Merge branch 'master' into test_nest

Author: pgleeson

.github/workflows/ci.yml

@@ -26,16 +26,17 @@ jobs:
           - jNeuroML_PyNN_NEURON
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Set up Python  ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v3
       with:
         python-version:  ${{ matrix.python-version }}
 
     - name: Install OMV
       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 }}

.gitignore

@@ -121,3 +121,4 @@ report*.txt
 *_moose.py
 /utilities/tests/*.gen.c
 /utilities/tests/*_eden.py
+arm64

README.md

@@ -3,7 +3,10 @@
 
 # OSB Model Validation
 
-Tools for automated model validation in [Open Source Brain](http://www.opensourcebrain.org) projects, which can also be used for testing model behaviour on many [simulation engines](https://github.com/OpenSourceBrain/osb-model-validation/tree/master/omv/engines) on your local machine and on [GitHub Actions](https://github.com/features/actions).
+Tools for automated model validation in [Open Source Brain](http://www.opensourcebrain.org) projects, which can also be used for testing model behaviour on many [simulation engines](https://github.com/OpenSourceBrain/osb-model-validation/tree/master/omv/engines) both:
+
+- on your local machine when developing models
+- on [GitHub Actions](https://github.com/features/actions), to ensure tests pass on every commit.
 
 To see this framework in action, click on some of the green buttons below:
 

omv/__init__.py

@@ -1 +1 @@
-__version__ = '0.1.15'
+__version__ = '0.2.6'

omv/analyzers/utils/timeseries.py

@@ -1,6 +1,6 @@
-
 from omv.common.inout import inform
 
+
 def detect_spikes(v, method='threshold', threshold=0.):
     from numpy import flatnonzero, bitwise_and, roll, diff, array
 
@@ -27,10 +27,11 @@ def load_data_file(fname, columns=(0, 1), header_lines=0, scaling=1):
 
 def load_spike_file(fname, format='ID_TIME', ids=0, scaling=1.0):
     from numpy import loadtxt
-    ts = loadtxt(fname)
+    ts = loadtxt(fname, skiprows=3) if format=='ID_TIME_NEST_DAT' else loadtxt(fname)
     spike_map = {}
     for l in ts:
-        if format=='ID_TIME':
+        #print('Interpreting: %s'%l)
+        if format=='ID_TIME' or format=='ID_TIME_NEST_DAT':
             t = l[1]*scaling
             id = l[0]
         elif format=='TIME_ID':
@@ -45,8 +46,13 @@ def load_spike_file(fname, format='ID_TIME', ids=0, scaling=1.0):
 
 def compare_arrays(arrays, tolerance):
     from numpy import allclose, array, max, abs, atleast_1d
-    
-    a1, a2 = array(arrays)
+
+    # if array conversion fails, also fail test
+    try:
+        a1, a2 = array(arrays)
+    except ValueError as e:
+        print(e)
+        return (False, 0)
 
     if (hasattr(a1, '__len__') or hasattr(a2, '__len__')) and len(a1)!=len(a2):  # Different lengths!!
         return (False, 0)

omv/common/inout.py

@@ -65,7 +65,7 @@ def inform(msg, pars=None, indent=0, underline=False,
         block = map(centralize, block)
     if indent:
         block = map(lambda l: __INDENT__ * indent + l, block)
-          
+
     print('\n'.join(map(omvify, block)))
 
 
@@ -81,7 +81,7 @@ def trim_path(fname):
         return "."+fname[len(cwd):]
     else:
         return fname
-    
+
 def check_output(cmds, cwd='.', shell=False, verbosity=0, env=None):
     inform("Running the commands: [%s] in (%s; cwd=%s; shell=%s; env=%s)"%(' '.join(cmds), cwd, os.getcwd(),shell,env), indent=2, verbosity=verbosity)
     joint_env = {}
@@ -90,14 +90,14 @@ def check_output(cmds, cwd='.', shell=False, verbosity=0, env=None):
     for k in os.environ:
         if not k in joint_env:
             joint_env[k] = os.environ[k]
-    
+
     try:
-        ret_string = sp.check_output(cmds, cwd=cwd, shell=shell, env=joint_env)
+        ret_string = sp.check_output(cmds, cwd=cwd, shell=shell, env=joint_env, stderr=sp.STDOUT)
         inform("Commands: %s completed successfully"%(cmds), indent=2, verbosity=verbosity)
         if isinstance(ret_string, bytes):
                 ret_string = ret_string.decode('utf-8') # For Python 3...
         return ret_string
-        
+
     except sp.CalledProcessError as err:
         inform("Error running commands: %s in %s (return code: %s)"%(cmds, cwd,err.returncode), indent=2, verbosity=verbosity)
         inform("Error: %s"%(err), indent=2, verbosity=verbosity)
@@ -106,14 +106,19 @@ def check_output(cmds, cwd='.', shell=False, verbosity=0, env=None):
         inform("Error running commands: %s in (%s)!"%(cmds, cwd), indent=2, verbosity=verbosity)
         inform("Error: %s"%(err), indent=2, verbosity=verbosity)
         raise err
-    
-def pip_install(packages):
-    
-    pip = 'pip3' if sys.version_info.major == 3 else 'pip' 
+
+def pip_install(packages, version=None):
+
+    pip = 'pip3' if sys.version_info.major == 3 else 'pip'
     cmds = [pip, 'install']
     if type(packages)==str:
-        cmds.append(packages)
+        if version ==None:
+            cmds.append(packages)
+        else:
+            cmds.append('%s==%s'%(packages,version))
     else:
+        raise Exception('pip_install will only install single packages...')
+        '''
         for p in packages:
-            cmds.append(p)
-    print(check_output(cmds))
+            cmds.append(p)'''
+    print(check_output(cmds))

omv/engines/__init__.py

@@ -29,6 +29,7 @@
 from omv.engines.pynnneuron import PyNNNRNEngine
 from omv.engines.pyneuron import PyNRNEngine
 #from omv.engines.pynnbrian1 import PyNNBrian1Engine
+from omv.engines.pynnbrian2 import PyNNBrian2Engine
 from omv.engines.pynnnest import PyNNNestEngine
 from omv.engines.pynnneuroml import PyNNNeuroMLEngine
 from omv.engines.octave import OctaveEngine

omv/engines/arbor_.py

@@ -10,7 +10,7 @@ class ArborEngine(OMVEngine):
     name = "Arbor"
 
     @staticmethod
-    def is_installed(version):
+    def is_installed():
         ret = True
         try:
             import arbor

omv/engines/brian1.py

@@ -12,7 +12,7 @@ class Brian1Engine(OMVEngine):
     python3_compatible = False
 
     @staticmethod
-    def is_installed(version):
+    def is_installed():
         ret = False
         try:
             import brian

omv/engines/brian2_.py

@@ -10,7 +10,7 @@ class Brian2Engine(OMVEngine):
     name = "Brian2"
 
     @staticmethod
-    def is_installed(version):
+    def is_installed():
         ret = True
         try:
             import brian2