Merge pull request #82 from OpenSourceBrain/test_arbor_eden

Improved EDEN support

.github/workflows/ci.yml

@@ -32,6 +32,7 @@ jobs:
           - jLEMS
           - jNeuroML
           - jNeuroML_Brian2
+          - jNeuroML_EDEN
           - jNeuroML_NEURON
           - jNeuroML_NetPyNE
           - jNeuroML_PyNN_NEURON

.gitignore

@@ -119,3 +119,5 @@ report*.txt
 /getmoose
 /envpy*
 *_moose.py
+/utilities/tests/*.gen.c
+/utilities/tests/*_eden.py

omv/engines/__init__.py

@@ -9,6 +9,7 @@
 from omv.engines.jneuromlnetpyne_np4 import JNeuroMLNetPyNENP4Engine
 from omv.engines.jneuromlnetpyne_np2 import JNeuroMLNetPyNENP2Engine
 #from omv.engines.jneuromlbrian import JNeuroMLBrianEngine
+from omv.engines.jneuromleden import JNeuroMLEdenEngine
 from omv.engines.jneuromlbrian2 import JNeuroMLBrian2Engine
 from omv.engines.jneuromlmoose import JNeuroMLMooseEngine
 from omv.engines.jneuromlvalidate import JNeuroMLValidateEngine

omv/engines/eden_.py

@@ -35,9 +35,11 @@ def install(version):
 
     def run(self):
         try:
-            inform("Running a file %s with sim %s" % (trim_path(self.modelpath), self.name), indent=1)
+            inform("Running a file %s with the simulator %s" % (trim_path(self.modelpath), self.name), indent=1)
+
             self.stdout = check_output(['python', self.modelpath],
                                           cwd=os.path.dirname(self.modelpath))
+
             self.returncode = 0
         except sp.CalledProcessError as err:
             self.returncode = err.returncode

omv/engines/getjnml.py

@@ -5,7 +5,7 @@
 
 def install_jnml():
 
-    version='v0.11.1_pre'
+    version='v0.11.1_pre2'
 
     jnmlpath = os.path.join(os.environ['HOME'],'jnml')
     if not os.path.isdir(jnmlpath):

omv/engines/jneuromleden.py

@@ -0,0 +1,52 @@
+import os
+import subprocess as sp
+
+from omv.engines.jneuroml import JNeuroMLEngine
+from omv.engines.eden_ import EdenEngine
+from omv.common.inout import inform, trim_path, check_output, is_verbose
+from omv.engines.engine import EngineExecutionError
+
+
+class JNeuroMLEdenEngine(JNeuroMLEngine):
+
+    name = "jNeuroML_EDEN"
+
+    @staticmethod
+    def is_installed(version):
+        if is_verbose():
+            inform("Checking whether %s is installed..." %
+               JNeuroMLEdenEngine.name, indent=1)
+        return JNeuroMLEngine.is_installed(None) and EdenEngine.is_installed(None)
+
+    @staticmethod
+    def install(version):
+
+        if not JNeuroMLEngine.is_installed(None):
+            JNeuroMLEngine.install(None)
+        if not EdenEngine.is_installed(None):
+            EdenEngine.install(None)
+
+        JNeuroMLEdenEngine.path = JNeuroMLEngine.path + \
+            ":" + EdenEngine.path
+        JNeuroMLEdenEngine.environment_vars = {}
+        JNeuroMLEdenEngine.environment_vars.update(
+            JNeuroMLEngine.environment_vars)
+        JNeuroMLEdenEngine.environment_vars.update(
+            EdenEngine.environment_vars)
+        inform("PATH: " + JNeuroMLEdenEngine.path)
+        inform("Env vars: %s" % JNeuroMLEdenEngine.environment_vars)
+
+    def run(self):
+        try:
+            inform("Running file %s with %s" % (trim_path(self.modelpath), JNeuroMLEdenEngine.name), indent=1)
+            from omv.engines.jneuroml import JNeuroMLEngine
+            jnml = JNeuroMLEngine.get_executable()
+            self.stdout = check_output([jnml, self.modelpath, '-eden'], cwd=os.path.dirname(self.modelpath),env=JNeuroMLEngine.get_environment())
+            self.stdout += check_output(['python', self.modelpath.replace('.xml', '_eden.py')], cwd=os.path.dirname(self.modelpath))
+            inform("Success with running ", JNeuroMLEdenEngine.name, indent=1)
+            self.returncode = 0
+        except sp.CalledProcessError as err:
+            inform("Error with ", JNeuroMLEdenEngine.name, indent=1)
+            self.returncode = err.returncode
+            self.stdout = err.output
+            raise EngineExecutionError

utilities/tests/.test.ex5.jnmleden.omt

@@ -0,0 +1,17 @@
+# Script for running automated tests on OSB using Travis-CI, see https://github.com/OpenSourceBrain/osb-model-validation
+
+target: LEMS_NML2_Ex5_DetCell.xml
+engine: jNeuroML_EDEN
+mep: .test.ex5.mep
+experiments:
+  v:
+    observables:
+      spike times:
+        file:
+          path: ex5_v.dat
+          columns: [0,1]
+          scaling: [1000, 1000]
+        spike detection:
+          method: threshold
+          threshold: 0
+        tolerance: 0.001963746223565029

utilities/tests/.test.ex9.jnmlbrian.omt → utilities/tests/.test.ex9.jnmleden.omt

@@ -1,26 +1,26 @@
 # Script for running automated tests on OSB using Travis-CI, see https://github.com/OpenSourceBrain/osb-model-validation
- 
-target: LEMS_NML2_Ex9_FN.xml 
-engine: jNeuroML_Brian
+
+target: LEMS_NML2_Ex9_FN.xml
+engine: jNeuroML_EDEN
 mep: .test.ex9.mep
 experiments:
   V:
     observables:
       spike times:
-        file: 
+        file:
           path: ex9.dat
           columns: [0,1]
           scaling: [1000, 1000]
-        spike detection: 
+        spike detection:
           method: derivative
-        tolerance: 0.004099
+        tolerance: 4.098360645390339e-08
   W:
     observables:
       spike times:
-        file: 
+        file:
           path: ex9.dat
           columns: [0,2]
           scaling: [1000, 1]
-        spike detection: 
+        spike detection:
           method: derivative
-        tolerance: 0.000616
+        tolerance: 5.0276520911579816e-8

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

@@ -0,0 +1,16 @@
+# Script for running automated tests on OSB using Travis-CI, see https://github.com/OpenSourceBrain/osb-model-validation
+
+target: LEMS_2007One.xml
+engine: jNeuroML_EDEN
+mep: .test.exIzh.mep
+experiments:
+  v:
+    observables:
+      spike times:
+        file:
+          path: exIzh.dat
+          columns: [0,1]
+          scaling: [1000, 1000]
+        spike detection:
+          method: threshold
+        tolerance: 0.00014888369126089628