Merge branch 'development' into test_pyversions

Author: pgleeson

.github/workflows/ci.yml

@@ -11,14 +11,14 @@ on:
 jobs:
   build:
 
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     strategy:
       fail-fast: false
       matrix:
         python-version: [ "3.11" ]
         engine:
           - Arbor
-          - "Brian2:2.4"
+          - "Brian2:2.9.0"
           - Brian2
           - EDEN
           - "NEST:3.3"
@@ -63,8 +63,9 @@ jobs:
     - name: Install OMV
       run: |
         pip install .
-        pip install scipy sympy matplotlib cython pandas tables
+        pip install scipy sympy matplotlib "cython<3.1.0" pandas tables
         #sudo apt install octave
+        sudo apt-get install -y subversion # for neuroConstruct full install...
 
     - name: Run OMV tests on engine ${{ matrix.engine }}
       run: |

.github/workflows/ci_versions.yml

@@ -14,10 +14,10 @@ jobs:
       fail-fast: false
       matrix:
         python-version: ["3.9", "3.10", "3.11", "3.12"]
-        runs-on: [ubuntu-latest, macos-latest]
+        runs-on: [ubuntu-latest, macos-latest, ubuntu-24.04 ]
         exclude:
           - runs-on: macos-latest
-            python-version: "3.9"
+            python-version: ["3.9"]
 
     steps:
     - uses: actions/checkout@v4
@@ -50,4 +50,4 @@ jobs:
       run: |
         omv list -V # list installed engines
         env
-        pip list
+        pip list

README.md

@@ -157,3 +157,4 @@ Since you can run the validation with different [engines](https://github.com/Ope
 ### Running tests automatically on GitHub Actions
 
 To use OMV with GHA, copy an existing configuration file, e.g. https://github.com/OpenSourceBrain/ACnet2/blob/master/.github/workflows/omv-ci.yml and place it in the required repository.
+

omv/autogen.py

@@ -27,7 +27,7 @@ def read_option(options, default=0):
     opt = None
     while opt is None:
         try:
-            sel = int(raw_input("Select option number [default: %s]: " % default))
+            sel = int(input("Select option number [default: %s]: " % default))
             opt = options[sel]
         except IndexError:
             print("invalid index!")

omv/common/inout.py

@@ -103,7 +103,7 @@ def check_output(cmds, cwd=".", shell=False, verbosity=0, env=None):
     if env:
         joint_env.update(env)
     for k in os.environ:
-        if not k in joint_env:
+        if k not in joint_env:
             joint_env[k] = os.environ[k]
 
     try:

omv/engines/engine.py

@@ -1,6 +1,5 @@
 from os.path import realpath
 from os import environ
-import sys
 from omv.common.inout import inform
 import platform
 
@@ -78,8 +77,8 @@ def build_query_string(self, name, cmd):
     def set_environment(self):
         if self.environment_vars:
             for name, val in self.environment_vars.items():
-                if name in environ and not "HOME" in name:
-                    if not ":%s:" % val in environ[name]:
+                if name in environ and "HOME" not in name:
+                    if ":%s:" % val not in environ[name]:
                         environ[name] = "%s:%s" % (environ[name], val)
                 else:
                     environ[name] = val

omv/engines/getarbor.py

@@ -8,7 +8,7 @@ def install_arbor(version=None):
         pip_install("arbor==%s" % version)
         import arbor
 
-        m = "Successfully installed Arbor..."
+        m = "Successfully installed Arbor %s..."%arbor.__version__
     except Exception as e:
         m = "ERROR installing Arbor: " + str(e)
     finally:

omv/engines/getbrian1.py

@@ -1,5 +1,4 @@
 import os
-import pip
 from omv.common.inout import inform, check_output
 from omv.engines.utils.wdir import working_dir
 

omv/engines/getbrian2.py

@@ -5,12 +5,12 @@
 
 def install_brian2(version):
     if not version:
-        version = "2.5.3"
+        version = "2.7.1"
     try:
         pip_install("brian2", version)
         import brian2
 
-        m = "Successfully installed Brian2..."
+        m = "Successfully installed Brian2 %s..."%brian2.__version__
     except Exception as e:
         m = "ERROR installing Brian2: " + str(e)
     finally:

omv/engines/getjnml.py

@@ -8,9 +8,8 @@
 
 
 def install_jnml(version):
-
     if not version:
-        version = "v0.13.3"
+        version = "v0.14.0"
 
     try:
         jnmlhome = os.environ["JNML_HOME"]
@@ -45,4 +44,4 @@ def install_jnml(version):
         )
         check_output(["unzip", "jNeuroML.zip"])
 
-    inform("Successfully installed jNeuroML "+version, indent=1)
+    inform("Successfully installed jNeuroML " + version, indent=1)