Merge pull request #112 from LEMS/development

Updates for NML v2.3

.github/workflows/ci.yml

@@ -16,8 +16,8 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        java: [ '8', '11', '16', '17' ]
-        runs-on: [ubuntu-latest, macos-11, windows-latest]
+        java: [ '8', '11', '16', '17', '19' ]
+        runs-on: [ubuntu-latest, macos-latest, windows-latest]
 
     name: Test on Java ${{ matrix.Java }} on ${{ matrix.runs-on }}
     steps:

.github/workflows/examples.yml

@@ -3,7 +3,7 @@ name: Check LEMS examples
 
 on:
   push:
-    branches:  [ master, development, experimental ]
+    branches:  [ master, development ]
 
 jobs:
   verify:

lems

@@ -1,6 +1,6 @@
 #!/bin/sh
 
-export LEMS_VERSION=0.10.6
+export LEMS_VERSION=0.10.8
 
 export CLASSPATH=.:./target/jlems-$LEMS_VERSION.jar:$LEMS_HOME/target/jlems-$LEMS_VERSION.jar
 

lems.bat

@@ -1,6 +1,6 @@
 @echo off
 
-set LEMS_VERSION=0.10.6
+set LEMS_VERSION=0.10.8
 
 set CLASSPATH=target\jlems-%LEMS_VERSION%.jar;%LEMS_HOME%\target\jlems-%LEMS_VERSION%.jar
 

pom.xml

@@ -3,8 +3,11 @@
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>org.lemsml</groupId>
 	<artifactId>jlems</artifactId>
-	<version>0.10.6</version>
-	<packaging>bundle</packaging>
+	<version>0.10.8</version>
+	<packaging>bundle</packaging>  
+	<properties>
+    	<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+  	</properties>
 	<dependencies>
 		<dependency>
 			<groupId>junit</groupId>
@@ -34,10 +37,6 @@
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-surefire-plugin</artifactId>
                 <version>2.22.2</version>
-				<configuration>
-					<source>1.7</source>
-					<target>1.7</target>
-				</configuration>
 			</plugin>
 			<plugin>
 				<groupId>org.apache.felix</groupId>

src/main/java/org/lemsml/jlems/core/reader/LemsFactory.java

@@ -4,6 +4,7 @@
 import org.lemsml.jlems.core.type.dynamics.*;
 import org.lemsml.jlems.core.type.structure.*;
 import org.lemsml.jlems.core.type.simulation.Record;
+
 import org.lemsml.jlems.core.type.simulation.*;
 
 import org.lemsml.jlems.core.type.procedure.*;
@@ -764,10 +765,10 @@ private Child buildChild(XMLElement xel) {
                 ret.name = parseString(xv);
             } else if (xn.equals("type")) {
                 ret.type = parseString(xv);
-            } else if (xn.equals("description")) {
-                ret.description = parseString(xv);
             } else if (xn.equals("substitute")) {
                 ret.substitute = parseString(xv);
+            } else if (xn.equals("description")) {
+                ret.description = parseString(xv);
             } else {
                 E.warning("Unrecognized attribute " + xa + " " + xv);
             }
@@ -810,6 +811,8 @@ private Link buildLink(XMLElement xel) {
                 ret.name = parseString(xv);
             } else if (xn.equals("type")) {
                 ret.type = parseString(xv);
+            } else if (xn.equals("description")) {
+                ret.description = parseString(xv);
             } else if (xn.equals("root")) {
                 ret.root = parseString(xv);
             } else if (xn.equals("isAny")) {
@@ -2423,6 +2426,8 @@ private Simulation buildSimulation(XMLElement xel) {
                 ret.dataWriters.add((DataWriter)obj);
             } else if (obj instanceof EventWriter) {
                 ret.eventWriters.add((EventWriter)obj);
+            } else if (obj instanceof Meta) {
+                ret.metas.add((Meta)obj);
             } else {
                 E.warning("Unrecognized element ("+xn+"): " + cel);
             }

src/main/java/org/lemsml/jlems/core/type/Attachments.java

@@ -11,9 +11,9 @@
 		"and access purposes they are like child components. The cannonical use of attachments is in " +
 		"adding synapses to a cell when a network connection is made.")
 public class Attachments implements Named {
-	@ModelProperty(info="")
+	@ModelProperty(info="A name for the Attachments")
 	public String name;
-	@ModelProperty(info="")
+	@ModelProperty(info="The type of the Attachments")
 	public String type;
 	public ComponentType r_type;
 

src/main/java/org/lemsml/jlems/core/type/Child.java

@@ -11,7 +11,7 @@
 		"children of the same type but with different roles, such as the forward and reverse transition rates in a channel.")
 public class Child implements Named {
 
-	@ModelProperty(info="")
+	@ModelProperty(info="Name of the child")
     public String name;
 
 	@ModelProperty(info="Reference to a component class, the value should be the name of the target class.")
@@ -20,6 +20,7 @@ public class Child implements Named {
 
     public String substitute;
 
+	@ModelProperty(info="An optional description of the child")
     public String description;
 
 

src/main/java/org/lemsml/jlems/core/type/Children.java

@@ -12,7 +12,7 @@
 		"child components")
 public class Children implements Named  {
 
-	@ModelProperty(info="")
+	@ModelProperty(info="Name of the children")
     public String name;
 
 	@ModelProperty(info="The class of component allowed as children.")

src/main/java/org/lemsml/jlems/core/type/ComponentReference.java

@@ -12,11 +12,12 @@
 		"same way as a child component, but can be defined independently")
 public class ComponentReference implements Named  {
 
-	@ModelProperty(info="")
+	@ModelProperty(info="A name for the ComponentReference")
 	public String name;
 
-	@ModelProperty(info="Target type")
+	@ModelProperty(info="The type of the target Component")
 	public String type;
+	@ModelProperty(info="An optional description of the ComponentReference")
     public String description;
 	public ComponentType r_type;
 

src/main/java/org/lemsml/jlems/core/type/ComponentType.java

@@ -22,7 +22,7 @@
 import org.lemsml.jlems.core.type.structure.Structure;
 import org.lemsml.jlems.core.xml.XMLElement;
 
-@ModelElement(info="Root element for defining component types.")
+@ModelElement(info="Root element for defining LEMS Component Types.")
 
 @SuppressWarnings("StringConcatenationInsideStringBufferAppend")
 public class ComponentType extends Base implements Named, Summaried, Inheritor {

src/main/java/org/lemsml/jlems/core/type/DerivedParameter.java

@@ -6,7 +6,7 @@
 import org.lemsml.jlems.core.sim.ContentError;
 import org.lemsml.jlems.core.type.dynamics.ExpressionValued;
 
-@ModelElement(info="A parameter that comes from other parameter values in the model rather than being set explicitly. Its value " +
+@ModelElement(info="A parameter that is a function of the Component's Parameters, which does not change with time. Its value " +
 		"can be supplied either with the 'value' attribute that evaluates within the scope of the definition, or with the " +
 		"'select' attribute which gives a path to 'primary' version of the parameter. For example, " +
 		" setting select='//MembranePotential[species=channel/species]/reversal' within the appropriate context allows " +
@@ -15,8 +15,13 @@
 
 public class DerivedParameter extends ExpressionValued implements Named {
 
+	@ModelProperty(info="The name of the derived parameter")
 	public String name;
+
+	@ModelProperty(info="The dimension, or 'none'. This should be the name of an already defined dimension element")
 	public String dimension;
+
+	@ModelProperty(info="An optional description of the derived parameter")
 	public String description;
 	public Dimension r_dimension;
 

src/main/java/org/lemsml/jlems/core/type/EventPort.java

@@ -5,14 +5,15 @@
 import org.lemsml.jlems.core.logging.E;
 import org.lemsml.jlems.core.sim.ContentError;
 
-@ModelElement(info = "A port on a component that can send or receive events, depending on the direction speicfied.")
+@ModelElement(info = "A port on a component that can send or receive events, depending on the direction specified")
 
 public class EventPort implements Named {
 
-    @ModelProperty(info = "")
+    @ModelProperty(info = "Name of the EventPort")
     public String name;
     @ModelProperty(info = "'IN' or 'OUT'")
     public String direction;
+	@ModelProperty(info="An optional description of the EventPort")
     public String description;
 
     public Dimension r_dimension;

src/main/java/org/lemsml/jlems/core/type/Exposure.java

@@ -5,15 +5,16 @@
 import org.lemsml.jlems.core.logging.E;
 import org.lemsml.jlems.core.sim.ContentError;
 
-@ModelElement(info = "A quantity that is made available to other component in the simulation. All variables in a Dynamics "
-+ "definition are private. If other components need access to them then the definition has to explicitly link them "
+@ModelElement(info = "A quantity that is made available to other components in the simulation. Note that all variables in a Dynamics "
++ "definition are private. If other components need access to them, then the definition should explicitly link them "
 + "to an exposure defined in the component class")
 public class Exposure implements Named {
 
-    @ModelProperty(info = "name")
+    @ModelProperty(info = "Name of the exposure element")
     public String name;
-    @ModelProperty(info = "Reference to a dimension")
+	@ModelProperty(info="The dimension, or 'none'. This should be the name of an already defined dimension element")
     public String dimension;
+	@ModelProperty(info="An optional description of the element")
     public String description;
     public Dimension r_dimension;
 

src/main/java/org/lemsml/jlems/core/type/Meta.java

@@ -3,34 +3,36 @@
 import java.util.ArrayList;
 import java.util.HashMap;
 
+import org.lemsml.jlems.core.annotation.ModelElement;
 import org.lemsml.jlems.core.sim.ContentError;
 import org.lemsml.jlems.core.xml.XMLAttribute;
 import org.lemsml.jlems.core.xml.XMLElement;
-
 
-// RawValued indicates that XML found inside Meta elements should be treated 
+
+// RawValued indicates that XML found inside Meta elements should be treated
 // processed into an element tree, but not interpreted as lems elements.
 // other tools can do their own thing with the content
+@ModelElement(info="Meta element to provide arbitrary metadata to LEMS simulations. Note that this is not processed by the LEMS interpreter.")
 public class Meta {
 
 	public String context;
-	
+
 	public XMLElement valueWrapper = new XMLElement("wrapper");
-	
+
 	private XMLElement p_sourceXML;
-	
+
 	public ArrayList<MetaItem> items = new ArrayList<MetaItem>();
 
-	
-	
+
+
 	public Meta() {
-		
+
 	}
-	
+
 	public void setSource(XMLElement xe) {
 		p_sourceXML = xe;
 	}
-	
+
 	public void addXMLElement(XMLElement xe) {
 		valueWrapper.add(xe);
 		// E.info("Set VW " + xe.toXMLString(""));
@@ -45,15 +47,15 @@ public HashMap<String, String> getAttributes() {
 		}
 		return ret;
 	}
-	 
+
 
 	public void add(Object obj) throws ContentError {
 		if (obj instanceof MetaItem) {
 			items.add((MetaItem)obj);
 		} else {
 			throw new ContentError("cant add " + obj);
 		}
-	} 
+	}
 
 	public MetaItem newItem(String nm) {
 		 MetaItem ret = new MetaItem(nm);

src/main/java/org/lemsml/jlems/core/type/Parameter.java

@@ -5,18 +5,19 @@
 import org.lemsml.jlems.core.logging.E;
 import org.lemsml.jlems.core.sim.ContentError;
 
-@ModelElement(info = "Sets the name an dimensionality of a parameter that must be supplied when a component is defined "
-+ "curresponding to the enclosing ComponentType")
+@ModelElement(info = "A quantity, defined by name and dimension, that must be supplied when a Component of the "
++ "enclosing ComponentType is defined")
 public class Parameter implements Named {
 
-	@ModelProperty(info="The name of the parameter. This is the attibute name when the parameter is supplied in a component definition")
+	@ModelProperty(info="The name of the parameter. This is the name of the attribute to be used when the parameter is supplied in a component definition")
 	public String name;
 
-	@ModelProperty(info="The dimension, or 'none'. This should be the ID of a dimension element defined elsewhere")
+	@ModelProperty(info="The dimension, or 'none'. This should be the name of an already defined dimension element")
 	public String dimension;
 
 	public Dimension r_dimension;
 
+	@ModelProperty(info="An optional description of the parameter")
     public String description;
 
     public String exposure;

src/main/java/org/lemsml/jlems/core/type/Requirement.java

@@ -19,10 +19,11 @@ public class Requirement implements Named {
     @ModelProperty(info = "name")
     public String name;
 
-    @ModelProperty(info = "reference to a dimension")
+	@ModelProperty(info="The dimension, or 'none'. This should be the name of an already defined dimension element")
     public String dimension;
     public Dimension r_dimension;
 
+	@ModelProperty(info="An optional description of the requirement")
     public String description;
 
 

src/main/java/org/lemsml/jlems/core/type/Text.java

@@ -7,9 +7,10 @@
 @ModelElement(info="Holds textual information that does not change the model but is needed for other purposes such as " +
 		"labelling graphs.")
 public class Text implements Named  {
-	@ModelProperty(info="")
+	@ModelProperty(info="The textual content")
 	public String name;
 
+	@ModelProperty(info="An optional description of the element")
     public String description;
 
 	public Text() {

src/main/java/org/lemsml/jlems/core/type/dynamics/AbstractStateChange.java

@@ -11,9 +11,11 @@
 import org.lemsml.jlems.core.sim.ContentError;
 import org.lemsml.jlems.core.type.Dimension;
 import org.lemsml.jlems.core.type.LemsCollection;
+import org.lemsml.jlems.core.annotation.ModelProperty;
 
 public abstract class AbstractStateChange extends ExpressionValued {
 
+	@ModelProperty(info="The name of the variable")
 	public String variable;
 
 	private StateVariable r_variable;

src/main/java/org/lemsml/jlems/core/type/dynamics/DerivedVariable.java

@@ -18,21 +18,22 @@
 import org.lemsml.jlems.core.type.LemsCollection;
 
 @ModelElement(info="A quantity that depends algebraically on other quantities in the model. The 'value' field can be " +
-		"set to a mathematical expression, or the select field to a path expression. If the path expression " +
+		"set to a mathematical expression, or the 'select' field to a path expression. If the path expression " +
 		"produces multiple matches, then the 'reduce' field says how these are reduced to a single value by " +
 		"taking the sum or product. ")
 public class DerivedVariable extends ExpressionValued implements Valued {
 
-	@ModelProperty(info="")
+	@ModelProperty(info="Name of the derived variable")
 	public String name;
 
-	@ModelProperty(info="")
+	@ModelProperty(info="A path to the variable that supplies the value. Note that to select a variable from another component, the variable must be marked as an Exposure. Exactly one of 'select' and 'value' is required")
 	public String select;
 
-	@ModelProperty(info="")
+	@ModelProperty(info="The dimension, or 'none'. This should be the name of an already defined dimension element")
 	public String dimension;
 	public Dimension r_dimension;
 
+	@ModelProperty(info="An optional description of the derived variable")
     public String description;
 
 	@ModelProperty(info="Either 'add' or 'multiply'. This applies if ther are multiple " +

src/main/java/org/lemsml/jlems/core/type/dynamics/Dynamics.java

@@ -34,7 +34,11 @@
 import org.lemsml.jlems.core.type.Requirement;
 
 
-@ModelElement(info="Specifies the dynamical behavior of components build from this ComponentType. ")
+@ModelElement(info="Specifies the dynamical behavior of components build from this ComponentType. "
++ "Note that all variables in a Dynamics "
++ "definition are private. If other components need access to them, then the definition should explicitly link them "
++ "to an Exposure defined in the component class"
+)
 public class Dynamics  {
 
 	public String name;