Improve gap example

Author: pgleeson

.github/workflows/non-omv.yml

@@ -40,6 +40,7 @@ jobs:
         omv install neuron
         omv install netpyne
         omv install pyNeuroML
+        omv install pynn
 
         pip list
 

.gitignore

@@ -201,3 +201,7 @@ arm64
 /NeuroML2/gaps/report.SimExampleGJ.txt
 /NeuroML2/gaps/SimExampleGJ.json
 /NeuroML2/TwoCells/LEMS_TwoCell_netpyne_data.json-e
+/NeuroML2/gaps/*_netpyne.py
+/NeuroML2/gaps/*_nrn.py
+/NeuroML2/gaps/*.mod
+/NeuroML2/gaps/*.hoc

NeuroML2/gaps/ExampleGaps.py

@@ -1,5 +1,5 @@
 from neuromllite import Network, Cell, InputSource, Population, Synapse
-from neuromllite import Projection, RandomConnectivity, Input, Simulation
+from neuromllite import Projection, RandomConnectivity, Input, Simulation, RandomLayout, RectangularRegion
 import sys
 
 ################################################################################
@@ -23,12 +23,15 @@
 
 net.input_sources.append(input_source)
 
+r1 = RectangularRegion(id="region1", x=0, y=0, z=0, width=1000, height=100, depth=1000)
+net.regions.append(r1)
 
 pop_pre = Population(
     id="PopPre",
     size="1",
     component=cell.id,
     properties={"color": ".7 0 0"},
+    random_layout = RandomLayout(region=r1.id),
 )
 pop_post = Population(
     id="PopPost",

NeuroML2/gaps/Example_GapJunctions.net.nml

@@ -12,15 +12,21 @@
         <notes>Example: testing gap junctions...</notes>
         <property tag="recommended_dt_ms" value="0.025"/>
         <property tag="recommended_duration_ms" value="300.0"/>
-        <population id="PopPre" component="pascell" size="1"/>
+        <population id="PopPre" component="pascell" size="1" type="populationList">
+            <property tag="color" value=".7 0 0"/>
+            <property tag="region" value="region1"/>
+            <instance id="0">
+                <location x="52.363598850944328" y="8.718667752263231" z="407.241763670398313"/>
+            </instance>
+        </population>
         <population id="PopPost" component="pascell" size="3"/>
         <electricalProjection id="projGJ" presynapticPopulation="PopPre" postsynapticPopulation="PopPost">
-            <electricalConnection id="0" preCell="0" postCell="0" synapse="gj"/>
-            <electricalConnection id="1" preCell="0" postCell="1" synapse="gj"/>
-            <electricalConnection id="2" preCell="0" postCell="2" synapse="gj"/>
+            <electricalConnectionInstance id="0" preCell="../PopPre/0/pascell" postCell="../PopPost[0]" synapse="gj"/>
+            <electricalConnectionInstance id="1" preCell="../PopPre/0/pascell" postCell="../PopPost[1]" synapse="gj"/>
+            <electricalConnectionInstance id="2" preCell="../PopPre/0/pascell" postCell="../PopPost[2]" synapse="gj"/>
         </electricalProjection>
         <inputList id="stim" population="PopPre" component="iclamp0">
-            <input id="0" target="../PopPre[0]" destination="synapses"/>
+            <input id="0" target="../PopPre/0/pascell" destination="synapses"/>
         </inputList>
     </network>
 </neuroml>

NeuroML2/gaps/LEMS_SimExampleGJ.xml

@@ -26,7 +26,7 @@
         </Display>
 
         <Display id="PopPre_v" title="Plots of PopPre_v" timeScale="1ms" xmin="-30.0" xmax="330.0" ymin="-80" ymax="40">
-            <Line id="PopPre_0__v" quantity="PopPre[0]/v" scale="1mV" color="#bca074" timeScale="1ms"/>
+            <Line id="PopPre_0_pascell_v" quantity="PopPre/0/pascell/v" scale="1mV" color="#bca074" timeScale="1ms"/>
         </Display>
 
         <OutputFile id="SimExampleGJ_PopPost_v_dat" fileName="SimExampleGJ.PopPost.v.dat">
@@ -36,7 +36,7 @@
         </OutputFile>
 
         <OutputFile id="SimExampleGJ_PopPre_v_dat" fileName="SimExampleGJ.PopPre.v.dat">
-            <OutputColumn id="PopPre_0__v" quantity="PopPre[0]/v"/>
+            <OutputColumn id="PopPre_0_pascell_v" quantity="PopPre/0/pascell/v"/>
         </OutputFile>
 
     </Simulation>