From 6288ccb040eefe25cf02d6f7b1e0270a632a1a02 Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Tue, 25 Nov 2025 18:01:47 +0000 Subject: [PATCH 1/5] Careful about numpy<2 --- .github/workflows/ci_pip.yml | 12 ++++++++++++ .github/workflows/omv-ci.yml | 10 +++++----- 2 files changed, 17 insertions(+), 5 deletions(-) diff --git a/.github/workflows/ci_pip.yml b/.github/workflows/ci_pip.yml index 5ccd708..4cd87a3 100644 --- a/.github/workflows/ci_pip.yml +++ b/.github/workflows/ci_pip.yml @@ -57,6 +57,18 @@ jobs: cd NeuroML2 python run_hhcell.py -nogui + + - name: Install OMV + run: | + pip install git+https://github.com/OpenSourceBrain/osb-model-validation + pip install scipy sympy matplotlib cython pandas tables + + - name: Run OMV tests + run: | + omv all -V + - name: Final version info run: | + + omv list -V # list installed engines pip list diff --git a/.github/workflows/omv-ci.yml b/.github/workflows/omv-ci.yml index de11a73..03d0a1d 100644 --- a/.github/workflows/omv-ci.yml +++ b/.github/workflows/omv-ci.yml @@ -25,17 +25,17 @@ jobs: with: python-version: ${{ matrix.python-version }} + - name: Install numpy < 2 if necessary... + run: | + if [[ ${{ matrix.python-version }} == '3.10' ]] || [[ ${{ matrix.python-version }} == '3.11' ]] || [[ ${{ matrix.python-version }} == '3.12' ]]; 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 - - name: Install numpy < 2 if necessary... - run: | - if [[ ${{ matrix.python-version }} == '3.10' ]] || [[ ${{ matrix.python-version }} == '3.11' ]]; then pip install "numpy<2" ; fi ; - pip list - - name: Run OMV tests on engine ${{ matrix.engine }} run: | omv all -V --engine=${{ matrix.engine }} From 3b229e1ec4345ae95409cb4b345180f598a2426d Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Tue, 25 Nov 2025 19:27:33 +0000 Subject: [PATCH 2/5] More test options --- .github/workflows/ci_pip.yml | 4 ++-- .github/workflows/omv-ci.yml | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/ci_pip.yml b/.github/workflows/ci_pip.yml index 4cd87a3..fd290c0 100644 --- a/.github/workflows/ci_pip.yml +++ b/.github/workflows/ci_pip.yml @@ -11,10 +11,11 @@ on: jobs: build: - runs-on: ubuntu-latest + runs-on: ${{ matrix.runs-on }} strategy: fail-fast: false matrix: + runs-on: [ubuntu-latest, ubuntu-22.04] python-version: ["3.9", "3.10", "3.11", "3.12"] # not yet working: "3.12"?? steps: @@ -34,7 +35,6 @@ jobs: pip list - name: Install numpy < 2 if necessary... - if: ${{ matrix.python-version == '3.11' }} run: | pip install "numpy<2" pip list diff --git a/.github/workflows/omv-ci.yml b/.github/workflows/omv-ci.yml index 03d0a1d..3a23c01 100644 --- a/.github/workflows/omv-ci.yml +++ b/.github/workflows/omv-ci.yml @@ -3,9 +3,9 @@ name: Continuous build using OMV on: push: - branches: [ master, development, experimental ] + branches: [ master, development, experimental, test* ] pull_request: - branches: [ master, development, experimental ] + branches: [ master, development, experimental, test* ] jobs: build: From 274d4f40b9450ba1e48090ee04b3e64ebe3fc18f Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Tue, 25 Nov 2025 19:36:02 +0000 Subject: [PATCH 3/5] Tweak test install & tolerance... --- .github/workflows/omv-ci.yml | 6 ++++-- NeuroML2/test_files/.test.hh.jnmlmoose.omt | 2 +- 2 files changed, 5 insertions(+), 3 deletions(-) diff --git a/.github/workflows/omv-ci.yml b/.github/workflows/omv-ci.yml index 3a23c01..509fcbe 100644 --- a/.github/workflows/omv-ci.yml +++ b/.github/workflows/omv-ci.yml @@ -14,7 +14,7 @@ jobs: strategy: fail-fast: false matrix: - python-version: [ "3.9", "3.10", "3.11", "3.12"] # not yet working: "3.12"?? + python-version: [ "3.9", "3.10", "3.11"] # not yet working: "3.12"?? engine: [ jNeuroML, jNeuroML_NEURON, jNeuroML_validate, jNeuroML_Moose, jNeuroML_EDEN, jNeuroML_NetPyNE ] steps: @@ -25,15 +25,17 @@ jobs: with: python-version: ${{ matrix.python-version }} + - name: Install numpy < 2 if necessary... run: | - if [[ ${{ matrix.python-version }} == '3.10' ]] || [[ ${{ matrix.python-version }} == '3.11' ]] || [[ ${{ matrix.python-version }} == '3.12' ]]; then pip install "numpy<2" ; fi ; + 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 --upgrade # needed for Eden on py 3.12 - name: Run OMV tests on engine ${{ matrix.engine }} diff --git a/NeuroML2/test_files/.test.hh.jnmlmoose.omt b/NeuroML2/test_files/.test.hh.jnmlmoose.omt index 90e43fe..88ba65e 100644 --- a/NeuroML2/test_files/.test.hh.jnmlmoose.omt +++ b/NeuroML2/test_files/.test.hh.jnmlmoose.omt @@ -14,4 +14,4 @@ experiments: spike detection: method: threshold threshold: 0 - tolerance: 0.0009566968781470178 + tolerance: 0.0014602215508559518 From 1d6114d2daf949f73c3d3ac9ae7841baf3f72b5d Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Tue, 25 Nov 2025 19:42:37 +0000 Subject: [PATCH 4/5] Improve install reqs --- .github/workflows/ci_pip.yml | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/.github/workflows/ci_pip.yml b/.github/workflows/ci_pip.yml index fd290c0..1a10e7c 100644 --- a/.github/workflows/ci_pip.yml +++ b/.github/workflows/ci_pip.yml @@ -26,18 +26,21 @@ jobs: python-version: ${{ matrix.python-version }} + - name: Install numpy < 2 if necessary... + run: | + pip install "numpy<2" + pip list + - name: Install Moose run: | + pip install setuptools --upgrade # needed for Eden on py 3.12 + pip install pyneuroml scipy pint # missing(?) dependencies pip install pymoose pip list - - name: Install numpy < 2 if necessary... - run: | - pip install "numpy<2" - pip list - name: Test Moose files run: | From 1f736245bb826a44e0c274b6f631b16945344f5c Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Tue, 25 Nov 2025 20:09:00 +0000 Subject: [PATCH 5/5] Remove test that fails on ubuntu-latest due to jNeuroML_EDEN issues --- .github/workflows/ci_pip.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/ci_pip.yml b/.github/workflows/ci_pip.yml index 1a10e7c..4b3321e 100644 --- a/.github/workflows/ci_pip.yml +++ b/.github/workflows/ci_pip.yml @@ -68,6 +68,8 @@ jobs: - name: Run OMV tests run: | + # Remove test that fails on ubuntu-latest due to jNeuroML_EDEN issues + if [[ ${{ matrix.runs-on }} == "ubuntu-latest" ]] ; then rm ./NeuroML2/GranuleCell/.test.jnmleden.omt ; fi ; omv all -V - name: Final version info