Update brian, nrn, nest, pynn

.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"
@@ -49,14 +49,14 @@ 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@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 }}
 
@@ -67,9 +67,13 @@ jobs:
         #sudo apt install octave
         sudo apt-get install -y subversion # for neuroConstruct full install...
 
+        pip install setuptools==80 # needed for eden on Python 3.12...
+
     - name: Install numpy < 2 if necessary...
       run: |
+
         if [[  ${{ matrix.engine }} == *"MOOSE"* ]] || [[  ${{ matrix.engine }} == *"Moose"* ]]; then pip install "numpy<2" ; fi ;
+
         pip list
 
     - name: Run OMV tests on engine ${{ matrix.engine }}

.github/workflows/ci_versions.yml

@@ -16,8 +16,10 @@ 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-14, macos-latest ]
         exclude:
+          - runs-on: macos-14
+            python-version: "3.9"
           - runs-on: macos-latest
             python-version: "3.9"
 

.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

omv/engines/getbrian2.py

@@ -5,7 +5,7 @@
 
 def install_brian2(version):
     if not version:
-        version = "2.7.1"
+        version = "2.10.1"
     try:
         pip_install("brian2", version)
         import brian2

omv/engines/getmoose.py

@@ -4,8 +4,10 @@
 def install_moose(version):
     if not version:
         version = "4.0.0.dev20240411"
+        version = "4.1.4" # temp test this, it is the latest on pypi... 
     try:
         pip_install("pymoose", version)
+        pip_install("pint")
         import moose
 
         m = "Successfully installed MOOSE..."

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")

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"
 

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

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

utilities/tests/.test.exIzh.jnmleden.omt

@@ -13,4 +13,4 @@ experiments:
           scaling: [1000, 1000]
         spike detection:
           method: threshold
-        tolerance: 0.00014888369126089628
+        tolerance: 0.00014884116521364865