More tests: Brain2 and PyNN...

Author: pgleeson

.gitignore

@@ -25,3 +25,4 @@ Tutorial/Source/*json
 /Tutorial2/NeuroML2/*nrn.py
 /Tutorial2/NeuroML2/*.hoc
 /Tutorial/Source/LEMS_HH_Simulation_netpyne.py
+/Tutorial/Source/LEMS_HH_SingleAP_brian2.py

.travis.yml

@@ -25,6 +25,8 @@ env:
     - OMV_ENGINE=jNeuroML_NEURON
     - OMV_ENGINE=jNeuroML_validate
     - OMV_ENGINE=jNeuroML_NetPyNE
+    - OMV_ENGINE=jNeuroML_PyNN_NEURON
+    - OMV_ENGINE=jNeuroML_Brian2
 
 install: 
     - pip install git+https://github.com/OpenSourceBrain/osb-model-validation

Tutorial/Source/LEMS_HH_SingleAP.xml

@@ -29,21 +29,6 @@
             <Line id="V" quantity="hhpop/0/hhcell/v" scale="1mV" color="#000000" timeScale="1ms"/>
         </Display>
 
-        <Display id="d2" title="Hodgkin-Huxley Neuron: Gating Variables" timeScale="1ms" xmin="-5" xmax="55" ymin="-0.1" ymax="1.1">
-            <Line id="m" quantity="hhpop/0/hhcell/bioPhys1/membraneProperties/naChans/naChan/m/q" scale="1"  color="#ff0000" timeScale="1ms"/>
-            <Line id="h" quantity="hhpop/0/hhcell/bioPhys1/membraneProperties/naChans/naChan/h/q" scale="1"  color="#00dd00" timeScale="1ms"/>
-            <Line id="n" quantity="hhpop/0/hhcell/bioPhys1/membraneProperties/kChans/kChan/n/q" scale="1"  color="#0000ff" timeScale="1ms"/>
-        </Display>
-
-        <Display id="d3" title="Hodgkin-Huxley Neuron: Current" timeScale="1ms" xmin="-5" xmax="55" ymin="-10" ymax="10">
-            <Line id="I_na" quantity="hhpop/0/hhcell/bioPhys1/membraneProperties/naChans/iDensity" scale="1"  color="#00ffff" timeScale="1ms"/>
-            <Line id="I_k" quantity="hhpop/0/hhcell/bioPhys1/membraneProperties/kChans/iDensity" scale="1"  color="#ffff00" timeScale="1ms"/>
-            <Line id="I_l" quantity="hhpop/0/hhcell/bioPhys1/membraneProperties/leak/iDensity" scale="1"  color="#ff00ff" timeScale="1ms"/>
-        </Display>
-
-        <Display id="d4" title="Hodgkin-Huxley Neuron: I_inj (nA)" timeScale="1ms" xmin="-5" xmax="55" ymin="-0.01" ymax="0.4">
-            <Line id="I_inj" quantity="hhpop/0/hhcell/pulseGen1/i" scale="1nA"  color="#ffffff" timeScale="1ms"/>
-        </Display>
 
         <OutputFile id="of0" fileName="hh_v.dat">
             <OutputColumn id="v" quantity="hhpop/0/hhcell/v"/> 

Tutorial/Source/test/.test.singleap.jnmlbrian2.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_HH_SingleAP.xml 
+engine: jNeuroML_Brian2
+mep: .test.singleap.mep
+experiments:
+  Current clamp:
+    observables:
+      spike times:
+        file: 
+          path: ../hh_v.dat
+          columns: [0,1]
+          scaling: [1000, 1000]
+        spike detection: 
+          method: threshold
+          threshold: 0
+        tolerance: 0.000375281461096

Tutorial/Source/test/.test.singleap.jnmlnrn.omt

@@ -2,3 +2,16 @@
 
 target: ../LEMS_HH_SingleAP.xml 
 engine: jNeuroML_NEURON
+mep: .test.singleap.mep
+experiments:
+  Current clamp:
+    observables:
+      spike times:
+        file: 
+          path: ../hh_v.dat
+          columns: [0,1]
+          scaling: [1000, 1000]
+        spike detection: 
+          method: threshold
+          threshold: 0
+        tolerance: 0.0

Tutorial/Source/test/.test.singleap.jnmlpynnnrn.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_HH_SingleAP.xml 
+engine: jNeuroML_PyNN_NEURON
+mep: .test.singleap.mep
+experiments:
+  Current clamp:
+    observables:
+      spike times:
+        file: 
+          path: ../hh_v.dat
+          columns: [0,1]
+          scaling: [1000, 1000]
+        spike detection: 
+          method: threshold
+          threshold: 0
+        tolerance: 0.0

Tutorial/Source/test/.test.singleap.mep

@@ -0,0 +1,6 @@
+system: Testing a single compartment cell
+
+experiments:
+  Current clamp:
+    expected:
+      spike times: [7.994]