Merge pull request #100 from OpenSourceBrain/test_pynn0101

Uses PyNN v0.10.1, nrn v8.1, nest v3.3

Author: pgleeson

.github/workflows/ci.yml

@@ -27,6 +27,7 @@ jobs:
           - "NEURON:7.8.2"
           - "PyNEURON:8.0.2"
           - PyNN
+          - PyNN_Brian2
           - PyNN_NEURON
           - PyNN_Nest
           - PyNN_NeuroML

.gitignore

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

omv/__init__.py

@@ -1 +1 @@
-__version__ = '0.2.2'
+__version__ = '0.2.4'

omv/analyzers/utils/timeseries.py

@@ -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':

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/getnest.py

@@ -8,7 +8,7 @@
 def install_nest(version):
 
     if not version:
-        version='2.20.0'
+        version='3.3'
 
     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='7.8.2'
+            version='8.1' # 8.1 works with pynn 0.10.1
         else:
             version='7.6'
 

omv/engines/getpynn.py

@@ -5,10 +5,14 @@
 from omv.engines.utils.wdir import working_dir
 
 def install_pynn(version=None):
+
+    if not version:
+        version='0.10.1'
+
     try:
 
         #pip_install('lazyarray')  # This should ideally be automatically installed with PyNN...
-        pip_install('neo==0.9.0')  # This should ideally be automatically installed with PyNN, some issues with 0.10.0...
+        #pip_install('neo>=0.11.0')  # This should ideally be automatically installed with PyNN...
 
         install_root = os.environ['HOME']
 
@@ -19,7 +23,6 @@ def install_pynn(version=None):
         path = os.path.join(install_root, pyNN_src)
 
         with working_dir(path):
-            if version==None: version = '0.9.6'
             print(check_output(['git','checkout',version]))  # neuroml branch has the latest NML2 import/export code!
             #check_output(['git','checkout','master'])
             #print(check_output(['python', 'setup.py', 'install']))

omv/engines/nestsli.py

@@ -18,6 +18,8 @@ def get_nest_environment():
         nestpath = os.path.join(os.environ['HOME'],'nest/nest/')
         if 'NEST_INSTALL_DIR' in os.environ:
             nestpath = os.environ['NEST_INSTALL_DIR']+'/'
+        elif 'NEST_HOME' in os.environ:
+            nestpath = os.environ['NEST_HOME']+'/'
 
         environment_vars = {'NEST_HOME': nestpath,
                             'PYTHONPATH': nestpath+'/lib/python%s.%s/site-packages/'%(sys.version_info.major, sys.version_info.minor)}
@@ -28,7 +30,6 @@ def get_nest_environment():
     @staticmethod
     def is_installed():
         ret = True
-
         environment_vars = NestEngine.get_nest_environment()
         try:
             FNULL = open(os.devnull, 'w')
@@ -39,6 +40,8 @@ def is_installed():
             if '-' in ret:
                 ret = 'v%s'%ret.split('-')[-1]
 
+            if not 'v' in ret: ret='v%s'%ret
+
             inform("NEST %s is correctly installed..." % ret, indent=2, verbosity=1)
 
         except OSError as err:

omv/engines/pynnbrian2.py

@@ -0,0 +1,71 @@
+import os
+import subprocess as sp
+
+from omv.engines.brian2_ import Brian2Engine
+from omv.engines.pynn import PyNNEngine
+
+from omv.common.inout import inform, trim_path, check_output, is_verbose
+from omv.engines.engine import EngineExecutionError
+
+
+class PyNNBrian2Engine(PyNNEngine):
+    
+    name = "PyNN_Brian2"
+    python3_compatible = Brian2Engine.python3_compatible
+
+    @staticmethod
+    def is_installed():
+        if is_verbose():
+            inform("Checking whether %s is installed..." %
+                   PyNNBrian2Engine.name, indent=1)
+        return PyNNEngine.is_installed() and Brian2Engine.is_installed()
+        
+    @staticmethod
+    def install(version):
+        if not Brian2Engine.is_installed():
+            Brian2Engine.install(version)  # interpret version as version of Brian!
+            inform("%s installed Brian..." % PyNNBrian2Engine.name, indent=2, verbosity =1)
+        if not PyNNEngine.is_installed():
+            PyNNEngine.install(None)
+            inform("%s installed PyNN..." % PyNNBrian2Engine.name, indent=2, verbosity =1)
+
+        PyNNBrian2Engine.path = PyNNEngine.path + \
+            ":" + Brian2Engine.path
+        PyNNBrian2Engine.environment_vars = {}
+        PyNNBrian2Engine.environment_vars.update(
+            PyNNEngine.environment_vars)
+        PyNNBrian2Engine.environment_vars.update(
+            Brian2Engine.environment_vars)
+        inform("PATH: " + PyNNBrian2Engine.path)
+
+
+    def run(self):
+        try:
+            inform("Running file %s with %s" % (trim_path(self.modelpath), self.name), indent=1)
+            self.stdout = check_output(['python', self.modelpath, 'brian2'],
+                                          cwd=os.path.dirname(self.modelpath))
+            self.returncode = 0
+        except sp.CalledProcessError as err:
+            self.returncode = err.returncode
+            self.stdout = err.output
+            raise EngineExecutionError
+        except Exception as err:
+            inform("Another error with running %s: "%self.name, err, indent=1)
+            self.returncode = -1
+            self.stdout = "???"
+
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