From 5980ed45b04643555c9c8e086a6664be586cddcf Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Fri, 16 Jan 2026 10:53:44 +0000 Subject: [PATCH 1/9] Remove pin on numpy; quantities issue solved... --- .github/workflows/ci.yml | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 6e001e7..782fb45 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -67,10 +67,9 @@ jobs: #sudo apt install octave sudo apt-get install -y subversion # for neuroConstruct full install... - - name: Install numpy < 2 (or <2.4) if necessary... + - name: Install numpy < 2 if necessary... run: | - pip install "numpy<2.4" # Issue with numpy 2.4 and quantities, see https://github.com/OpenSourceBrain/osb-model-validation/issues/150 - + if [[ ${{ matrix.engine }} == *"MOOSE"* ]] || [[ ${{ matrix.engine }} == *"Moose"* ]]; then pip install "numpy<2" ; fi ; pip list From ea7d17e8a5847ba930c57fd48253cd39ed29f587 Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Fri, 16 Jan 2026 11:38:47 +0000 Subject: [PATCH 2/9] Update default Brian2 version to 2.10.1 - test if it works with numpy>=2.4 --- omv/engines/getbrian2.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/omv/engines/getbrian2.py b/omv/engines/getbrian2.py index dc42663..6b98ad2 100644 --- a/omv/engines/getbrian2.py +++ b/omv/engines/getbrian2.py @@ -5,7 +5,7 @@ def install_brian2(version): if not version: - version = "2.9.0" + version = "2.10.1" try: pip_install("brian2", version) import brian2 From e782f49b26d3c31daeded849e2f861ce65fd3ff5 Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Mon, 2 Feb 2026 14:15:56 +0000 Subject: [PATCH 3/9] Update Python version to 3.12 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 782fb45..dc2c6ba 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -15,7 +15,7 @@ jobs: strategy: fail-fast: false matrix: - python-version: [ "3.11" ] + python-version: [ "3.12" ] engine: - Arbor - "Brian2:2.9.0" From 260ceea9c24650e0746feb4703045162e01df176 Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Fri, 20 Mar 2026 11:03:45 +0000 Subject: [PATCH 4/9] Back to py3.11 for now --- .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 dc2c6ba..782fb45 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -15,7 +15,7 @@ jobs: strategy: fail-fast: false matrix: - python-version: [ "3.12" ] + python-version: [ "3.11" ] engine: - Arbor - "Brian2:2.9.0" From 9207aec61c91af21d9838722574cfbb3a066ffb4 Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Fri, 20 Mar 2026 11:11:35 +0000 Subject: [PATCH 5/9] Back to py3.12 for brian, setuptools install for eden... --- .github/workflows/ci.yml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 782fb45..d0ebd16 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -15,7 +15,7 @@ jobs: strategy: fail-fast: false matrix: - python-version: [ "3.11" ] + python-version: [ "3.12" ] engine: - Arbor - "Brian2:2.9.0" @@ -67,6 +67,8 @@ jobs: #sudo apt install octave sudo apt-get install -y subversion # for neuroConstruct full install... + pip install setuptools --upgrade # needed for Eden on Python 3.12 + - name: Install numpy < 2 if necessary... run: | From 84aa94261487920726f55e8fcf82af8270eb5ad1 Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Fri, 20 Mar 2026 11:31:37 +0000 Subject: [PATCH 6/9] Test fix for eden --- .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 d0ebd16..2262a26 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -67,7 +67,7 @@ jobs: #sudo apt install octave sudo apt-get install -y subversion # for neuroConstruct full install... - pip install setuptools --upgrade # needed for Eden on Python 3.12 + pip install setuptools==80 # needed for eden on Python 3.12... - name: Install numpy < 2 if necessary... run: | From 7f4b7190c07841a33bc72abf189682d4351dd8d5 Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Fri, 20 Mar 2026 11:54:00 +0000 Subject: [PATCH 7/9] test moose v4.1.4 --- .github/workflows/ci.yml | 4 ++-- .github/workflows/python-publish.yml | 4 ++-- omv/engines/getmoose.py | 1 + 3 files changed, 5 insertions(+), 4 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 2262a26..6842e3a 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -54,9 +54,9 @@ jobs: - XPP 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 }} diff --git a/.github/workflows/python-publish.yml b/.github/workflows/python-publish.yml index c6848ef..3778433 100644 --- a/.github/workflows/python-publish.yml +++ b/.github/workflows/python-publish.yml @@ -11,9 +11,9 @@ jobs: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@v6 - name: Set up Python - uses: actions/setup-python@v5 + uses: actions/setup-python@v6 with: python-version: "3.x" - name: Install pypa/build diff --git a/omv/engines/getmoose.py b/omv/engines/getmoose.py index fbc2da4..acafe69 100644 --- a/omv/engines/getmoose.py +++ b/omv/engines/getmoose.py @@ -4,6 +4,7 @@ def install_moose(version): if not version: version = "4.0.0.dev20240411" + version = "4.1.4" try: pip_install("pymoose", version) import moose From 51eb85646d7d0742b5f9ad5b9139993fdc3ebd7c Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Fri, 20 Mar 2026 11:57:28 +0000 Subject: [PATCH 8/9] Add install of pint for moose --- omv/engines/getmoose.py | 1 + 1 file changed, 1 insertion(+) diff --git a/omv/engines/getmoose.py b/omv/engines/getmoose.py index acafe69..c892f25 100644 --- a/omv/engines/getmoose.py +++ b/omv/engines/getmoose.py @@ -7,6 +7,7 @@ def install_moose(version): version = "4.1.4" try: pip_install("pymoose", version) + pip_install("pint") import moose m = "Successfully installed MOOSE..." From f3c370574a37483e9df421c4843cec8fc6b19e65 Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Fri, 20 Mar 2026 12:03:00 +0000 Subject: [PATCH 9/9] Temp disable moose test... --- .github/workflows/ci.yml | 2 +- omv/engines/getmoose.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 6842e3a..ffaec20 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -49,9 +49,9 @@ jobs: - pyNeuroML - pyNeuroML_validate_sbml - pyNEURON_XPP_LEMS - - jNeuroML_Moose - MOOSE:3.1.5 - XPP + # - jNeuroML_Moose # not yet working on py3.12 steps: - uses: actions/checkout@v6 diff --git a/omv/engines/getmoose.py b/omv/engines/getmoose.py index c892f25..3e258c2 100644 --- a/omv/engines/getmoose.py +++ b/omv/engines/getmoose.py @@ -4,7 +4,7 @@ def install_moose(version): if not version: version = "4.0.0.dev20240411" - version = "4.1.4" + version = "4.1.4" # temp test this, it is the latest on pypi... try: pip_install("pymoose", version) pip_install("pint")