Merge pull request #126 from OpenSourceBrain/test_pynn011

Update to use PyNN v0.11.0, NEST 3.5, NEURON 8.2.2 in tests

Author: pgleeson

.github/workflows/ci.yml

@@ -66,7 +66,6 @@ jobs:
       run: |
         pip install .
         pip install scipy sympy matplotlib cython pandas tables
-        pip install 'numpy<=1.23.0' # temp fix for https://levelup.gitconnected.com/fix-attributeerror-module-numpy-has-no-attribute-float-d7d68c5a4971
         #sudo apt install octave
 
     - name: Run OMV tests on engine ${{ matrix.engine }}

omv/engines/getnest.py

@@ -8,7 +8,7 @@
 
 def install_nest(version):
     if not version:
-        version = "3.3"
+        version = "3.5"
 
     inform("Installing NEST", indent=2, verbosity=1)
     nestpath = os.path.join(os.environ["HOME"], "nest")

omv/engines/getnrn.py

@@ -11,7 +11,7 @@
 def install_neuron(version):
     if not version:
         if sys.version_info.major == 3:
-            version = "8.1"  # 8.1 works with pynn 0.10.1
+            version = "8.2.2"  # for pynn 0.11.0
         else:
             version = "7.6"
 

omv/engines/getpynn.py

@@ -7,12 +7,15 @@
 
 def install_pynn(version=None):
     if not version:
-        version = "0.10.1"
+        version = "0.11.0"
 
     try:
         # pip_install('lazyarray')  # This should ideally be automatically installed with PyNN...
         # pip_install('neo>=0.11.0')  # This should ideally be automatically installed with PyNN...
 
+        pip_install("pynn", version)
+        import pyNN
+        '''
         install_root = os.environ["HOME"]
 
         pyNN_src = "PyNN_src"
@@ -33,6 +36,7 @@ def install_pynn(version=None):
             print(check_output(["pwd"]))
             print("Finished attempting to install PyNN")
         # import pyNN
+        '''
         m = "Successfully installed pyNN..."
     except Exception as e:
         m = "ERROR during install_pynn: %s" % e

setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = OSBModelValidation
-version = 0.2.22
+version = 0.3.1
 author = Boris Marin, Padraig Gleeson
 author_email = [email protected]
 url = https://github.com/OpenSourceBrain/osb-model-validation
@@ -24,7 +24,7 @@ classifiers=
 [options]
 install_requires =
     PyYAML
-    numpy
+    numpy<2.0.0  # Due to other packages (e.g. tables) not working yet with numpy v2
     pyrx
     pathlib; python_version<'3.4'
     docopt