From 4cfcdaca8e527d72b31ad644978f7abb63d1bd93 Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Fri, 13 Jun 2025 16:22:32 +0100 Subject: [PATCH 1/7] Update non-omv.yml --- .github/workflows/non-omv.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/non-omv.yml b/.github/workflows/non-omv.yml index 518096a..64a66f0 100644 --- a/.github/workflows/non-omv.yml +++ b/.github/workflows/non-omv.yml @@ -14,7 +14,7 @@ jobs: strategy: fail-fast: false matrix: - python-version: [ 3.9, "3.10", "3.11"] + python-version: [ 3.9, "3.10", "3.12"] steps: - uses: actions/checkout@v4 From e46d6e9b0c38671500c9d7c0ce5c395156745393 Mon Sep 17 00:00:00 2001 From: pgleeson Date: Fri, 13 Jun 2025 17:03:00 +0100 Subject: [PATCH 2/7] ensure latest numpy --- .github/workflows/non-omv.yml | 3 +-- .github/workflows/omv-ci.yml | 10 +++------- 2 files changed, 4 insertions(+), 9 deletions(-) diff --git a/.github/workflows/non-omv.yml b/.github/workflows/non-omv.yml index 64a66f0..51aa9a8 100644 --- a/.github/workflows/non-omv.yml +++ b/.github/workflows/non-omv.yml @@ -28,13 +28,12 @@ jobs: run: | pip install git+https://github.com/OpenSourceBrain/osb-model-validation - #pip install 'numpy<=1.23.0' # see https://github.com/OpenSourceBrain/osb-model-validation/issues/91 - - name: Test some scripts run: | pip install pyneuroml omv install PyNN ./regenerate.sh + omv all -V - name: OMV final version info run: | diff --git a/.github/workflows/omv-ci.yml b/.github/workflows/omv-ci.yml index a8d28d4..217dbfb 100644 --- a/.github/workflows/omv-ci.yml +++ b/.github/workflows/omv-ci.yml @@ -14,11 +14,8 @@ jobs: strategy: fail-fast: false matrix: - python-version: [ 3.8, "3.10" ] + python-version: [ "3.10", "3.12" ] engine: [ PyNEST, "PyNEST:3.4", "PyNEST:3.5", PyNN_Nest, PyNN_NEURON, PyNN_Brian2, PyNN_NeuroML, jNeuroML_validate, jNeuroML, jNeuroML_NEURON ] - exclude: - - python-version: 3.8 - engine: PyNN_Brian2 steps: - uses: actions/checkout@v4 @@ -31,9 +28,8 @@ jobs: - name: Install OMV run: | pip install git+https://github.com/OpenSourceBrain/osb-model-validation - pip install scipy sympy matplotlib cython pandas tables - - #pip install 'numpy<=1.23.0' # see https://github.com/OpenSourceBrain/osb-model-validation/issues/91 + + pip install matplotlib "cython<3.1.0" # let omv handle other deps... - name: Run OMV tests on engine ${{ matrix.engine }} run: | From e48e9bd293d2bd3bed3b82adba6b940e754aa146 Mon Sep 17 00:00:00 2001 From: pgleeson Date: Fri, 13 Jun 2025 17:26:24 +0100 Subject: [PATCH 3/7] Better dep installs --- .github/workflows/non-omv.yml | 2 ++ .github/workflows/omv-ci.yml | 4 ++-- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/.github/workflows/non-omv.yml b/.github/workflows/non-omv.yml index 51aa9a8..7b8bda4 100644 --- a/.github/workflows/non-omv.yml +++ b/.github/workflows/non-omv.yml @@ -27,6 +27,8 @@ jobs: - name: Install OMV run: | pip install git+https://github.com/OpenSourceBrain/osb-model-validation + + pip install scipy sympy matplotlib "cython<3.1.0" pandas tables - name: Test some scripts run: | diff --git a/.github/workflows/omv-ci.yml b/.github/workflows/omv-ci.yml index 217dbfb..c96c67e 100644 --- a/.github/workflows/omv-ci.yml +++ b/.github/workflows/omv-ci.yml @@ -28,8 +28,8 @@ jobs: - name: Install OMV run: | pip install git+https://github.com/OpenSourceBrain/osb-model-validation - - pip install matplotlib "cython<3.1.0" # let omv handle other deps... + + pip install scipy sympy matplotlib "cython<3.1.0" pandas tables - name: Run OMV tests on engine ${{ matrix.engine }} run: | From f0908f18fda82bc46ce2ecba4e257193695d4f0a Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Wed, 12 Nov 2025 18:36:39 +0000 Subject: [PATCH 4/7] Update CI workflow to remove PyNEST:3.4 Removed 'PyNEST:3.4' from the engine matrix in CI workflow. --- .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 c96c67e..164bf2a 100644 --- a/.github/workflows/omv-ci.yml +++ b/.github/workflows/omv-ci.yml @@ -15,7 +15,7 @@ jobs: fail-fast: false matrix: python-version: [ "3.10", "3.12" ] - engine: [ PyNEST, "PyNEST:3.4", "PyNEST:3.5", PyNN_Nest, PyNN_NEURON, PyNN_Brian2, PyNN_NeuroML, jNeuroML_validate, jNeuroML, jNeuroML_NEURON ] + engine: [ PyNEST, "PyNEST:3.5", PyNN_Nest, PyNN_NEURON, PyNN_Brian2, PyNN_NeuroML, jNeuroML_validate, jNeuroML, jNeuroML_NEURON ] steps: - uses: actions/checkout@v4 From 570ce26c2b9cbbd3b20ac50012a7f0adcc9554e9 Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Sat, 21 Mar 2026 10:07:01 +0000 Subject: [PATCH 5/7] Update GitHub Actions to use latest versions --- .github/workflows/non-omv.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/non-omv.yml b/.github/workflows/non-omv.yml index 7b8bda4..23f4844 100644 --- a/.github/workflows/non-omv.yml +++ b/.github/workflows/non-omv.yml @@ -17,10 +17,10 @@ jobs: python-version: [ 3.9, "3.10", "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 }} From 25fd5b665004e4257004f08b545817a570611e84 Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Tue, 19 May 2026 09:09:24 +0100 Subject: [PATCH 6/7] Update Python version and actions in CI workflow --- .github/workflows/omv-ci.yml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/.github/workflows/omv-ci.yml b/.github/workflows/omv-ci.yml index 164bf2a..977e727 100644 --- a/.github/workflows/omv-ci.yml +++ b/.github/workflows/omv-ci.yml @@ -14,14 +14,14 @@ jobs: strategy: fail-fast: false matrix: - python-version: [ "3.10", "3.12" ] + python-version: [ "3.11", "3.12" ] engine: [ PyNEST, "PyNEST:3.5", PyNN_Nest, PyNN_NEURON, PyNN_Brian2, PyNN_NeuroML, jNeuroML_validate, jNeuroML, jNeuroML_NEURON ] 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 }} @@ -29,8 +29,10 @@ jobs: run: | pip install git+https://github.com/OpenSourceBrain/osb-model-validation + pip install 'numpy==2.2.6' # TODO: remove when pynn v0.12 used! pip install scipy sympy matplotlib "cython<3.1.0" pandas tables + - name: Run OMV tests on engine ${{ matrix.engine }} run: | omv all -V --engine=${{ matrix.engine }} From 6cb342f30a21bb83a117cbc6176605a55b3fb1b1 Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Tue, 19 May 2026 09:27:14 +0100 Subject: [PATCH 7/7] test on py 3.12 & 3.13 --- .github/workflows/non-omv.yml | 3 ++- .github/workflows/omv-ci.yml | 2 +- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/.github/workflows/non-omv.yml b/.github/workflows/non-omv.yml index 23f4844..312d8e3 100644 --- a/.github/workflows/non-omv.yml +++ b/.github/workflows/non-omv.yml @@ -14,7 +14,7 @@ jobs: strategy: fail-fast: false matrix: - python-version: [ 3.9, "3.10", "3.12"] + python-version: [ "3.12", "3.13" ] steps: - uses: actions/checkout@v6 @@ -28,6 +28,7 @@ jobs: run: | pip install git+https://github.com/OpenSourceBrain/osb-model-validation + pip install 'numpy==2.2.6' # TODO: remove when pynn v0.12 used! pip install scipy sympy matplotlib "cython<3.1.0" pandas tables - name: Test some scripts diff --git a/.github/workflows/omv-ci.yml b/.github/workflows/omv-ci.yml index 977e727..a819b60 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: [ "3.11", "3.12" ] + python-version: [ "3.12", "3.13" ] engine: [ PyNEST, "PyNEST:3.5", PyNN_Nest, PyNN_NEURON, PyNN_Brian2, PyNN_NeuroML, jNeuroML_validate, jNeuroML, jNeuroML_NEURON ] steps: