Merge pull request #73 from NeuroML/development

Changes for NeuroML v2.3.1 release
NeuroML · Aug 20, 2024 · b0bb24e · b0bb24e
2 parents 7ca95b5 + 476b1f5
commit b0bb24e
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -19,9 +19,9 @@ jobs:
       HDF5_DISABLE_VERSION_CHECK: 1
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python  ${{ matrix.python-version }}
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@v5
       with:
         python-version:  ${{ matrix.python-version }}
 
@@ -35,7 +35,7 @@ jobs:
           pip install .
           pip install -r requirements-extra.txt
                   
-          pip install 'numpy<=1.23.0' # temp fix, see https://github.com/OpenSourceBrain/osb-model-validation/issues/91
+          #pip install 'numpy<=1.23.0' # temp fix, see https://github.com/OpenSourceBrain/osb-model-validation/issues/91
 
 
     - name: Lint with flake8

diff --git a/.github/workflows/python-publish.yml b/.github/workflows/python-publish.yml
@@ -18,9 +18,9 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@v5
       with:
         python-version: '3.x'
     - name: Install dependencies

diff --git a/docs/NeuroMLlite_specification.json b/docs/NeuroMLlite_specification.json
@@ -1,5 +1,5 @@
 {
-    "version": "NeuroMLlite v0.5.7",
+    "version": "NeuroMLlite v0.6.0",
     "specification": {
         "Network": {
             "definition": "A Network containing multiple Population's, connected by Projection's and receiving Input's",

diff --git a/docs/NeuroMLlite_specification.yaml b/docs/NeuroMLlite_specification.yaml
@@ -1,4 +1,4 @@
-version: NeuroMLlite v0.5.7
+version: NeuroMLlite v0.6.0
 specification:
     Network:
         definition: A Network containing multiple Population's, connected by Projection's

diff --git a/docs/README.md b/docs/README.md
@@ -1,4 +1,4 @@
-# Specification of NeuroMLlite v0.5.7
+# Specification of NeuroMLlite v0.6.0
 **Note: the NeuroMLlite specification is still in development! Subject to change...**
 
 ## Network

diff --git a/examples/Example10_Lorenz.json b/examples/Example10_Lorenz.json
@@ -1,6 +1,6 @@
 {
     "Example10_Lorenz": {
-        "version": "NeuroMLlite v0.5.7",
+        "version": "NeuroMLlite v0.6.0",
         "notes": "Example 10: Lorenz",
         "parameters": {
             "N": 1,

diff --git a/examples/Example11_Synapses.json b/examples/Example11_Synapses.json
@@ -1,6 +1,6 @@
 {
     "Example11_Synapses": {
-        "version": "NeuroMLlite v0.5.7",
+        "version": "NeuroMLlite v0.6.0",
         "notes": "Example 11: synaptic properties",
         "parameters": {
             "input_amp": 0.23,

diff --git a/examples/Example11_Synapses.net.nml b/examples/Example11_Synapses.net.nml
@@ -1,5 +1,5 @@
-<neuroml xmlns="http://www.neuroml.org/schema/neuroml2"  xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.xsd" id="Example11_Synapses">
-    <notes>Generated by NeuroMLlite v0.5.7
+<neuroml xmlns="http://www.neuroml.org/schema/neuroml2"  xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.1.xsd" id="Example11_Synapses">
+    <notes>Generated by NeuroMLlite v0.6.0
     Generated network: Example11_Synapses
     Generation seed: 1234
     NeuroMLlite parameters: 

diff --git a/examples/Example12_MultiComp.json b/examples/Example12_MultiComp.json
@@ -1,6 +1,6 @@
 {
     "Example12_MultiComp": {
-        "version": "NeuroMLlite v0.5.7",
+        "version": "NeuroMLlite v0.6.0",
         "notes": "Example 12: Multicompartmental cells...",
         "parameters": {
             "N": 20,

diff --git a/examples/Example1_TestNetwork.json b/examples/Example1_TestNetwork.json
@@ -1,6 +1,6 @@
 {
     "TestNetwork": {
-        "version": "NeuroMLlite v0.5.7",
+        "version": "NeuroMLlite v0.6.0",
         "notes": "A simple network with 2 populations & projection between them. No info yet on what the cells are so network can't be simulated.",
         "populations": {
             "pop0": {

diff --git a/examples/Example2_TestNetwork.json b/examples/Example2_TestNetwork.json
@@ -1,6 +1,6 @@
 {
     "Example2_TestNetwork": {
-        "version": "NeuroMLlite v0.5.7",
+        "version": "NeuroMLlite v0.6.0",
         "notes": "A simple network with 2 populations & projection between them. Cells are specified to be NeuroML 2 HH cell models & pre population is given a spiking input.",
         "cells": {
             "hhcell": {

diff --git a/examples/Example2_TestNetwork.net.nml b/examples/Example2_TestNetwork.net.nml
@@ -1,5 +1,5 @@
-<neuroml xmlns="http://www.neuroml.org/schema/neuroml2"  xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.xsd" id="Example2_TestNetwork">
-    <notes>Generated by NeuroMLlite v0.5.7
+<neuroml xmlns="http://www.neuroml.org/schema/neuroml2"  xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.1.xsd" id="Example2_TestNetwork">
+    <notes>Generated by NeuroMLlite v0.6.0
     Generated network: Example2_TestNetwork
     Generation seed: 1234</notes>
     <include href="test_files/inputs.nml"/>

diff --git a/examples/Example3_Network.json b/examples/Example3_Network.json
@@ -1,6 +1,6 @@
 {
     "Example3_Network": {
-        "version": "NeuroMLlite v0.5.7",
+        "version": "NeuroMLlite v0.6.0",
         "notes": "Example 3: simple network with 2 populations of NeuroML2 cells, a projection between them and spiking input.",
         "cells": {
             "hhcell": {

diff --git a/examples/Example3_Network.net.nml b/examples/Example3_Network.net.nml
@@ -1,5 +1,5 @@
-<neuroml xmlns="http://www.neuroml.org/schema/neuroml2"  xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.xsd" id="Example3_Network">
-    <notes>Generated by NeuroMLlite v0.5.7
+<neuroml xmlns="http://www.neuroml.org/schema/neuroml2"  xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.1.xsd" id="Example3_Network">
+    <notes>Generated by NeuroMLlite v0.6.0
     Generated network: Example3_Network
     Generation seed: 1234</notes>
     <include href="test_files/inputs.nml"/>

diff --git a/examples/Example4.py b/examples/Example4.py
@@ -109,6 +109,7 @@
 print(net.to_json())
 net_json_file = net.to_json_file("%s.json" % net.id)
 net_yaml_file = net.to_yaml_file("%s.yaml" % net.id)
+net_xml_file = net.to_xml_file("%s.nmllite.xml" % net.id)
 
 
 ################################################################################

diff --git a/examples/Example4_PyNN.json b/examples/Example4_PyNN.json
@@ -1,6 +1,6 @@
 {
     "Example4_PyNN": {
-        "version": "NeuroMLlite v0.5.7",
+        "version": "NeuroMLlite v0.6.0",
         "notes": "Example 4: a network with PyNN cells & inputs",
         "parameters": {
             "input_amp": 0.99

diff --git a/examples/Example4_PyNN.net.nml b/examples/Example4_PyNN.net.nml
@@ -1,5 +1,5 @@
-<neuroml xmlns="http://www.neuroml.org/schema/neuroml2"  xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.xsd" id="Example4_PyNN">
-    <notes>Generated by NeuroMLlite v0.5.7
+<neuroml xmlns="http://www.neuroml.org/schema/neuroml2"  xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.1.xsd" id="Example4_PyNN">
+    <notes>Generated by NeuroMLlite v0.6.0
     Generated network: Example4_PyNN
     Generation seed: 1234
     NeuroMLlite parameters: 

diff --git a/examples/Example4_PyNN.yaml b/examples/Example4_PyNN.yaml
@@ -1,5 +1,5 @@
 Example4_PyNN:
-    version: NeuroMLlite v0.5.7
+    version: NeuroMLlite v0.6.0
     notes: 'Example 4: a network with PyNN cells & inputs'
     parameters:
         input_amp: 0.99

diff --git a/examples/Example6_PyNN.json b/examples/Example6_PyNN.json
@@ -1,6 +1,6 @@
 {
     "Example6_PyNN": {
-        "version": "NeuroMLlite v0.5.7",
+        "version": "NeuroMLlite v0.6.0",
         "notes": "Another network for PyNN - work in progress...",
         "parameters": {
             "N_scaling": 0.005,

diff --git a/examples/Example6_PyNN.net.nml b/examples/Example6_PyNN.net.nml
@@ -1,5 +1,5 @@
-<neuroml xmlns="http://www.neuroml.org/schema/neuroml2"  xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.xsd" id="Example6_PyNN">
-    <notes>Generated by NeuroMLlite v0.5.7
+<neuroml xmlns="http://www.neuroml.org/schema/neuroml2"  xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.1.xsd" id="Example6_PyNN">
+    <notes>Generated by NeuroMLlite v0.6.0
     Generated network: Example6_PyNN
     Generation seed: 1234
     NeuroMLlite parameters: 

diff --git a/examples/Example6_PyNN_noinputs.json b/examples/Example6_PyNN_noinputs.json
@@ -1,6 +1,6 @@
 {
     "Example6_PyNN_noinputs": {
-        "version": "NeuroMLlite v0.5.7",
+        "version": "NeuroMLlite v0.6.0",
         "notes": "Another network for PyNN - work in progress...",
         "parameters": {
             "N_scaling": 0.005,

diff --git a/examples/Example6_PyNN_noinputs.net.nml b/examples/Example6_PyNN_noinputs.net.nml
@@ -1,5 +1,5 @@
-<neuroml xmlns="http://www.neuroml.org/schema/neuroml2"  xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.xsd" id="Example6_PyNN_noinputs">
-    <notes>Generated by NeuroMLlite v0.5.7
+<neuroml xmlns="http://www.neuroml.org/schema/neuroml2"  xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.1.xsd" id="Example6_PyNN_noinputs">
+    <notes>Generated by NeuroMLlite v0.6.0
     Generated network: Example6_PyNN_noinputs
     Generation seed: 1234
     NeuroMLlite parameters: 

diff --git a/examples/Example7_Brunel2000.json b/examples/Example7_Brunel2000.json
@@ -1,6 +1,6 @@
 {
     "Example7_Brunel2000": {
-        "version": "NeuroMLlite v0.5.7",
+        "version": "NeuroMLlite v0.6.0",
         "notes": "Example 7: based on network of Brunel 2000",
         "parameters": {
             "g": 4,

diff --git a/examples/Example7_Brunel2000.net.nml b/examples/Example7_Brunel2000.net.nml
@@ -1,5 +1,5 @@
-<neuroml xmlns="http://www.neuroml.org/schema/neuroml2"  xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.xsd" id="Example7_Brunel2000">
-    <notes>Generated by NeuroMLlite v0.5.7
+<neuroml xmlns="http://www.neuroml.org/schema/neuroml2"  xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.1.xsd" id="Example7_Brunel2000">
+    <notes>Generated by NeuroMLlite v0.6.0
     Generated network: Example7_Brunel2000
     Generation seed: 1234
     NeuroMLlite parameters: 

diff --git a/examples/Example8_Extension.json b/examples/Example8_Extension.json
@@ -1,6 +1,6 @@
 {
     "Example8_Extension": {
-        "version": "NeuroMLlite v0.5.7",
+        "version": "NeuroMLlite v0.6.0",
         "notes": "Example 8: general testing...",
         "parameters": {
             "N": 10,

diff --git a/examples/Example9_HindmarshRose.json b/examples/Example9_HindmarshRose.json
@@ -1,6 +1,6 @@
 {
     "Example9_HindmarshRose": {
-        "version": "NeuroMLlite v0.5.7",
+        "version": "NeuroMLlite v0.6.0",
         "notes": "Example 9: HindmarshRose",
         "parameters": {
             "N": 1,

diff --git a/examples/LEMS_SimExample3.xml b/examples/LEMS_SimExample3.xml
@@ -1,34 +1,33 @@
 <Lems>
-    
+
     <!-- 
 
-        This LEMS file has been automatically generated using PyNeuroML v1.0.10 (libNeuroML v0.5.3)
+        This LEMS file has been automatically generated using PyNeuroML v1.3.7 (libNeuroML v0.6.3)
 
      -->
-    
+
     <!-- Specify which component to run -->
     <Target component="SimExample3" reportFile="report.SimExample3.txt"/>
 
     <!-- Include core NeuroML2 ComponentType definitions -->
     <Include file="Cells.xml"/>
     <Include file="Networks.xml"/>
     <Include file="Simulation.xml"/>
-    
+
     <Include file="PyNN.xml"/>
     <Include file="Example3_Network.net.nml"/>
     <Include file="test_files/inputs.nml"/>
     <Include file="test_files/hhcell.cell.nml"/>
-   
+
     <Simulation id="SimExample3" length="1000.0ms" step="0.025ms" target="Example3_Network" seed="5678">  <!-- Note seed: ensures same random numbers used every run -->
-
         <Display id="pop0_v" title="Plots of pop0_v" timeScale="1ms" xmin="-100.0" xmax="1100.0" ymin="-80" ymax="40">
             <Line id="pop0_0_hhcell_v" quantity="pop0/0/hhcell/v" scale="1mV" color="#d54f33" timeScale="1ms"/>
             <Line id="pop0_1_hhcell_v" quantity="pop0/1/hhcell/v" scale="1mV" color="#0534e4" timeScale="1ms"/>
             <Line id="pop0_2_hhcell_v" quantity="pop0/2/hhcell/v" scale="1mV" color="#98e752" timeScale="1ms"/>
             <Line id="pop0_3_hhcell_v" quantity="pop0/3/hhcell/v" scale="1mV" color="#bca074" timeScale="1ms"/>
             <Line id="pop0_4_hhcell_v" quantity="pop0/4/hhcell/v" scale="1mV" color="#632794" timeScale="1ms"/>
         </Display>
-        
+
         <Display id="pop1_v" title="Plots of pop1_v" timeScale="1ms" xmin="-100.0" xmax="1100.0" ymin="-80" ymax="40">
             <Line id="pop1_0_hhcell_v" quantity="pop1/0/hhcell/v" scale="1mV" color="#8a5d88" timeScale="1ms"/>
             <Line id="pop1_1_hhcell_v" quantity="pop1/1/hhcell/v" scale="1mV" color="#df5954" timeScale="1ms"/>
@@ -41,28 +40,28 @@
             <Line id="pop1_8_hhcell_v" quantity="pop1/8/hhcell/v" scale="1mV" color="#5fa56f" timeScale="1ms"/>
             <Line id="pop1_9_hhcell_v" quantity="pop1/9/hhcell/v" scale="1mV" color="#b5b5a2" timeScale="1ms"/>
         </Display>
-        
+
         <OutputFile id="SimExample3_pop0_v_dat" fileName="SimExample3.pop0.v.dat">
-            <OutputColumn id="pop0_0_hhcell_v" quantity="pop0/0/hhcell/v"/> 
-            <OutputColumn id="pop0_1_hhcell_v" quantity="pop0/1/hhcell/v"/> 
-            <OutputColumn id="pop0_2_hhcell_v" quantity="pop0/2/hhcell/v"/> 
-            <OutputColumn id="pop0_3_hhcell_v" quantity="pop0/3/hhcell/v"/> 
-            <OutputColumn id="pop0_4_hhcell_v" quantity="pop0/4/hhcell/v"/> 
+            <OutputColumn id="pop0_0_hhcell_v" quantity="pop0/0/hhcell/v"/>
+            <OutputColumn id="pop0_1_hhcell_v" quantity="pop0/1/hhcell/v"/>
+            <OutputColumn id="pop0_2_hhcell_v" quantity="pop0/2/hhcell/v"/>
+            <OutputColumn id="pop0_3_hhcell_v" quantity="pop0/3/hhcell/v"/>
+            <OutputColumn id="pop0_4_hhcell_v" quantity="pop0/4/hhcell/v"/>
         </OutputFile>
-        
+
         <OutputFile id="SimExample3_pop1_v_dat" fileName="SimExample3.pop1.v.dat">
-            <OutputColumn id="pop1_0_hhcell_v" quantity="pop1/0/hhcell/v"/> 
-            <OutputColumn id="pop1_1_hhcell_v" quantity="pop1/1/hhcell/v"/> 
-            <OutputColumn id="pop1_2_hhcell_v" quantity="pop1/2/hhcell/v"/> 
-            <OutputColumn id="pop1_3_hhcell_v" quantity="pop1/3/hhcell/v"/> 
-            <OutputColumn id="pop1_4_hhcell_v" quantity="pop1/4/hhcell/v"/> 
-            <OutputColumn id="pop1_5_hhcell_v" quantity="pop1/5/hhcell/v"/> 
-            <OutputColumn id="pop1_6_hhcell_v" quantity="pop1/6/hhcell/v"/> 
-            <OutputColumn id="pop1_7_hhcell_v" quantity="pop1/7/hhcell/v"/> 
-            <OutputColumn id="pop1_8_hhcell_v" quantity="pop1/8/hhcell/v"/> 
-            <OutputColumn id="pop1_9_hhcell_v" quantity="pop1/9/hhcell/v"/> 
+            <OutputColumn id="pop1_0_hhcell_v" quantity="pop1/0/hhcell/v"/>
+            <OutputColumn id="pop1_1_hhcell_v" quantity="pop1/1/hhcell/v"/>
+            <OutputColumn id="pop1_2_hhcell_v" quantity="pop1/2/hhcell/v"/>
+            <OutputColumn id="pop1_3_hhcell_v" quantity="pop1/3/hhcell/v"/>
+            <OutputColumn id="pop1_4_hhcell_v" quantity="pop1/4/hhcell/v"/>
+            <OutputColumn id="pop1_5_hhcell_v" quantity="pop1/5/hhcell/v"/>
+            <OutputColumn id="pop1_6_hhcell_v" quantity="pop1/6/hhcell/v"/>
+            <OutputColumn id="pop1_7_hhcell_v" quantity="pop1/7/hhcell/v"/>
+            <OutputColumn id="pop1_8_hhcell_v" quantity="pop1/8/hhcell/v"/>
+            <OutputColumn id="pop1_9_hhcell_v" quantity="pop1/9/hhcell/v"/>
         </OutputFile>
-        
+
     </Simulation>
 
 </Lems>
diff --git a/examples/LEMS_SimExample4.xml b/examples/LEMS_SimExample4.xml
@@ -1,57 +1,56 @@
 <Lems>
-    
+
     <!-- 
 
-        This LEMS file has been automatically generated using PyNeuroML v1.0.10 (libNeuroML v0.5.3)
+        This LEMS file has been automatically generated using PyNeuroML v1.3.7 (libNeuroML v0.6.3)
 
      -->
-    
+
     <!-- Specify which component to run -->
     <Target component="SimExample4" reportFile="report.SimExample4.txt"/>
 
     <!-- Include core NeuroML2 ComponentType definitions -->
     <Include file="Cells.xml"/>
     <Include file="Networks.xml"/>
     <Include file="Simulation.xml"/>
-    
+
     <Include file="PyNN.xml"/>
     <Include file="Example4_PyNN.net.nml"/>
-   
+
     <Simulation id="SimExample4" length="1000.0ms" step="0.01ms" target="Example4_PyNN" seed="5678">  <!-- Note seed: ensures same random numbers used every run -->
-
         <Display id="pop0_v" title="Plots of pop0_v" timeScale="1ms" xmin="-100.0" xmax="1100.0" ymin="-80" ymax="40">
             <Line id="pop0_0_testcell_v" quantity="pop0/0/testcell/v" scale="1mV" color="#d54f33" timeScale="1ms"/>
             <Line id="pop0_1_testcell_v" quantity="pop0/1/testcell/v" scale="1mV" color="#0534e4" timeScale="1ms"/>
         </Display>
-        
+
         <Display id="pop1_v" title="Plots of pop1_v" timeScale="1ms" xmin="-100.0" xmax="1100.0" ymin="-80" ymax="40">
             <Line id="pop1_0_testcell2_v" quantity="pop1/0/testcell2/v" scale="1mV" color="#98e752" timeScale="1ms"/>
             <Line id="pop1_1_testcell2_v" quantity="pop1/1/testcell2/v" scale="1mV" color="#bca074" timeScale="1ms"/>
         </Display>
-        
+
         <Display id="pop2_v" title="Plots of pop2_v" timeScale="1ms" xmin="-100.0" xmax="1100.0" ymin="-80" ymax="40">
             <Line id="pop2_0_testcell2_v" quantity="pop2/0/testcell2/v" scale="1mV" color="#632794" timeScale="1ms"/>
         </Display>
-        
+
         <OutputFile id="SimExample4_pop0_v_dat" fileName="SimExample4.pop0.v.dat">
-            <OutputColumn id="pop0_0_testcell_v" quantity="pop0/0/testcell/v"/> 
-            <OutputColumn id="pop0_1_testcell_v" quantity="pop0/1/testcell/v"/> 
+            <OutputColumn id="pop0_0_testcell_v" quantity="pop0/0/testcell/v"/>
+            <OutputColumn id="pop0_1_testcell_v" quantity="pop0/1/testcell/v"/>
         </OutputFile>
-        
+
         <OutputFile id="SimExample4_pop1_v_dat" fileName="SimExample4.pop1.v.dat">
-            <OutputColumn id="pop1_0_testcell2_v" quantity="pop1/0/testcell2/v"/> 
-            <OutputColumn id="pop1_1_testcell2_v" quantity="pop1/1/testcell2/v"/> 
+            <OutputColumn id="pop1_0_testcell2_v" quantity="pop1/0/testcell2/v"/>
+            <OutputColumn id="pop1_1_testcell2_v" quantity="pop1/1/testcell2/v"/>
         </OutputFile>
-        
+
         <OutputFile id="SimExample4_pop2_v_dat" fileName="SimExample4.pop2.v.dat">
-            <OutputColumn id="pop2_0_testcell2_v" quantity="pop2/0/testcell2/v"/> 
+            <OutputColumn id="pop2_0_testcell2_v" quantity="pop2/0/testcell2/v"/>
         </OutputFile>
-        
+
         <EventOutputFile id="SimExample4_pop0_spikes" fileName="SimExample4.pop0.spikes" format="ID_TIME">
-            <EventSelection id="0" select="pop0/0/testcell" eventPort="spike"/> 
-            <EventSelection id="1" select="pop0/1/testcell" eventPort="spike"/> 
+            <EventSelection id="0" select="pop0/0/testcell" eventPort="spike"/>
+            <EventSelection id="1" select="pop0/1/testcell" eventPort="spike"/>
         </EventOutputFile>
-        
+
     </Simulation>
 
 </Lems>
diff --git a/examples/SimExample10.json b/examples/SimExample10.json
@@ -1,6 +1,6 @@
 {
     "SimExample10": {
-        "version": "NeuroMLlite v0.5.7",
+        "version": "NeuroMLlite v0.6.0",
         "network": "Example10_Lorenz.json",
         "duration": 10000.0,
         "dt": 1.0,

diff --git a/examples/SimExample11.json b/examples/SimExample11.json
@@ -1,6 +1,6 @@
 {
     "SimExample11": {
-        "version": "NeuroMLlite v0.5.7",
+        "version": "NeuroMLlite v0.6.0",
         "network": "Example11_Synapses.json",
         "duration": 1000.0,
         "dt": 0.01,