else: fcolor = "#ffffff" - print_v('Color %s -> %s -> %s'%(properties['color'], rgb, color)) + print_v("Color %s -> %s -> %s" % (properties["color"], rgb, color)) if properties and "type" in properties: self.pop_types[population_id] = properties["type"] @@ -634,7 +634,6 @@ def handle_projection( self.proj_post_pops[projName] = postPop self.proj_types[projName] = type - if type == "continuousProjection": shape = self.CONT_CONN_ARROW_SHAPE line = "solid" @@ -646,7 +645,7 @@ def handle_projection( if type == "electricalProjection": shape = self.GAP_CONN_ARROW_SHAPE line = "dashed" - + if synapse_obj: self.proj_syn_objs[projName] = synapse_obj erev = self.get_reversal_potential_mV(synapse_obj) From 21614612aa898232e001b702910bc481e8326ab7 Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Fri, 31 Jul 2026 11:55:47 +0100 Subject: [PATCH 11/12] To v0.6.2 --- docs/NeuroMLlite_specification.json | 2 +- docs/NeuroMLlite_specification.yaml | 2 +- docs/README.md | 2 +- examples/BBP_5percent.json | 2 +- examples/Example10_Lorenz.json | 2 +- examples/Example11_Synapses.json | 2 +- examples/Example11_Synapses.net.nml | 2 +- examples/Example12_MultiComp.json | 2 +- examples/Example1_TestNetwork.json | 2 +- examples/Example2_TestNetwork.json | 2 +- examples/Example2_TestNetwork.net.nml | 2 +- examples/Example3_Network.json | 2 +- examples/Example3_Network.net.nml | 2 +- examples/Example4_PyNN.json | 2 +- examples/Example4_PyNN.net.nml | 2 +- examples/Example4_PyNN.yaml | 2 +- examples/Example6_PyNN.json | 2 +- examples/Example6_PyNN.net.nml | 2 +- examples/Example6_PyNN_noinputs.json | 2 +- examples/Example6_PyNN_noinputs.net.nml | 2 +- examples/Example7_Brunel2000.json | 2 +- examples/Example7_Brunel2000.net.nml | 2 +- examples/Example8_Extension.json | 2 +- examples/Example9_HindmarshRose.json | 2 +- examples/SimExample10.json | 2 +- examples/SimExample11.json | 2 +- examples/SimExample12_MultiComp.json | 2 +- examples/SimExample3.json | 2 +- examples/SimExample4.json | 2 +- examples/SimExample4.yaml | 2 +- examples/SimExample6_PyNN.json | 2 +- examples/SimExample7.json | 2 +- examples/SimExample8.json | 2 +- examples/SimExample9.json | 2 +- examples/arbor/ArborExample.json | 2 +- examples/arbor/ArborExample.yaml | 2 +- examples/arbor/SimArborExample.json | 2 +- examples/arbor/SimArborExample.yaml | 2 +- examples/spikeratetest/SimSpikers.json | 2 +- examples/spikeratetest/Spikers.json | 2 +- neuromllite/__init__.py | 2 +- 41 files changed, 41 insertions(+), 41 deletions(-) diff --git a/docs/NeuroMLlite_specification.json b/docs/NeuroMLlite_specification.json index 199830d..aa4c1e7 100644 --- a/docs/NeuroMLlite_specification.json +++ b/docs/NeuroMLlite_specification.json @@ -1,5 +1,5 @@ { - "version": "NeuroMLlite v0.6.1", + "version": "NeuroMLlite v0.6.2", "specification": { "Network": { "definition": "A Network containing multiple Population's, connected by Projection's and receiving Input's", diff --git a/docs/NeuroMLlite_specification.yaml b/docs/NeuroMLlite_specification.yaml index 1fdd1db..406cf37 100644 --- a/docs/NeuroMLlite_specification.yaml +++ b/docs/NeuroMLlite_specification.yaml @@ -1,4 +1,4 @@ -version: NeuroMLlite v0.6.1 +version: NeuroMLlite v0.6.2 specification: Network: definition: A Network containing multiple Population's, connected by Projection's diff --git a/docs/README.md b/docs/README.md index d7901b8..1065238 100644 --- a/docs/README.md +++ b/docs/README.md @@ -1,4 +1,4 @@ -# Specification of NeuroMLlite v0.6.1 +# Specification of NeuroMLlite v0.6.2 **Note: the NeuroMLlite specification is still in development! Subject to change...** ## Network diff --git a/examples/BBP_5percent.json b/examples/BBP_5percent.json index ed1ce36..c8bdfc7 100644 --- a/examples/BBP_5percent.json +++ b/examples/BBP_5percent.json @@ -1,6 +1,6 @@ { "BBP_5percent": { - "version": "NeuroMLlite v0.6.1", + "version": "NeuroMLlite v0.6.2", "notes": "A network with the Blue Brain Project connectivity data (%s% of total cells)", "cells": { "hhcell": { diff --git a/examples/Example10_Lorenz.json b/examples/Example10_Lorenz.json index 9a51de5..bf759f3 100644 --- a/examples/Example10_Lorenz.json +++ b/examples/Example10_Lorenz.json @@ -1,6 +1,6 @@ { "Example10_Lorenz": { - "version": "NeuroMLlite v0.6.1", + "version": "NeuroMLlite v0.6.2", "notes": "Example 10: Lorenz", "parameters": { "N": 1, diff --git a/examples/Example11_Synapses.json b/examples/Example11_Synapses.json index 50a0e2f..5665f58 100644 --- a/examples/Example11_Synapses.json +++ b/examples/Example11_Synapses.json @@ -1,6 +1,6 @@ { "Example11_Synapses": { - "version": "NeuroMLlite v0.6.1", + "version": "NeuroMLlite v0.6.2", "notes": "Example 11: synaptic properties", "parameters": { "input_amp": 0.23, diff --git a/examples/Example11_Synapses.net.nml b/examples/Example11_Synapses.net.nml index 024d122..b8705c8 100644 --- a/examples/Example11_Synapses.net.nml +++ b/examples/Example11_Synapses.net.nml @@ -1,5 +1,5 @@ - Generated by NeuroMLlite v0.6.1 + Generated by NeuroMLlite v0.6.2 Generated network: Example11_Synapses Generation seed: 1234 NeuroMLlite parameters: diff --git a/examples/Example12_MultiComp.json b/examples/Example12_MultiComp.json index 705a841..66d64e5 100644 --- a/examples/Example12_MultiComp.json +++ b/examples/Example12_MultiComp.json @@ -1,6 +1,6 @@ { "Example12_MultiComp": { - "version": "NeuroMLlite v0.6.1", + "version": "NeuroMLlite v0.6.2", "notes": "Example 12: Multicompartmental cells...", "parameters": { "N": 20, diff --git a/examples/Example1_TestNetwork.json b/examples/Example1_TestNetwork.json index e291fad..649b77f 100644 --- a/examples/Example1_TestNetwork.json +++ b/examples/Example1_TestNetwork.json @@ -1,6 +1,6 @@ { "TestNetwork": { - "version": "NeuroMLlite v0.6.1", + "version": "NeuroMLlite v0.6.2", "notes": "A simple network with 2 populations & projection between them. No info yet on what the cells are so network can't be simulated.", "populations": { "pop0": { diff --git a/examples/Example2_TestNetwork.json b/examples/Example2_TestNetwork.json index d6f09a9..7d45160 100644 --- a/examples/Example2_TestNetwork.json +++ b/examples/Example2_TestNetwork.json @@ -1,6 +1,6 @@ { "Example2_TestNetwork": { - "version": "NeuroMLlite v0.6.1", + "version": "NeuroMLlite v0.6.2", "notes": "A simple network with 2 populations & projection between them. Cells are specified to be NeuroML 2 HH cell models & pre population is given a spiking input.", "cells": { "hhcell": { diff --git a/examples/Example2_TestNetwork.net.nml b/examples/Example2_TestNetwork.net.nml index 9e77286..db7a6f9 100644 --- a/examples/Example2_TestNetwork.net.nml +++ b/examples/Example2_TestNetwork.net.nml @@ -1,5 +1,5 @@ - Generated by NeuroMLlite v0.6.1 + Generated by NeuroMLlite v0.6.2 Generated network: Example2_TestNetwork Generation seed: 1234 diff --git a/examples/Example3_Network.json b/examples/Example3_Network.json index 85909f7..80e36a7 100644 --- a/examples/Example3_Network.json +++ b/examples/Example3_Network.json @@ -1,6 +1,6 @@ { "Example3_Network": { - "version": "NeuroMLlite v0.6.1", + "version": "NeuroMLlite v0.6.2", "notes": "Example 3: simple network with 2 populations of NeuroML2 cells, a projection between them and spiking input.", "cells": { "hhcell": { diff --git a/examples/Example3_Network.net.nml b/examples/Example3_Network.net.nml index 26d8500..1ebcb8c 100644 --- a/examples/Example3_Network.net.nml +++ b/examples/Example3_Network.net.nml @@ -1,5 +1,5 @@ - Generated by NeuroMLlite v0.6.1 + Generated by NeuroMLlite v0.6.2 Generated network: Example3_Network Generation seed: 1234 diff --git a/examples/Example4_PyNN.json b/examples/Example4_PyNN.json index 572561e..9e79d1f 100644 --- a/examples/Example4_PyNN.json +++ b/examples/Example4_PyNN.json @@ -1,6 +1,6 @@ { "Example4_PyNN": { - "version": "NeuroMLlite v0.6.1", + "version": "NeuroMLlite v0.6.2", "notes": "Example 4: a network with PyNN cells & inputs", "parameters": { "input_amp": 0.99 diff --git a/examples/Example4_PyNN.net.nml b/examples/Example4_PyNN.net.nml index cb4202c..f6a9d7f 100644 --- a/examples/Example4_PyNN.net.nml +++ b/examples/Example4_PyNN.net.nml @@ -1,5 +1,5 @@ - Generated by NeuroMLlite v0.6.1 + Generated by NeuroMLlite v0.6.2 Generated network: Example4_PyNN Generation seed: 1234 NeuroMLlite parameters: diff --git a/examples/Example4_PyNN.yaml b/examples/Example4_PyNN.yaml index 783a442..1be96ec 100644 --- a/examples/Example4_PyNN.yaml +++ b/examples/Example4_PyNN.yaml @@ -1,5 +1,5 @@ Example4_PyNN: - version: NeuroMLlite v0.6.1 + version: NeuroMLlite v0.6.2 notes: 'Example 4: a network with PyNN cells & inputs' parameters: input_amp: 0.99 diff --git a/examples/Example6_PyNN.json b/examples/Example6_PyNN.json index ed7929d..6d8ada3 100644 --- a/examples/Example6_PyNN.json +++ b/examples/Example6_PyNN.json @@ -1,6 +1,6 @@ { "Example6_PyNN": { - "version": "NeuroMLlite v0.6.1", + "version": "NeuroMLlite v0.6.2", "notes": "Another network for PyNN - work in progress...", "parameters": { "N_scaling": 0.005, diff --git a/examples/Example6_PyNN.net.nml b/examples/Example6_PyNN.net.nml index 3bf815f..84d0427 100644 --- a/examples/Example6_PyNN.net.nml +++ b/examples/Example6_PyNN.net.nml @@ -1,5 +1,5 @@ - Generated by NeuroMLlite v0.6.1 + Generated by NeuroMLlite v0.6.2 Generated network: Example6_PyNN Generation seed: 1234 NeuroMLlite parameters: diff --git a/examples/Example6_PyNN_noinputs.json b/examples/Example6_PyNN_noinputs.json index 71664a8..22c1e7b 100644 --- a/examples/Example6_PyNN_noinputs.json +++ b/examples/Example6_PyNN_noinputs.json @@ -1,6 +1,6 @@ { "Example6_PyNN_noinputs": { - "version": "NeuroMLlite v0.6.1", + "version": "NeuroMLlite v0.6.2", "notes": "Another network for PyNN - work in progress...", "parameters": { "N_scaling": 0.005, diff --git a/examples/Example6_PyNN_noinputs.net.nml b/examples/Example6_PyNN_noinputs.net.nml index d110bb3..ad33567 100644 --- a/examples/Example6_PyNN_noinputs.net.nml +++ b/examples/Example6_PyNN_noinputs.net.nml @@ -1,5 +1,5 @@ - Generated by NeuroMLlite v0.6.1 + Generated by NeuroMLlite v0.6.2 Generated network: Example6_PyNN_noinputs Generation seed: 1234 NeuroMLlite parameters: diff --git a/examples/Example7_Brunel2000.json b/examples/Example7_Brunel2000.json index 05d3376..bc59c06 100644 --- a/examples/Example7_Brunel2000.json +++ b/examples/Example7_Brunel2000.json @@ -1,6 +1,6 @@ { "Example7_Brunel2000": { - "version": "NeuroMLlite v0.6.1", + "version": "NeuroMLlite v0.6.2", "notes": "Example 7: based on network of Brunel 2000", "parameters": { "g": 4, diff --git a/examples/Example7_Brunel2000.net.nml b/examples/Example7_Brunel2000.net.nml index 2944bea..f46a110 100644 --- a/examples/Example7_Brunel2000.net.nml +++ b/examples/Example7_Brunel2000.net.nml @@ -1,5 +1,5 @@ - Generated by NeuroMLlite v0.6.1 + Generated by NeuroMLlite v0.6.2 Generated network: Example7_Brunel2000 Generation seed: 1234 NeuroMLlite parameters: diff --git a/examples/Example8_Extension.json b/examples/Example8_Extension.json index 71dc1ac..c66269f 100644 --- a/examples/Example8_Extension.json +++ b/examples/Example8_Extension.json @@ -1,6 +1,6 @@ { "Example8_Extension": { - "version": "NeuroMLlite v0.6.1", + "version": "NeuroMLlite v0.6.2", "notes": "Example 8: general testing...", "parameters": { "N": 10, diff --git a/examples/Example9_HindmarshRose.json b/examples/Example9_HindmarshRose.json index c0302df..01bb7b2 100644 --- a/examples/Example9_HindmarshRose.json +++ b/examples/Example9_HindmarshRose.json @@ -1,6 +1,6 @@ { "Example9_HindmarshRose": { - "version": "NeuroMLlite v0.6.1", + "version": "NeuroMLlite v0.6.2", "notes": "Example 9: HindmarshRose", "parameters": { "N": 1, diff --git a/examples/SimExample10.json b/examples/SimExample10.json index 7c2ab4f..46ccc90 100644 --- a/examples/SimExample10.json +++ b/examples/SimExample10.json @@ -1,6 +1,6 @@ { "SimExample10": { - "version": "NeuroMLlite v0.6.1", + "version": "NeuroMLlite v0.6.2", "network": "Example10_Lorenz.json", "duration": 10000.0, "dt": 1.0, diff --git a/examples/SimExample11.json b/examples/SimExample11.json index 2e3abbf..c6208b7 100644 --- a/examples/SimExample11.json +++ b/examples/SimExample11.json @@ -1,6 +1,6 @@ { "SimExample11": { - "version": "NeuroMLlite v0.6.1", + "version": "NeuroMLlite v0.6.2", "network": "Example11_Synapses.json", "duration": 1000.0, "dt": 0.01, diff --git a/examples/SimExample12_MultiComp.json b/examples/SimExample12_MultiComp.json index 894aac7..dc462d4 100644 --- a/examples/SimExample12_MultiComp.json +++ b/examples/SimExample12_MultiComp.json @@ -1,6 +1,6 @@ { "SimExample12_MultiComp": { - "version": "NeuroMLlite v0.6.1", + "version": "NeuroMLlite v0.6.2", "network": "Example12_MultiComp.json", "duration": 1000.0, "dt": 0.025, diff --git a/examples/SimExample3.json b/examples/SimExample3.json index edeaf23..765e33f 100644 --- a/examples/SimExample3.json +++ b/examples/SimExample3.json @@ -1,6 +1,6 @@ { "SimExample3": { - "version": "NeuroMLlite v0.6.1", + "version": "NeuroMLlite v0.6.2", "network": "Example3_Network.json", "duration": 1000.0, "dt": 0.025, diff --git a/examples/SimExample4.json b/examples/SimExample4.json index 1c7a811..5f07d6e 100644 --- a/examples/SimExample4.json +++ b/examples/SimExample4.json @@ -1,6 +1,6 @@ { "SimExample4": { - "version": "NeuroMLlite v0.6.1", + "version": "NeuroMLlite v0.6.2", "network": "Example4_PyNN.json", "duration": 1000.0, "dt": 0.01, diff --git a/examples/SimExample4.yaml b/examples/SimExample4.yaml index 275a147..d5a3a6c 100644 --- a/examples/SimExample4.yaml +++ b/examples/SimExample4.yaml @@ -1,5 +1,5 @@ SimExample4: - version: NeuroMLlite v0.6.1 + version: NeuroMLlite v0.6.2 network: Example4_PyNN.yaml duration: 1000.0 dt: 0.01 diff --git a/examples/SimExample6_PyNN.json b/examples/SimExample6_PyNN.json index 4eb841e..dc3e71b 100644 --- a/examples/SimExample6_PyNN.json +++ b/examples/SimExample6_PyNN.json @@ -1,6 +1,6 @@ { "SimExample6_PyNN": { - "version": "NeuroMLlite v0.6.1", + "version": "NeuroMLlite v0.6.2", "network": "Example6_PyNN.json", "duration": 100.0, "dt": 0.025, diff --git a/examples/SimExample7.json b/examples/SimExample7.json index bceaae3..89ee354 100644 --- a/examples/SimExample7.json +++ b/examples/SimExample7.json @@ -1,6 +1,6 @@ { "SimExample7": { - "version": "NeuroMLlite v0.6.1", + "version": "NeuroMLlite v0.6.2", "network": "Example7_Brunel2000.json", "duration": 1000.0, "dt": 0.025, diff --git a/examples/SimExample8.json b/examples/SimExample8.json index bcc3ff1..89a340d 100644 --- a/examples/SimExample8.json +++ b/examples/SimExample8.json @@ -1,6 +1,6 @@ { "SimExample8": { - "version": "NeuroMLlite v0.6.1", + "version": "NeuroMLlite v0.6.2", "network": "Example8_Extension.json", "duration": 1000.0, "dt": 0.025, diff --git a/examples/SimExample9.json b/examples/SimExample9.json index f6effbe..f1da93b 100644 --- a/examples/SimExample9.json +++ b/examples/SimExample9.json @@ -1,6 +1,6 @@ { "SimExample9": { - "version": "NeuroMLlite v0.6.1", + "version": "NeuroMLlite v0.6.2", "network": "Example9_HindmarshRose.json", "duration": 1000000.0, "dt": 25.0, diff --git a/examples/arbor/ArborExample.json b/examples/arbor/ArborExample.json index b07b57e..08236ca 100644 --- a/examples/arbor/ArborExample.json +++ b/examples/arbor/ArborExample.json @@ -1,6 +1,6 @@ { "ArborExample": { - "version": "NeuroMLlite v0.6.1", + "version": "NeuroMLlite v0.6.2", "notes": "Example for testing Arbor", "parameters": { "v_init": -50, diff --git a/examples/arbor/ArborExample.yaml b/examples/arbor/ArborExample.yaml index d35eeb9..4faeb01 100644 --- a/examples/arbor/ArborExample.yaml +++ b/examples/arbor/ArborExample.yaml @@ -1,5 +1,5 @@ ArborExample: - version: NeuroMLlite v0.6.1 + version: NeuroMLlite v0.6.2 notes: Example for testing Arbor parameters: v_init: -50 diff --git a/examples/arbor/SimArborExample.json b/examples/arbor/SimArborExample.json index 9ef4674..c8cf787 100644 --- a/examples/arbor/SimArborExample.json +++ b/examples/arbor/SimArborExample.json @@ -1,6 +1,6 @@ { "SimArborExample": { - "version": "NeuroMLlite v0.6.1", + "version": "NeuroMLlite v0.6.2", "network": "ArborExample.json", "duration": 100.0, "dt": 0.01, diff --git a/examples/arbor/SimArborExample.yaml b/examples/arbor/SimArborExample.yaml index 06869d1..9474578 100644 --- a/examples/arbor/SimArborExample.yaml +++ b/examples/arbor/SimArborExample.yaml @@ -1,5 +1,5 @@ SimArborExample: - version: NeuroMLlite v0.6.1 + version: NeuroMLlite v0.6.2 network: ArborExample.yaml duration: 100.0 dt: 0.01 diff --git a/examples/spikeratetest/SimSpikers.json b/examples/spikeratetest/SimSpikers.json index dded3da..a05f1fc 100644 --- a/examples/spikeratetest/SimSpikers.json +++ b/examples/spikeratetest/SimSpikers.json @@ -1,6 +1,6 @@ { "SimSpikers": { - "version": "NeuroMLlite v0.6.1", + "version": "NeuroMLlite v0.6.2", "network": "Spikers.json", "duration": 10000.0, "dt": 0.025, diff --git a/examples/spikeratetest/Spikers.json b/examples/spikeratetest/Spikers.json index 34d090b..2831cde 100644 --- a/examples/spikeratetest/Spikers.json +++ b/examples/spikeratetest/Spikers.json @@ -1,6 +1,6 @@ { "Spikers": { - "version": "NeuroMLlite v0.6.1", + "version": "NeuroMLlite v0.6.2", "notes": "Example with spiking entities..", "parameters": { "N": 10, diff --git a/neuromllite/__init__.py b/neuromllite/__init__.py index 7d2898c..ecde2a4 100644 --- a/neuromllite/__init__.py +++ b/neuromllite/__init__.py @@ -1,6 +1,6 @@ import collections -__version__ = "0.6.1" +__version__ = "0.6.2" # import pyNN # import nest From 03c21362878fb9de53aa753b9edc97507a9e0418 Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Fri, 31 Jul 2026 12:24:32 +0100 Subject: [PATCH 12/12] Disable 3.14 due to neuron --- .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 9551b23..d850fa1 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"] #, "3.14" # Neuron not yet supported on 3.14 (need nrn<9.0) env: JNML_HOME: "/home/runner/work/NeuroMLlite/NeuroMLlite/jNeuroML" HDF5_DISABLE_VERSION_CHECK: 1