Updates for NMLv2.3

.github/workflows/ci.yml

@@ -1,7 +1,5 @@
-# This workflow will build a Java project with Maven
-# For more information see: https://help.github.com/actions/language-and-framework-guides/building-and-testing-java-with-maven
 
-name: Test commits
+name: Build all NML Java
 
 on:
   push:
@@ -11,20 +9,21 @@ on:
 
 jobs:
   build:
-
     runs-on: ubuntu-latest
     strategy:
+      fail-fast: false
       matrix:
-        java: [ 8, 11, 16, 17 ]
+        java: [ '8', '11', '16', '17', '19' ]
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
 
     - name: Set up JDK ${{ matrix.java }}
-      uses: actions/setup-java@v1
+      uses: actions/setup-java@v3
       with:
         java-version: ${{ matrix.java }}
         java-package: jdk
+        distribution: 'adopt'
 
     - name: Install NeuroML 2 with Maven
       run: |
@@ -44,7 +43,7 @@ jobs:
         mvn dependency:tree
         ./jnml -v
         cd ..
-        
+
     - name: Install OMV
       run: |
         pwd
@@ -55,7 +54,7 @@ jobs:
         omv list -V
         env
         pip freeze
-        
+
     - name: Test examples using OMV
       run: |
         cd $GITHUB_WORKSPACE/NeuroML2/LEMSexamples

.github/workflows/omv-ci.yml

@@ -0,0 +1,51 @@
+name: Run OMV tests
+
+on:
+  push:
+    branches: [ master, development, experimental, documentation_update, osb* ]
+  pull_request:
+    branches: [ master, development, experimental, documentation_update, osb* ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: [ 3.9 ]
+        engine:
+          - jNeuroML
+          - jNeuroML_Brian2
+          - jNeuroML_EDEN
+          - jNeuroML_NEURON
+          - jNeuroML_NetPyNE
+          - jNeuroML_MOOSE
+          - jNeuroML_validate
+          - PyLEMS_NeuroML2
+
+    steps:
+    - uses: actions/checkout@v3
+
+    - name: Set up Python  ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version:  ${{ matrix.python-version }}
+
+    - name: Install OMV
+      run: |
+        pip install git+https://github.com/OpenSourceBrain/osb-model-validation
+        pip install scipy sympy matplotlib cython pandas tables
+
+        pip install 'numpy<=1.23.0' # see https://github.com/OpenSourceBrain/osb-model-validation/issues/91
+
+
+    - name: Run OMV tests on engine ${{ matrix.engine }}
+      run: |
+        omv all -V --engine=${{ matrix.engine }}
+
+    - name: OMV final version info
+      run: |
+        omv list -V # list installed engines
+        env
+        pip list

.gitignore

@@ -64,3 +64,7 @@ examples/*.pov
 /LEMSexamples/test/x86_64
 /LEMSexamples/report.ex*.txt
 /LEMSexamples/results/*.spikes
+/LEMSexamples/*.gen.so
+/LEMSexamples/tmp
+arm64
+/examples/NML2_SingleCompHHCell.nml__flattened.xml

HISTORY.md

@@ -8,6 +8,17 @@ and [LEMS](https://github.com/LEMS/LEMS), but also the Python ([libNeuroML](http
 
 **Only contributors who are not [NeuroML Editors](https://neuroml.org/editors) are specifically pointed out below.**
 
+v2.3 / 2022-??-??
+--------------------
+
+* **Renamed the main Schema from NeuroML_v2.2.xsd to [NeuroML_v2.3.xsd](https://github.com/NeuroML/NeuroML2/blob/master/Schemas/NeuroML2/NeuroML_v2.3).**
+
+* Added new cell type `<hindmarshRose1984Cell>`
+
+
+
+...
+
 v2.2 / 2021-12-15
 --------------------
 

LEMSexamples/LEMS_NML2_Ex15_CaDynamics.xml

@@ -253,7 +253,7 @@
     </ComponentType>
 
 
-    <decayingPoolConcentrationModel id="Gran_CaPool" 
+    <decayingPoolConcentrationModel id="Gran_CaPool"
                          ion="ca"
                          restingConc="7.55E-11 mol_per_cm3"
                          decayConstant="10.0 ms"
@@ -273,7 +273,7 @@
 
             <segmentGroup id="Soma" neuroLexId="sao864921383">    <!--
                 This group contains an unbranched set of segments, and all of the segmentGroups marked with
-                neuroLexId = sao864921383 form a non-overlapping set of all of the segments. 
+                neuroLexId = sao864921383 form a non-overlapping set of all of the segments.
                 These segmentGroups correspond to the 'cables' of NeuroML v1.8.1. -->
                 <member segment="0"/>
             </segmentGroup>
@@ -286,7 +286,7 @@
                 <include segmentGroup="Soma"/>
             </segmentGroup>
 
-            
+
         </morphology>
 
             <!--Adding the biophysical parameters-->
@@ -315,8 +315,8 @@
 
                 <species id="ca"
                          ion="ca"
-                         concentrationModel="Gran_CaPool" 
-                         initialConcentration="7.55E-11 mol_per_cm3" 
+                         concentrationModel="Gran_CaPool"
+                         initialConcentration="7.55E-11 mol_per_cm3"
                          initialExtConcentration="2.4E-6 mol_per_cm3"/>
 
                 <resistivity value="0.1 kohm_cm"/>
@@ -353,20 +353,21 @@
             <Line id="Gran_NaF_98/m" quantity="hhpop[0]/biophys/membraneProperties/Gran_NaF_98_all/Gran_NaF_98/m/q" scale="1"  color="#000000" timeScale="1ms"/>
             <Line id="Gran_NaF_98/h" quantity="hhpop[0]/biophys/membraneProperties/Gran_NaF_98_all/Gran_NaF_98/h/q" scale="1"  color="#0000ff" timeScale="1ms"/>
             <Line id="Gran_H_98/n" quantity="hhpop[0]/biophys/membraneProperties/Gran_H_98_all/Gran_H_98/n/q" scale="1"  color="#ff0000" timeScale="1ms"/>
-            
+
             <Line id="Gran_CaHVA_98/m" quantity="hhpop[0]/biophys/membraneProperties/Gran_CaHVA_98_all/Gran_CaHVA_98/m/q" scale="1"  color="#770fff" timeScale="1ms"/>
             <Line id="Gran_CaHVA_98/h" quantity="hhpop[0]/biophys/membraneProperties/Gran_CaHVA_98_all/Gran_CaHVA_98/h/q" scale="1"  color="#55f00f" timeScale="1ms"/>
-            
+
             <Line id="Gran_KA_98/m" quantity="hhpop[0]/biophys/membraneProperties/Gran_KA_98_all/Gran_KA_98/m/q" scale="1"  color="#ffff00" timeScale="1ms"/>
             <Line id="Gran_KA_98/h" quantity="hhpop[0]/biophys/membraneProperties/Gran_KA_98_all/Gran_KA_98/h/q" scale="1"  color="#ffffff" timeScale="1ms"/>
 
         </Display>
- 
+
         <Display id="d3" title="Ex15: Ca Dynamics: NaF, KDr, CaHVA, KA current densities (uA_per_cm2)" timeScale="1ms" xmin="0" xmax="700" ymin="-650" ymax="650">
             <Line id="NaF iDensity" quantity="hhpop[0]/biophys/membraneProperties/Gran_NaF_98_all/iDensity" scale="1uA_per_cm2"  color="#000000" timeScale="1ms"/>
-           <Line id="KDr iDensity" quantity="hhpop[0]/biophys/membraneProperties/Gran_KDr_98_all/iDensity" scale="1uA_per_cm2"  color="#0000ff" timeScale="1ms"/>
             <Line id="CaHVA iDensity" quantity="hhpop[0]/biophys/membraneProperties/Gran_CaHVA_98_all/iDensity" scale="1uA_per_cm2"  color="#00ff00" timeScale="1ms"/>
+            <Line id="KDr iDensity" quantity="hhpop[0]/biophys/membraneProperties/Gran_KDr_98_all/iDensity" scale="1uA_per_cm2"  color="#0000ff" timeScale="1ms"/>
             <Line id="KA iDensity" quantity="hhpop[0]/biophys/membraneProperties/Gran_KA_98_all/iDensity" scale="1uA_per_cm2"  color="#ff0000" timeScale="1ms"/>
+            <Line id="KCa iDensity" quantity="hhpop[0]/biophys/membraneProperties/Gran_KCa_98_all/iDensity" scale="1uA_per_cm2"  color="#ffff00" timeScale="1ms"/>
         </Display>
 
         <Display id="d4" title="Ex15: Ca Dynamics: Ca concentration (mM)" timeScale="1ms" xmin="0" xmax="700" ymin="-0.0005" ymax="0.003">
@@ -392,11 +393,24 @@
         <OutputFile id="of0" fileName="results/ex15_v.dat">
             <OutputColumn id="v" quantity="hhpop[0]/v"/>
         </OutputFile>
-
-        <!--<OutputFile id="of1" fileName="results/ex15_ha.dat">
-            <OutputColumn id="v" quantity="hhpop[0]/biophys/membraneProperties/Gran_KDr_98_all/Gran_KDr_98/h/alpha"/>
+
+        <OutputFile id="of1" fileName="results/ex15_curr_dens.dat">
+            <OutputColumn id="ina" quantity="hhpop[0]/biophys/membraneProperties/Gran_NaF_98_all/iDensity"/>
+            <OutputColumn id="ica" quantity="hhpop[0]/biophys/membraneProperties/Gran_CaHVA_98_all/iDensity"/>
+            <OutputColumn id="ikdr" quantity="hhpop[0]/biophys/membraneProperties/Gran_KDr_98_all/iDensity"/>
+            <OutputColumn id="ika" quantity="hhpop[0]/biophys/membraneProperties/Gran_KA_98_all/iDensity"/>
+            <OutputColumn id="ikca" quantity="hhpop[0]/biophys/membraneProperties/Gran_KCa_98_all/iDensity"/>
+        </OutputFile>
+
+        <OutputFile id="of2" fileName="results/ex15_cond_dens.dat">
+            <OutputColumn id="gna" quantity="hhpop[0]/biophys/membraneProperties/Gran_NaF_98_all/gDensity"/>
+            <OutputColumn id="gca" quantity="hhpop[0]/biophys/membraneProperties/Gran_CaHVA_98_all/gDensity"/>
+            <OutputColumn id="gkdr" quantity="hhpop[0]/biophys/membraneProperties/Gran_KDr_98_all/gDensity"/>
+            <OutputColumn id="gka" quantity="hhpop[0]/biophys/membraneProperties/Gran_KA_98_all/gDensity"/>
+            <OutputColumn id="gkca" quantity="hhpop[0]/biophys/membraneProperties/Gran_KCa_98_all/gDensity"/>
         </OutputFile>
-        <OutputFile id="of2" fileName="results/ex15_hb.dat">
+
+        <!--<OutputFile id="of2" fileName="results/ex15_hb.dat">
             <OutputColumn id="v" quantity="hhpop[0]/biophys/membraneProperties/Gran_KDr_98_all/Gran_KDr_98/h/beta"/>
         </OutputFile>-->
 
@@ -405,4 +419,4 @@
     </Simulation>
 
 
-</Lems>
+</Lems>

LEMSexamples/LEMS_NML2_Ex18_GHK.xml

@@ -13,7 +13,7 @@
   <!-- Membrane mechanisms -->
 
   <ionChannelPassive id="leak" conductance="10pS" species="non_specific"/>
-  
+
 
   <ionChannelHH id="na_chan" conductance="10pS" species="na">
 
@@ -22,7 +22,7 @@
       <forwardRate type="HHExpLinearRate" rate="1per_ms" midpoint="-40mV" scale="10mV"/>
       <reverseRate type="HHExpRate" rate="4per_ms" midpoint="-65mV" scale="-18mV"/>
     </gateHHrates>
-    
+
     <gateHHrates id="h" instances="1">
       <q10Settings type="q10ExpTemp" q10Factor="3" experimentalTemp="6.3 degC"/>
       <forwardRate type="HHExpRate" rate="0.07per_ms" midpoint="-65mV" scale="-20mV"/>
@@ -53,7 +53,7 @@
     </gateHHrates>
 
   </ionChannelHH>
-  
+
   <!-- Intracellular Calcium dynamics -->
   <concentrationModel id="simple_decay" type="fixedFactorConcentrationModel"
                       ion="ca"
@@ -157,7 +157,7 @@
       <OutputColumn id="ica" quantity="pop/0/na_k_ca/biophys/membraneProperties/ca_all/iDensity"/>
       <OutputColumn id="ca" quantity="pop/0/na_k_ca/caConc"/>
     </OutputFile>
-    
+
   </Simulation>