From b998dac1eac25567267a09c316f61bdfcce2caa2 Mon Sep 17 00:00:00 2001 From: pgleeson Date: Fri, 13 Jun 2025 17:20:40 +0100 Subject: [PATCH 1/9] Update brian, nrn, nest, pynn --- omv/engines/getbrian2.py | 2 +- omv/engines/getnest.py | 2 +- omv/engines/getnrn.py | 2 +- omv/engines/getpynn.py | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/omv/engines/getbrian2.py b/omv/engines/getbrian2.py index e5c4de8..dc42663 100644 --- a/omv/engines/getbrian2.py +++ b/omv/engines/getbrian2.py @@ -5,7 +5,7 @@ def install_brian2(version): if not version: - version = "2.7.1" + version = "2.9.0" try: pip_install("brian2", version) import brian2 diff --git a/omv/engines/getnest.py b/omv/engines/getnest.py index 6b46388..931fcbd 100644 --- a/omv/engines/getnest.py +++ b/omv/engines/getnest.py @@ -8,7 +8,7 @@ def install_nest(version): if not version: - version = "3.5" + version = "3.7" inform("Installing NEST", indent=2, verbosity=1) nestpath = os.path.join(os.environ["HOME"], "nest") diff --git a/omv/engines/getnrn.py b/omv/engines/getnrn.py index 4ee83e6..db7260a 100644 --- a/omv/engines/getnrn.py +++ b/omv/engines/getnrn.py @@ -10,7 +10,7 @@ def install_neuron(version): if not version: if sys.version_info.major == 3: - version = "8.2.7" # for pynn 0.11.0 + version = "8.2.7" else: version = "7.6" diff --git a/omv/engines/getpynn.py b/omv/engines/getpynn.py index dcc6cb6..b969d88 100644 --- a/omv/engines/getpynn.py +++ b/omv/engines/getpynn.py @@ -7,7 +7,7 @@ def install_pynn(version=None): if not version: - version = "0.11.0" + version = "0.12.4" try: # pip_install('lazyarray') # This should ideally be automatically installed with PyNN... From c748e3639afe254133a88ef4215a89527fb6fca2 Mon Sep 17 00:00:00 2001 From: pgleeson Date: Mon, 16 Jun 2025 14:30:42 +0100 Subject: [PATCH 2/9] Back to pynn 0.11.0 for now... --- omv/engines/getpynn.py | 2 +- utilities/tests/.test.exIzh.jnml.omt | 2 +- utilities/tests/.test.exIzh.jnmleden.omt | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/omv/engines/getpynn.py b/omv/engines/getpynn.py index b969d88..dcc6cb6 100644 --- a/omv/engines/getpynn.py +++ b/omv/engines/getpynn.py @@ -7,7 +7,7 @@ def install_pynn(version=None): if not version: - version = "0.12.4" + version = "0.11.0" try: # pip_install('lazyarray') # This should ideally be automatically installed with PyNN... diff --git a/utilities/tests/.test.exIzh.jnml.omt b/utilities/tests/.test.exIzh.jnml.omt index 23dd326..c958e7b 100644 --- a/utilities/tests/.test.exIzh.jnml.omt +++ b/utilities/tests/.test.exIzh.jnml.omt @@ -13,4 +13,4 @@ experiments: scaling: [1000, 1000] spike detection: method: threshold - tolerance: 0.000051 + tolerance: 5.0862371508887715e-05 diff --git a/utilities/tests/.test.exIzh.jnmleden.omt b/utilities/tests/.test.exIzh.jnmleden.omt index 0d32d25..59ed240 100644 --- a/utilities/tests/.test.exIzh.jnmleden.omt +++ b/utilities/tests/.test.exIzh.jnmleden.omt @@ -13,4 +13,4 @@ experiments: scaling: [1000, 1000] spike detection: method: threshold - tolerance: 0.00014888369126089628 + tolerance: 0.00014884116521364865 From 81ecb25ad0fd24c6fee0c934da352da5db4fd383 Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Tue, 29 Jul 2025 11:17:52 +0100 Subject: [PATCH 3/9] Test on macos-15 --- .github/workflows/ci_versions.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci_versions.yml b/.github/workflows/ci_versions.yml index 5345fcc..cef0f97 100644 --- a/.github/workflows/ci_versions.yml +++ b/.github/workflows/ci_versions.yml @@ -16,7 +16,7 @@ jobs: fail-fast: false matrix: python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"] - runs-on: [ubuntu-latest, macos-latest ] + runs-on: [ubuntu-latest, macos-latest, macos-15 ] exclude: - runs-on: macos-latest python-version: ["3.9"] From a2b58232da88d11b16c94fda0f1cb98fc1163bd1 Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Mon, 4 Aug 2025 18:08:11 +0100 Subject: [PATCH 4/9] To v0.3.11 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 6d6e513..8281b2a 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,6 +1,6 @@ [metadata] name = OSBModelValidation -version = 0.3.10 +version = 0.3.11 author = Boris Marin, Padraig Gleeson author_email = borismarin@gmail.com url = https://github.com/OpenSourceBrain/osb-model-validation From 17cd6ca107bc97d6ae25f9fd7b602d2ea8b353eb Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Mon, 15 Sep 2025 09:50:45 +0100 Subject: [PATCH 5/9] Fix YAML syntax for Python version exclusion --- .github/workflows/ci_versions.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci_versions.yml b/.github/workflows/ci_versions.yml index 5345fcc..c229b07 100644 --- a/.github/workflows/ci_versions.yml +++ b/.github/workflows/ci_versions.yml @@ -19,7 +19,7 @@ jobs: runs-on: [ubuntu-latest, macos-latest ] exclude: - runs-on: macos-latest - python-version: ["3.9"] + python-version: "3.9" steps: - uses: actions/checkout@v4 From 41739e733e262b75435a8e410f9df4eb85e67161 Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Tue, 6 Jan 2026 14:09:41 +0000 Subject: [PATCH 6/9] Test pinning numpy < 2.4 --- .github/workflows/ci.yml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index a56bb74..f2d2538 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -67,9 +67,12 @@ jobs: #sudo apt install octave sudo apt-get install -y subversion # for neuroConstruct full install... - - name: Install numpy < 2 if necessary... + - name: Install numpy < 2 (or <2.4) if necessary... run: | + pip install "numpy<2.4" # 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 - name: Run OMV tests on engine ${{ matrix.engine }} From e0c72baf4480f6e17a47306323ce9ef2ba3a20e6 Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Tue, 6 Jan 2026 17:29:36 +0000 Subject: [PATCH 7/9] Test macos-14 as latest is 15 --- .github/workflows/ci_versions.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci_versions.yml b/.github/workflows/ci_versions.yml index a935b04..33c9486 100644 --- a/.github/workflows/ci_versions.yml +++ b/.github/workflows/ci_versions.yml @@ -16,7 +16,7 @@ jobs: fail-fast: false matrix: python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"] - runs-on: [ubuntu-latest, macos-latest, macos-15 ] + runs-on: [ubuntu-latest, macos-14, macos-latest ] exclude: - runs-on: macos-latest python-version: "3.9" From 4d7c5860d502c720a0865ebd885580f56001f697 Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Tue, 6 Jan 2026 17:46:02 +0000 Subject: [PATCH 8/9] Correct exclusion --- .github/workflows/ci.yml | 2 +- .github/workflows/ci_versions.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index f2d2538..6e001e7 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -69,7 +69,7 @@ jobs: - name: Install numpy < 2 (or <2.4) if necessary... run: | - pip install "numpy<2.4" # See https://github.com/OpenSourceBrain/osb-model-validation/issues/150 + 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 ; diff --git a/.github/workflows/ci_versions.yml b/.github/workflows/ci_versions.yml index 33c9486..fb50eab 100644 --- a/.github/workflows/ci_versions.yml +++ b/.github/workflows/ci_versions.yml @@ -18,7 +18,7 @@ jobs: python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"] runs-on: [ubuntu-latest, macos-14, macos-latest ] exclude: - - runs-on: macos-latest + - runs-on: macos-14 python-version: "3.9" steps: From 35a37da03b11fa497206e5ebef5112be932486af Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Tue, 6 Jan 2026 18:03:52 +0000 Subject: [PATCH 9/9] More exclusions --- .github/workflows/ci_versions.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/ci_versions.yml b/.github/workflows/ci_versions.yml index fb50eab..f733cef 100644 --- a/.github/workflows/ci_versions.yml +++ b/.github/workflows/ci_versions.yml @@ -20,6 +20,8 @@ jobs: exclude: - runs-on: macos-14 python-version: "3.9" + - runs-on: macos-latest + python-version: "3.9" steps: - uses: actions/checkout@v4