From b998dac1eac25567267a09c316f61bdfcce2caa2 Mon Sep 17 00:00:00 2001
From: pgleeson <p.gleeson@gmail.com>
Date: Fri, 13 Jun 2025 17:20:40 +0100
Subject: [PATCH 01/18] 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 <p.gleeson@gmail.com>
Date: Mon, 16 Jun 2025 14:30:42 +0100
Subject: [PATCH 02/18] 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 <p.gleeson@gmail.com>
Date: Tue, 29 Jul 2025 11:17:52 +0100
Subject: [PATCH 03/18] 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 <p.gleeson@gmail.com>
Date: Mon, 4 Aug 2025 18:08:11 +0100
Subject: [PATCH 04/18] 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 <p.gleeson@gmail.com>
Date: Mon, 15 Sep 2025 09:50:45 +0100
Subject: [PATCH 05/18] 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 <p.gleeson@gmail.com>
Date: Tue, 6 Jan 2026 14:09:41 +0000
Subject: [PATCH 06/18] 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 <p.gleeson@gmail.com>
Date: Tue, 6 Jan 2026 17:29:36 +0000
Subject: [PATCH 07/18] 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 <p.gleeson@gmail.com>
Date: Tue, 6 Jan 2026 17:46:02 +0000
Subject: [PATCH 08/18] 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 <p.gleeson@gmail.com>
Date: Tue, 6 Jan 2026 18:03:52 +0000
Subject: [PATCH 09/18] 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

From 5980ed45b04643555c9c8e086a6664be586cddcf Mon Sep 17 00:00:00 2001
From: Padraig Gleeson <p.gleeson@gmail.com>
Date: Fri, 16 Jan 2026 10:53:44 +0000
Subject: [PATCH 10/18] 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 <p.gleeson@gmail.com>
Date: Fri, 16 Jan 2026 11:38:47 +0000
Subject: [PATCH 11/18] 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 <p.gleeson@gmail.com>
Date: Mon, 2 Feb 2026 14:15:56 +0000
Subject: [PATCH 12/18] 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 <p.gleeson@gmail.com>
Date: Fri, 20 Mar 2026 11:03:45 +0000
Subject: [PATCH 13/18] 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 <p.gleeson@gmail.com>
Date: Fri, 20 Mar 2026 11:11:35 +0000
Subject: [PATCH 14/18] 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 <p.gleeson@gmail.com>
Date: Fri, 20 Mar 2026 11:31:37 +0000
Subject: [PATCH 15/18] 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 <p.gleeson@gmail.com>
Date: Fri, 20 Mar 2026 11:54:00 +0000
Subject: [PATCH 16/18] 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 <p.gleeson@gmail.com>
Date: Fri, 20 Mar 2026 11:57:28 +0000
Subject: [PATCH 17/18] 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 <p.gleeson@gmail.com>
Date: Fri, 20 Mar 2026 12:03:00 +0000
Subject: [PATCH 18/18] 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")