From 431c333643b2574f5de787abbb2a4cbcc7cd4485 Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Tue, 19 May 2026 11:05:38 +0100 Subject: [PATCH 1/8] Update checkout action version in CI workflow --- .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 4b71468..5a76b69 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -16,7 +16,7 @@ jobs: java: [ '8', '11', '16', '17', '19', '21', '25' ] steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@v6 - name: Set up JDK ${{ matrix.java }} uses: actions/setup-java@v4 From 0368382fa5a4111a09365fd4ae489450b2ad8858 Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Tue, 19 May 2026 11:42:31 +0100 Subject: [PATCH 2/8] Update versions in GHA --- .github/workflows/ci.yml | 2 +- .github/workflows/omv-ci.yml | 8 ++++---- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 5a76b69..32a7cec 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -19,7 +19,7 @@ jobs: - uses: actions/checkout@v6 - name: Set up JDK ${{ matrix.java }} - uses: actions/setup-java@v4 + uses: actions/setup-java@v5 with: java-version: ${{ matrix.java }} java-package: jdk diff --git a/.github/workflows/omv-ci.yml b/.github/workflows/omv-ci.yml index 9c218ef..2d0c812 100644 --- a/.github/workflows/omv-ci.yml +++ b/.github/workflows/omv-ci.yml @@ -15,7 +15,7 @@ jobs: strategy: fail-fast: false matrix: - python-version: [ "3.10", "3.12" ] + python-version: [ "3.12", "3.13" ] engine: - jNeuroML - jNeuroML_Brian2 @@ -30,10 +30,10 @@ jobs: engine: jNeuroML_MOOSE # MOOSE not yet working on py 3.12... steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@v6 - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v5 + uses: actions/setup-python@v6 with: python-version: ${{ matrix.python-version }} @@ -46,7 +46,7 @@ jobs: run: | pip install git+https://github.com/OpenSourceBrain/osb-model-validation pip install scipy sympy matplotlib cython pandas tables - pip install setuptools --upgrade # needed for Eden on py 3.12 + pip install setuptools==80 # needed for Eden on py >=3.12 From b6f05da94c5c748d5cf17e97641eac435c27fc04 Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Tue, 19 May 2026 12:03:24 +0100 Subject: [PATCH 3/8] Update Python versions in CI workflow --- .github/workflows/omv-ci.yml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.github/workflows/omv-ci.yml b/.github/workflows/omv-ci.yml index 2d0c812..52d9fae 100644 --- a/.github/workflows/omv-ci.yml +++ b/.github/workflows/omv-ci.yml @@ -15,7 +15,7 @@ jobs: strategy: fail-fast: false matrix: - python-version: [ "3.12", "3.13" ] + python-version: [ "3.11", "3.12" ] engine: - jNeuroML - jNeuroML_Brian2 @@ -28,6 +28,8 @@ jobs: exclude: - python-version: "3.12" engine: jNeuroML_MOOSE # MOOSE not yet working on py 3.12... + - python-version: "3.11" + engine: jNeuroML_Brian2 # Brian latest no longer working on py <3.12... steps: - uses: actions/checkout@v6 From 45bd6d70a5373bacad4e0f78e4acbe2603ad7bc8 Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Tue, 19 May 2026 13:14:05 +0100 Subject: [PATCH 4/8] test moose on 3.10 --- .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 52d9fae..3ec3ff6 100644 --- a/.github/workflows/omv-ci.yml +++ b/.github/workflows/omv-ci.yml @@ -15,7 +15,7 @@ jobs: strategy: fail-fast: false matrix: - python-version: [ "3.11", "3.12" ] + python-version: [ "3.10", "3.12" ] engine: - jNeuroML - jNeuroML_Brian2 @@ -28,7 +28,7 @@ jobs: exclude: - python-version: "3.12" engine: jNeuroML_MOOSE # MOOSE not yet working on py 3.12... - - python-version: "3.11" + - python-version: "3.10" engine: jNeuroML_Brian2 # Brian latest no longer working on py <3.12... steps: From 0b5e0ca3fa10ad64e85e7b3f999b8ba0f04d0996 Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Tue, 19 May 2026 15:23:04 +0100 Subject: [PATCH 5/8] Test without moose --- .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 3ec3ff6..cb26126 100644 --- a/.github/workflows/omv-ci.yml +++ b/.github/workflows/omv-ci.yml @@ -22,9 +22,9 @@ jobs: - jNeuroML_EDEN - jNeuroML_NEURON - jNeuroML_NetPyNE - - jNeuroML_MOOSE - jNeuroML_validate - PyLEMS_NeuroML2 + # - jNeuroML_MOOSE exclude: - python-version: "3.12" engine: jNeuroML_MOOSE # MOOSE not yet working on py 3.12... From 28f9ef114db57ff7ff65c96e19a1a9ea7517d037 Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Tue, 19 May 2026 15:26:22 +0100 Subject: [PATCH 6/8] Comment on moose --- .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 cb26126..950cfc8 100644 --- a/.github/workflows/omv-ci.yml +++ b/.github/workflows/omv-ci.yml @@ -24,7 +24,7 @@ jobs: - jNeuroML_NetPyNE - jNeuroML_validate - PyLEMS_NeuroML2 - # - jNeuroML_MOOSE + # - jNeuroML_MOOSE # MOOSE disabled, due to latest version not supporting recording/plotting of channel variables, as used in ex5 exclude: - python-version: "3.12" engine: jNeuroML_MOOSE # MOOSE not yet working on py 3.12... From 5b390b48b5baa2150dc244c2d410cfc9205fc99c Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Tue, 19 May 2026 15:29:38 +0100 Subject: [PATCH 7/8] Update tests --- .github/workflows/ci.yml | 9 +++++---- .github/workflows/omv-ci.yml | 24 ++++++++++++++++++------ 2 files changed, 23 insertions(+), 10 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 5408614..d34efef 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -13,13 +13,13 @@ jobs: strategy: fail-fast: false matrix: - java: [ '8', '11', '16', '17', '19', '21' ] + java: [ '8', '11', '17', '19', '21', '25' ] steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@v6 - name: Set up JDK ${{ matrix.java }} - uses: actions/setup-java@v4 + uses: actions/setup-java@v6 with: java-version: ${{ matrix.java }} java-package: jdk @@ -32,7 +32,8 @@ jobs: - name: Install jNeuroML run: | - export main_repo_branch=${GITHUB_REF##*/} + export main_repo_branch=${GITHUB_REF##*/} + if [[ ${main_repo_branch} == "osb_test_master" ]]; then main_repo_branch=master ; fi if [[ ${main_repo_branch} != "master" && ${main_repo_branch} != "development" && ${main_repo_branch} != "experimental" && ${main_repo_branch} != *"osb"* ]]; then main_repo_branch=development ; fi echo Using branch $main_repo_branch git clone https://github.com/NeuroML/jNeuroML.git diff --git a/.github/workflows/omv-ci.yml b/.github/workflows/omv-ci.yml index 898510b..950cfc8 100644 --- a/.github/workflows/omv-ci.yml +++ b/.github/workflows/omv-ci.yml @@ -1,6 +1,8 @@ name: Run OMV tests on: + schedule: + - cron: "1 1 27 * *" push: branches: [ master, development, experimental, documentation_update, osb*, update* ] pull_request: @@ -9,35 +11,45 @@ on: jobs: build: - runs-on: ubuntu-latest + runs-on: ubuntu-22.04 # for eden... strategy: fail-fast: false matrix: - python-version: [ "3.9" ] + python-version: [ "3.10", "3.12" ] engine: - jNeuroML - jNeuroML_Brian2 - jNeuroML_EDEN - jNeuroML_NEURON - jNeuroML_NetPyNE - - jNeuroML_MOOSE - jNeuroML_validate - PyLEMS_NeuroML2 + # - jNeuroML_MOOSE # MOOSE disabled, due to latest version not supporting recording/plotting of channel variables, as used in ex5 + exclude: + - python-version: "3.12" + engine: jNeuroML_MOOSE # MOOSE not yet working on py 3.12... + - python-version: "3.10" + engine: jNeuroML_Brian2 # Brian latest no longer working on py <3.12... steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@v6 - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v5 + uses: actions/setup-python@v6 with: python-version: ${{ matrix.python-version }} + - name: Install numpy < 2 if necessary... + run: | + if [[ ${{ matrix.engine }} == *"MOOSE"* ]] || [[ ${{ matrix.engine }} == *"Moose"* ]]; then pip install "numpy<2" ; fi ; + pip list + - name: Install OMV run: | pip install git+https://github.com/OpenSourceBrain/osb-model-validation pip install scipy sympy matplotlib cython pandas tables + pip install setuptools==80 # needed for Eden on py >=3.12 - pip install 'numpy<=1.23.0' # see https://github.com/OpenSourceBrain/osb-model-validation/issues/91 - name: Run OMV tests on engine ${{ matrix.engine }} From 0cd6878f5aef6ac48266e2feb852dd2d33f9b579 Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Tue, 19 May 2026 15:33:03 +0100 Subject: [PATCH 8/8] Wrong action version --- .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 d34efef..9ebfab8 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -19,7 +19,7 @@ jobs: - uses: actions/checkout@v6 - name: Set up JDK ${{ matrix.java }} - uses: actions/setup-java@v6 + uses: actions/setup-java@v5 with: java-version: ${{ matrix.java }} java-package: jdk