Merge pull request #120 from NeuroML/development

Changes for NeuroML v2.3.1 release

Author: pgleeson

.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/[email protected]
 
     - 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>1.9.1</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>1.9.1</version>
+            <version>1.10.1</version>
         </dependency>
         <dependency>
             <groupId>org.lemsml</groupId>
             <artifactId>jlems</artifactId>
-            <version>0.10.8</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/DLemsKeywords.java

@@ -2,79 +2,83 @@
 
 /**
  * @author matteocantarelli
- * 
+ *
  */
 public enum DLemsKeywords
 {
-	DT, 
-	SEED, 
-	REPORT_FILE, 
-    DYNAMICS, 
-    EVENTS, 
-    CONDITION, 
-    DIRECTION, 
-    EFFECT, 
-    NAME, 
-    TYPE, 
-    TITLE, 
-    PARAMETERS, 
-    STATE, 
-    STATE_FUNCTIONS, 
-    T_END, 
-    T_START, 
-    COMMENT, 
-    DUMP_TO_FILE, 
-    OUTPUT_FILE, 
-    SPIKE_FILE, 
-    SPIKE_FILE_FORMAT, 
-    EVENT_SELECTIONS, 
-    EVENT_SELECTION_ID, 
-    SELECT, 
-    EVENT_PORT, 
-    FILE_NAME, 
-    OUTPUT_COLUMNS, 
-    VARIABLE, 
-    QUANTITY, 
-    DISPLAY, 
-    ABSCISSA_AXIS, 
-    MIN, MAX, 
-    ORDINATE_AXIS, 
-    CURVES, 
-    ABSCISSA, 
-    ORDINATE, 
-    POPULATION, 
-    POPULATION_INDEX, 
-    SEGMENT_ID, 
-    SEGMENT_NAME, 
-    FRACTION_ALONG, 
-    COLOUR, 
-    POPULATIONS, 
-    SIZE, 
+    DT,
+    SEED,
+    REPORT_FILE,
+    DYNAMICS,
+    EVENTS,
+    CONDITION,
+    DIRECTION,
+    EFFECT,
+    NAME,
+    TYPE,
+    TITLE,
+    PARAMETERS,
+    STATE,
+    STATE_FUNCTIONS,
+    T_END,
+    T_START,
+    COMMENT,
+    DUMP_TO_FILE,
+    OUTPUT_FILE,
+    SPIKE_FILE,
+    SPIKE_FILE_FORMAT,
+    EVENT_SELECTIONS,
+    EVENT_SELECTION_ID,
+    SELECT,
+    EVENT_PORT,
+    FILE_NAME,
+    OUTPUT_COLUMNS,
+    VARIABLE,
+    QUANTITY,
+    DISPLAY,
+    ABSCISSA_AXIS,
+    MIN, MAX,
+    ORDINATE_AXIS,
+    CURVES,
+    ABSCISSA,
+    ORDINATE,
+    POPULATION,
+    POPULATION_INDEX,
+    SEGMENT_ID,
+    SEGMENT_NAME,
+    FRACTION_ALONG,
+    COLOUR,
+    POPULATIONS,
+    SIZE,
     SYNAPSES,
     SYNAPSE,
     COMPONENT,
-    PROJECTIONS, 
-    PRE_POPULATION, 
-    POST_POPULATION, 
+    PROJECTIONS,
+    PRE_POPULATION,
+    POST_POPULATION,
     CONNECTIONS,
-    PRE_CELL_ID, 
-    POST_CELL_ID, 
-    WEIGHT, 
-    DELAY, 
+    PRE_CELL_ID,
+    POST_CELL_ID,
+    WEIGHT,
+    DELAY,
     INPUTS,
-    
-    
+
+
     TEMPERATURE,
     NEURON_VARIABLE_NAME,
     NEURON_MECHANISM_NAME,
     NEURON_SECTION_NAME,
     NEURON_FRACT_ALONG,
     NEURON_VARIABLE_SCALE,
-    
-    EXPORT_LIBRARY_VERSION;
 
-	public String get()
-	{
-		return this.toString().toLowerCase();
-	}
+    EXPORT_LIBRARY_VERSION,
+
+    CVODE,
+    ABS_TOL,
+    REL_TOL;
+
+    public String get()
+    {
+        return this.toString().toLowerCase();
+    }
 }

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

@@ -31,7 +31,9 @@
 import org.lemsml.jlems.core.type.Dimension;
 import org.lemsml.jlems.core.type.FinalParam;
 import org.lemsml.jlems.core.type.Lems;
+import org.lemsml.jlems.core.type.LemsCollection;
 import org.lemsml.jlems.core.type.ParamValue;
+import org.lemsml.jlems.core.type.Meta;
 import org.lemsml.jlems.core.type.Target;
 import org.lemsml.jlems.core.type.dynamics.DerivedVariable;
 import org.lemsml.jlems.core.type.dynamics.IVisitable;
@@ -203,6 +205,38 @@ public String getMainScript() throws LEMSException, IOException
 
         g.writeStringField(DLemsKeywords.DT.get(), convertTime(simCpt.getParamValue("step")));
 
+        boolean nrn_cvode = false;
+        /* defaults from NEURON */
+        String abs_tol = "None";
+        String rel_tol = "None";
+        LemsCollection<Meta> metas = simCpt.metas;
+        for(Meta m : metas)
+        {
+            HashMap<String, String> attributes = m.getAttributes();
+            if (attributes.getOrDefault("for", "").equals("neuron"))
+            {
+                if (attributes.getOrDefault("method", "").equals("cvode"))
+                {
+                    nrn_cvode = true;
+                    abs_tol = attributes.getOrDefault("abs_tolerance", abs_tol);
+                    rel_tol = attributes.getOrDefault("rel_tolerance", rel_tol);
+                    E.info("CVode with abs_tol="+abs_tol+" , rel_tol="+rel_tol+" selected for NEURON simulation");
+                }
+            }
+
+        }
+        if (nrn_cvode == true)
+        {
+            g.writeStringField(DLemsKeywords.CVODE.get(), "true");
+        }
+        else
+        {
+            g.writeStringField(DLemsKeywords.CVODE.get(), "false");
+        }
+        /* set them to something even if not provided by user */
+        g.writeStringField(DLemsKeywords.ABS_TOL.get(), abs_tol);
+        g.writeStringField(DLemsKeywords.REL_TOL.get(), rel_tol);
+
         int seed = DEFAULT_SEED;
         if (simCpt.hasStringValue("seed"))
             seed = Integer.parseInt(simCpt.getStringValue("seed"));
@@ -639,16 +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);
                 }
             }
 
@@ -860,7 +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);
@@ -899,7 +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());