feat(neuron/netpyne): use %r instead of %e or %s

.github/workflows/ci.yml

@@ -16,14 +16,19 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        java: [ '8', '11', '16', '17', '19']
-        runs-on: [ubuntu-latest, macos-latest, windows-2019 ]
+        java: [ '8', '11', '16', '17', '19', '21' ]
+        runs-on: [ubuntu-latest, macos-12, windows-2019] # Note macos-12, not latest/14, due to hdf5 install issue
+        exclude:
+          - runs-on: macos-latest
+            java: "8"
+          - runs-on: macos-latest
+            java: "16"
 
     name: Test on Java ${{ matrix.Java }} on ${{ matrix.runs-on }}
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up JDK ${{ matrix.Java }}
-      uses: actions/setup-java@v3
+      uses: actions/setup-java@v4
       with:
         java-version: ${{ matrix.Java }}
         distribution: 'temurin'

.github/workflows/docs.yml

@@ -13,18 +13,18 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - uses: nelonoel/branch-name@v1.0.1
 
     - name: Set up JDK 11
-      uses: actions/setup-java@v3
+      uses: actions/setup-java@v4
       with:
         java-version: 11
         distribution: 'temurin'
         java-package: jdk
 
     - name: Set up Python 3.9
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: 3.9
 
@@ -34,29 +34,29 @@ jobs:
         pip install ghp-import
 
     - name: Checkout NeuroML2
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         repository: NeuroML/NeuroML2
         ref: development
         path: NeuroML2
 
     - name: Checkout org.lemsml
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         repository: LEMS/jLEMS
         ref: development
         path: jLEMS
 
 
     - name: Checkout org.neuroml.model.injectingplugin
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         repository: NeuroML/org.neuroml.model.injectingplugin
         ref: development
         path: org.neuroml.model.injectingplugin
 
     - name: Checkout org.neuroml.model
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         repository: NeuroML/org.neuroml.model
         ref: development

pom.xml

@@ -4,7 +4,7 @@
     <groupId>org.neuroml.export</groupId>
     <artifactId>org.neuroml.export</artifactId>
     <packaging>bundle</packaging>
-    <version>1.10.0</version>
+    <version>1.10.1</version>
     <name>org.neuroml.export</name>
     <url>http://maven.apache.org</url>
 
@@ -18,12 +18,12 @@
         <dependency>
             <groupId>org.neuroml.model</groupId>
             <artifactId>org.neuroml.model</artifactId>
-            <version>1.10.0</version>
+            <version>1.10.1</version>
         </dependency>
         <dependency>
             <groupId>org.lemsml</groupId>
             <artifactId>jlems</artifactId>
-            <version>0.11.0</version>
+            <version>0.11.1</version>
         </dependency>
         <dependency>
             <groupId>org.apache.velocity</groupId>
@@ -49,7 +49,7 @@
                             &lt;br /&gt;
                             &lt;br /&gt;
                     </top>
-                    <bottom>Copyright NeuroML Contributors 2023</bottom>
+                    <bottom>Copyright NeuroML Contributors 2024</bottom>
                 </configuration>
             </plugin>
             <plugin>
@@ -91,8 +91,8 @@
                 <artifactId>maven-compiler-plugin</artifactId>
                 <version>3.0</version>
                 <configuration>
-                    <source>1.7</source>
-                    <target>1.7</target>
+                    <source>1.8</source>
+                    <target>1.8</target>
                 </configuration>
             </plugin>
             <plugin>

src/main/java/org/lemsml/export/dlems/DLemsWriter.java

@@ -673,16 +673,29 @@ private void writeDLemsForComponent(JsonGenerator g, Component comp, HashMap<Str
             g.writeObjectFieldStart(DLemsKeywords.PARAMETERS.get());
             writeParameters(g, comp);
             g.writeEndObject();
+
+            Component bpComp = comp.quietGetChild("biophysicalProperties");
+            if (bpComp==null)
+            {
+                try{
+                    Cell cell = (Cell)Utils.convertLemsComponentToNeuroML(comp, true, lems).get(comp.getID());
+                    bpComp = lems.getComponent(cell.getBiophysicalProperties().getId());
+                }
+                catch (NeuroMLException ne)
+                {
+                    throw new ContentError("Unable to parse cell's biophysicalProperties", ne);
+                }
+            }
 
-            for (Component specie: comp.getChild("biophysicalProperties").getChild("intracellularProperties").getChildrenAL("speciesList")) {
+            for (Component specie: bpComp.getChild("intracellularProperties").getChildrenAL("speciesList")) {
 
                 try{
                     g.writeStringField(specie.getID()+"_initial_internal_conc", ""+Utils.getMagnitudeInSI(specie.getAttributeValue("initialConcentration")));
                     g.writeStringField(specie.getID()+"_initial_external_conc", ""+Utils.getMagnitudeInSI(specie.getAttributeValue("initialExtConcentration")));
                 }
                 catch (NeuroMLException ne)
                 {
-                    throw new ContentError("Unabel to parse NeuroML", ne);
+                    throw new ContentError("Unable to parse NeuroML", ne);
                 }
             }
 
@@ -894,7 +907,7 @@ private void addNrnSecNameFract(Component comp, int segId, JsonGenerator g) thro
 
         if(!cachedNrnSecNames.get(comp.getID()).containsKey(segId))
         {
-            Cell cell = (Cell)Utils.convertLemsComponentToNeuroML(comp).get(comp.getID());
+            Cell cell = (Cell)Utils.convertLemsComponentToNeuroML(comp, true, lems).get(comp.getID());
 
             NamingHelper nh = new NamingHelper(cell);
             Segment segment = CellUtils.getSegmentWithId(cell, segId);
@@ -933,7 +946,14 @@ private void extractQuantityInfo(String quantity, JsonGenerator g) throws IOExce
             Component comp = popIdsVsComponents.get(lqp.getPopulation());
 
             if (comp.getComponentType().isOrExtends("cell")) {
-                for (Component seg: comp.getChild("morphology").getChildrenAL("segments")) {
+                Component morphComp = comp.quietGetChild("morphology");
+
+                if (morphComp==null) {
+                    morphComp=lems.getComponent(comp.getTextParam("morphology"));
+                }
+
+
+                for (Component seg: morphComp.getChildrenAL("segments")) {
                     if (seg.id.equals(lqp.getSegmentId()+"")) {
                         g.writeStringField(DLemsKeywords.SEGMENT_ID.get(), lqp.getSegmentId()+"");
                         g.writeStringField(DLemsKeywords.SEGMENT_NAME.get(), seg.getName());

src/main/java/org/neuroml/export/eden/EDENWriter.java

@@ -71,6 +71,7 @@ public void setSupportedFeatures()
 	{
 		sli.addSupportInfo(format, ModelFeature.ABSTRACT_CELL_MODEL, SupportLevelInfo.Level.HIGH);
 		sli.addSupportInfo(format, ModelFeature.COND_BASED_CELL_MODEL, SupportLevelInfo.Level.HIGH);
+        sli.addSupportInfo(format, ModelFeature.EXT_MORPH_BIOPHYS_CELL_MODEL, SupportLevelInfo.Level.HIGH);
 		sli.addSupportInfo(format, ModelFeature.SINGLE_COMP_MODEL, SupportLevelInfo.Level.HIGH);
 		sli.addSupportInfo(format, ModelFeature.NETWORK_MODEL, SupportLevelInfo.Level.HIGH);
 		sli.addSupportInfo(format, ModelFeature.MULTI_CELL_MODEL, SupportLevelInfo.Level.HIGH);

src/main/java/org/neuroml/export/info/InfoTreeCreator.java

@@ -65,7 +65,7 @@ public static InfoNode createInfoTreeFromComponent(final Component component) th
 	{
 		InfoNode infoRoot = new InfoNode();
 
-        LinkedHashMap<String, Standalone> standalones = Utils.convertLemsComponentToNeuroML(component);
+        LinkedHashMap<String, Standalone> standalones = Utils.convertLemsComponentToNeuroML(component, true, null);
 
 		for(Standalone element : standalones.values())
 		{

src/main/java/org/neuroml/export/netpyne/NetPyNEWriter.java

@@ -97,6 +97,7 @@ public void setSupportedFeatures()
 	{
 		sli.addSupportInfo(format, ModelFeature.ABSTRACT_CELL_MODEL, SupportLevelInfo.Level.HIGH);
 		sli.addSupportInfo(format, ModelFeature.COND_BASED_CELL_MODEL, SupportLevelInfo.Level.HIGH);
+        sli.addSupportInfo(format, ModelFeature.EXT_MORPH_BIOPHYS_CELL_MODEL, SupportLevelInfo.Level.HIGH);
 		sli.addSupportInfo(format, ModelFeature.SINGLE_COMP_MODEL, SupportLevelInfo.Level.HIGH);
 		sli.addSupportInfo(format, ModelFeature.NETWORK_MODEL, SupportLevelInfo.Level.HIGH);
 		sli.addSupportInfo(format, ModelFeature.MULTI_CELL_MODEL, SupportLevelInfo.Level.HIGH);
@@ -472,6 +473,11 @@ public static void main(String[] args) throws Exception
         //lemsFiles.add(new File("../neuroConstruct/osb/olfactorybulb/networks/MiglioreEtAl14_OlfactoryBulb3D/NeuroML2/Channels/test/LEMS_OlfactoryTest_12.xml"));
         //lemsFiles.add(new File("../neuroConstruct/osb/generic/hodgkin_huxley_tutorial/Tutorial/Source/LEMS_HH_Simulation.xml"));
         //lemsFiles.add(new File("../git/multi/temp/LEMS_ISN_net.xml"));
+        //lemsFiles.add(new File("../neuroConstruct/osb/cerebral_cortex/networks/ACnet2/neuroConstruct/generatedNeuroML2/LEMS_ACNet2.xml"));
+        lemsFiles.add(new File("../git/morphology_include/LEMS_m_in_b_in.xml"));
+        lemsFiles.add(new File("../git/morphology_include/LEMS_m_out_b_in.xml"));
+        lemsFiles.add(new File("../git/morphology_include/LEMS_m_out_b_out.xml"));
+        //lemsFiles.add(new File("../git/morphology_include/LEMS_m_in_b_out.xml"));
 
         for (File lemsFile : lemsFiles)
         {

src/main/java/org/neuroml/export/neuron/NamingHelper.java

@@ -13,6 +13,7 @@
 import org.neuroml.model.Segment;
 import org.neuroml.model.SegmentGroup;
 import org.neuroml.model.util.CellUtils;
+import org.neuroml.model.util.NeuroMLException;
 
 /**
  * 
@@ -31,7 +32,7 @@ public NamingHelper(Cell cell)
 		this.cell = cell;
 	}
 
-	public String getNrnSectionName(Segment seg)
+	public String getNrnSectionName(Segment seg) throws NeuroMLException
 	{
 
 		String uniqueId = cell.getId() + ":" + seg.getId();

src/main/java/org/neuroml/export/neuron/NeuronWriter.java

@@ -132,6 +132,7 @@ public void setSupportedFeatures()
     {
         sli.addSupportInfo(format, ModelFeature.ABSTRACT_CELL_MODEL, SupportLevelInfo.Level.MEDIUM);
         sli.addSupportInfo(format, ModelFeature.COND_BASED_CELL_MODEL, SupportLevelInfo.Level.MEDIUM);
+        sli.addSupportInfo(format, ModelFeature.EXT_MORPH_BIOPHYS_CELL_MODEL, SupportLevelInfo.Level.HIGH);
         sli.addSupportInfo(format, ModelFeature.SINGLE_COMP_MODEL, SupportLevelInfo.Level.MEDIUM);
         sli.addSupportInfo(format, ModelFeature.NETWORK_MODEL, SupportLevelInfo.Level.LOW);
         sli.addSupportInfo(format, ModelFeature.MULTI_CELL_MODEL, SupportLevelInfo.Level.MEDIUM);
@@ -1433,7 +1434,7 @@ else if(cc.getComponentType().isOrExtends(NeuroMLElements.CONTINUOUS_CONNECTION_
                     }
 
                     //columnsPostTraces.get(outfileId).add(bIndent+"    f_" + outfileId + "_f2.write('%e\\t'% py_v_" + timeRef + "[i] ");
-                    columnsPostTraces.get(outfileId).add(bIndent+"    f_" + outfileId + "_f2.write('%e\\t");
+                    columnsPostTraces.get(outfileId).add(bIndent+"    f_" + outfileId + "_f2.write('%r\\t");
                     writingVariables.get(outfileId).add("py_v_" + timeRef + "[i], ");
 
                     ArrayList<String> colIds = new ArrayList<String>();
@@ -1476,7 +1477,7 @@ else if(cc.getComponentType().isOrExtends(NeuroMLElements.CONTINUOUS_CONNECTION_
                             /*columnsPostTraces.get(outfileId).add(
                                     " + '%e\\t'%(py_v_" + colId + "[i]) ");*/
 
-                            columnsPostTraces.get(outfileId).add("%e\\t");
+                            columnsPostTraces.get(outfileId).add("%r\\t");
                             writingVariables.get(outfileId).add("py_v_" + colId + "[i], ");
 
                         }
@@ -2071,7 +2072,7 @@ private Cell getCellFromComponent(Component cellComponent) throws LEMSException,
         }
         else
         {
-            cell = Utils.getCellFromComponent(cellComponent);
+            cell = Utils.getCellFromComponent(cellComponent, lems);
             compIdsVsCells.put(cellComponent.getID(), cell);
         }
         return cell;
@@ -2105,7 +2106,11 @@ public IntracellularProperties convertCellWithMorphology(Component cellComponent
         {
             BiophysicalProperties bp = cell.getBiophysicalProperties();
             ip = bp.getIntracellularProperties();
-            bpComp = cellComponent.getChild("biophysicalProperties");
+            bpComp = cellComponent.quietGetChild("biophysicalProperties");
+            if (bpComp==null)
+            {
+                bpComp = lems.getComponent(bp.getId());
+            }
             mpComp = bpComp.getChild("membraneProperties");
             ipComp = bpComp.getChild("intracellularProperties");
         }
@@ -3936,8 +3941,8 @@ public static void main(String[] args) throws Exception
 
         ArrayList<File> lemsFiles = new ArrayList<File>();
 
-        lemsFiles.add(new File("../neuroConstruct/osb/hippocampus/interneurons/WangBuzsaki1996/NeuroML2/LEMS_ComponentType/LEMS_WangBuzsaki.xml"));
-        lemsFiles.add(new File("../neuroConstruct/osb/generic/HindmarshRose1984/NeuroML2/LEMS_Regular_HindmarshRoseNML.xml"));
+        //lemsFiles.add(new File("../neuroConstruct/osb/hippocampus/interneurons/WangBuzsaki1996/NeuroML2/LEMS_ComponentType/LEMS_WangBuzsaki.xml"));
+        //lemsFiles.add(new File("../neuroConstruct/osb/generic/HindmarshRose1984/NeuroML2/LEMS_Regular_HindmarshRoseNML.xml"));
         //lemsFiles.add(new File("../neuroConstruct/osb/showcase/StochasticityShowcase/NeuroML2/LEMS_Inputs0.xml"));
         //lemsFiles.add(new File("../neuroConstruct/osb/invertebrate/celegans/CElegansNeuroML/CElegans/pythonScripts/c302/examples/LEMS_c302_C1_Oscillator.xml"));
 
@@ -3947,14 +3952,14 @@ public static void main(String[] args) throws Exception
         //lemsFiles.add(new File("../neuroConstruct/osb/cerebellum/networks/VervaekeEtAl-GolgiCellNetwork/NeuroML2/LEMS_Pacemaking.xml"));
         //lemsFiles.add(new File("../NeuroML2/LEMSexamples/LEMS_NML2_Ex9_FN.xml"));
         lemsFiles.add(new File("../NeuroML2/LEMSexamples/LEMS_NML2_Ex5_DetCell.xml"));
-        lemsFiles.add(new File("../NeuroML2/LEMSexamples/LEMS_NML2_Ex15_CaDynamics.xml"));
-        lemsFiles.add(new File("../neuroConstruct/osb/cerebral_cortex/networks/IzhikevichModel/NeuroML2/LEMS_2007One.xml"));
+        //lemsFiles.add(new File("../NeuroML2/LEMSexamples/LEMS_NML2_Ex15_CaDynamics.xml"));
+        //lemsFiles.add(new File("../neuroConstruct/osb/cerebral_cortex/networks/IzhikevichModel/NeuroML2/LEMS_2007One.xml"));
         //lemsFiles.add(new File("../org.neuroml.export/src/test/resources/examples/LEMS_SpikePass2.xml"));
         /*
         lemsFiles.add(new File("../neuroConstruct/osb/showcase/StochasticityShowcase/NeuroML2/LEMS_NoisyCurrentInput.xml"));
         lemsFiles.add(new File("../neuroConstruct/osb/showcase/StochasticityShowcase/NeuroML2/LEMS_OUCurrentInput_test.xml"));
         lemsFiles.add(new File("../neuroConstruct/osb/cerebral_cortex/networks/IzhikevichModel/NeuroML2/LEMS_FiveCells.xml"));*/
-        lemsFiles.add(new File("../git/ca1/NeuroML2/channels/test_Cadynamics/NeuroML2/LEMS_test_Ca.xml"));
+        //lemsFiles.add(new File("../git/ca1/NeuroML2/channels/test_Cadynamics/NeuroML2/LEMS_test_Ca.xml"));
         //lemsFiles.add(new File("../NeuroML2/LEMSexamples/LEMS_NML2_Ex20a_AnalogSynapsesHH.xml"));
         //lemsFiles.add(new File("../NeuroML2/LEMSexamples/LEMS_NML2_Ex20_AnalogSynapses.xml"));
         //lemsFiles.add(new File("../NeuroMLlite/neuromllite/LEMS_Sim_ten_cells_spikes_nest.xml"));
@@ -3976,7 +3981,11 @@ public static void main(String[] args) throws Exception
 //
 //        lemsFiles.add(new File("../neuroConstruct/osb/cerebral_cortex/multiple/PospischilEtAl2008/NeuroML2/channels/Na/LEMS_Na.xml"));
 //        lemsFiles.add(new File("../neuroConstruct/osb/cerebral_cortex/multiple/PospischilEtAl2008/NeuroML2/channels/Kd/LEMS_Kd.xml"));
-//        lemsFiles.add(new File("../neuroConstruct/osb/cerebral_cortex/networks/ACnet2/neuroConstruct/generatedNeuroML2/LEMS_MediumNet.xml"));
+        lemsFiles.add(new File("../neuroConstruct/osb/cerebral_cortex/networks/ACnet2/neuroConstruct/generatedNeuroML2/LEMS_ACNet2.xml"));
+        lemsFiles.add(new File("../git/morphology_include/LEMS_m_in_b_in.xml"));
+        lemsFiles.add(new File("../git/morphology_include/LEMS_m_out_b_in.xml"));
+        lemsFiles.add(new File("../git/morphology_include/LEMS_m_in_b_out.xml"));
+
 //        lemsFiles.add(new File("../OpenCortex/examples/LEMS_ACNet.xml"));
 //
         //lemsFiles.add(new File("../OpenCortex/examples/LEMS_SpikingNet.xml"));
@@ -3995,7 +4004,7 @@ public static void main(String[] args) throws Exception
 //        lemsFiles.add(new File("../NeuroML2/LEMSexamples/LEMS_NML2_Ex25_MultiComp.xml"));
 //        lemsFiles.add(new File("../neuroConstruct/osb/showcase/NetPyNEShowcase/NeuroML2/LEMS_HybridTut.xml"));
 //        lemsFiles.add(new File("../OpenCortex/examples/LEMS_L23TraubDemo_1cells_0conns.xml"));
-        lemsFiles.add(new File("../NeuroML2/LEMSexamples/LEMS_NML2_Ex0_IaF.xml"));
+        //lemsFiles.add(new File("../NeuroML2/LEMSexamples/LEMS_NML2_Ex0_IaF.xml"));
 
         //lemsFiles.add(new File("../neuroConstruct/osb/invertebrate/celegans/CElegansNeuroML/CElegans/pythonScripts/c302/examples/LEMS_c302_C1_Muscles.xml"));
         //lemsFiles.add(new File("../neuroConstruct/osb/invertebrate/celegans/CElegansNeuroML/CElegans/pythonScripts/c302/examples/LEMS_c302_C1_Syns.xml"));

src/main/java/org/neuroml/export/svg/Network3D.java

@@ -6,6 +6,7 @@
 import java.util.HashMap;
 import java.util.List;
 import org.neuroml.model.util.CellUtils;
+import org.neuroml.model.util.NeuroMLException;
 
 public class Network3D
 {
@@ -19,13 +20,13 @@ public Network3D(String comment)
         lines = new ArrayList<Line3D>(100);
     }
 
-    public Network3D(Cell cell)
+    public Network3D(Cell cell) throws NeuroMLException
     {
         this.comment = "Cell: "+cell.getId();
         lines = extractLines(cell, null);
     }
 
-    public void addCell(Cell cell, float offsetX, float offsetY, float offsetZ, String defaultColor)
+    public void addCell(Cell cell, float offsetX, float offsetY, float offsetZ, String defaultColor) throws NeuroMLException
     {
         lines.addAll(extractLines(cell, offsetX, offsetY, offsetZ, defaultColor));
     }
@@ -201,13 +202,13 @@ private Network3D rotate(double degreesAroundZ, double degreesAroundY)
     }
 
 
-    private ArrayList<Line3D> extractLines(Cell cell, String defaultColor)
+    private ArrayList<Line3D> extractLines(Cell cell, String defaultColor) throws NeuroMLException
     {
         return extractLines(cell, 0, 0, 0, defaultColor);
     }
 
 
-    private ArrayList<Line3D> extractLines(Cell cell, float offsetX, float offsetY, float offsetZ, String defaultColor)
+    private ArrayList<Line3D> extractLines(Cell cell, float offsetX, float offsetY, float offsetZ, String defaultColor) throws NeuroMLException
     {
         ArrayList<Line3D> result = new ArrayList<Line3D>();