Merge pull request #64 from openworm/experimental

Add test on jnmlmoose

Author: pgleeson

.github/workflows/omv-ci.yml

@@ -15,7 +15,7 @@ jobs:
       fail-fast: false
       matrix:
         python-version: [ 3.7, 3.9 ]
-        engine: [ jNeuroML_Brian2, jNeuroML, jNeuroML_NEURON, jNeuroML_NetPyNE, jNeuroML_EDEN, jNeuroML_validate, jNeuroML_PyNN_NEURON, Brian2 ]
+        engine: [ jNeuroML_Brian2, jNeuroML, jNeuroML_NEURON, jNeuroML_NetPyNE, jNeuroML_EDEN, jNeuroML_validate, jNeuroML_PyNN_NEURON, Brian2, jNeuroML_Moose ]
 
     steps:
     - uses: actions/checkout@v2

.gitignore

@@ -38,3 +38,4 @@ Tutorial/Source/*json
 **/.ipynb_checkpoints/
 /Tutorial/Source/HHCellNetwork.net.nml__flattened.xml
 /notebooks/Python_HH_version/hh_py_v.dat
+/Tutorial/Source/HHCellSingleAP.net.nml__flattened.xml

Tutorial/Source/LEMS_HH_Simulation.xml

@@ -3,8 +3,8 @@
     <!-- Example with Simple Hodgkin-Huxley cell specifying segment details-->
 
     <!-- This is a file which can be read and executed by the LEMS Interpreter.
-         It imports the LEMS definitions of the core NeuroML 2 Components, 
-         imports in "pure" NeuroML 2 and contains some LEMS elements for running 
+         It imports the LEMS definitions of the core NeuroML 2 Components,
+         imports in "pure" NeuroML 2 and contains some LEMS elements for running
          a simulation -->
 
 
@@ -23,7 +23,7 @@
 
 
     <Simulation id="sim1" length="450ms" step="0.01ms" target="HHCellNetwork">
-    
+
         <Display id="d1" title="Hodgkin-Huxley Neuron: V (mV)" timeScale="1ms" xmin="-20" xmax="470" ymin="-90" ymax="50">
             <Line id="V" quantity="hhpop[0]/v" scale="1mV" color="#000000" timeScale="1ms"/>
         </Display>
@@ -44,25 +44,25 @@
             <Line id="I_inj1" quantity="hhpop[0]/pulseGen1/i" scale="1nA"  color="#ffffff" timeScale="1ms"/>
             <Line id="I_inj2" quantity="hhpop[0]/pulseGen2/i" scale="1nA"  color="#000000" timeScale="1ms"/>
         </Display>
-        
+
         <!-- Saved the membrane potential to file: hh_v.dat -->
         <OutputFile id="of0" fileName="hh_v.dat">
-            <OutputColumn id="v" quantity="hhpop[0]/v"/> 
+            <OutputColumn id="v" quantity="hhpop[0]/v"/>
         </OutputFile>
-        
+
         <!-- for plotting results in JupyterNotebook -->
         <OutputFile id="of1" fileName="hh_forJupyterNotebook.dat">
-            <OutputColumn id="v" quantity="hhpop[0]/v"/> 
-			<OutputColumn id="m" quantity="hhpop[0]/bioPhys1/membraneProperties/naChans/naChan/m/q"/> 
-			<OutputColumn id="h" quantity="hhpop[0]/bioPhys1/membraneProperties/naChans/naChan/h/q"/> 
-			<OutputColumn id="n" quantity="hhpop[0]/bioPhys1/membraneProperties/kChans/kChan/n/q"/> 
-			<OutputColumn id="I_na" quantity="hhpop[0]/bioPhys1/membraneProperties/naChans/iDensity"/>
+            <OutputColumn id="v" quantity="hhpop[0]/v"/>
+            <OutputColumn id="m" quantity="hhpop[0]/bioPhys1/membraneProperties/naChans/naChan/m/q"/>
+            <OutputColumn id="h" quantity="hhpop[0]/bioPhys1/membraneProperties/naChans/naChan/h/q"/> 
+            <OutputColumn id="n" quantity="hhpop[0]/bioPhys1/membraneProperties/kChans/kChan/n/q"/>
+            <OutputColumn id="I_na" quantity="hhpop[0]/bioPhys1/membraneProperties/naChans/iDensity"/>
             <OutputColumn id="I_k"  quantity="hhpop[0]/bioPhys1/membraneProperties/kChans/iDensity"/>
             <OutputColumn id="I_l"  quantity="hhpop[0]/bioPhys1/membraneProperties/leak/iDensity"/>
-			<OutputColumn id="I_inj1" quantity="hhpop[0]/pulseGen1/i"/>
+            <OutputColumn id="I_inj1" quantity="hhpop[0]/pulseGen1/i"/>
             <OutputColumn id="I_inj2" quantity="hhpop[0]/pulseGen2/i"/>
         </OutputFile>
-        
+
     </Simulation>
 
 

Tutorial/Source/test/.test.jnmlmoose.omt …Source/test/.test.singleap.jnmlmoose.omtTutorial/Source/test/.test.jnmlmoose.omt renamed to Tutorial/Source/test/.test.singleap.jnmlmoose.omt Tutorial/Source/test/.test.jnmlmoose.omt renamed to Tutorial/Source/test/.test.singleap.jnmlmoose.omt

@@ -1,17 +1,17 @@
 # Script for running automated tests on OSB using Travis-CI, see https://github.com/OpenSourceBrain/osb-model-validation
 
-target: ../LEMS_HH_Simulation.xml 
+target: ../LEMS_HH_SingleAP.xml
 engine: jNeuroML_Moose
-mep: .test.mep
+mep: .test.singleap.mep
 experiments:
   Current clamp:
     observables:
       spike times:
-        file: 
+        file:
           path: ../hh_v.dat
           columns: [0,1]
           scaling: [1000, 1000]
-        spike detection: 
+        spike detection:
           method: threshold
           threshold: 0
-        tolerance: 0.00147105180204
+        tolerance: 0.000750562922191561