Merge pull request #124 from LEMS/development

Changes for NeuroML v2.3.1 release

.github/workflows/ci.yml

@@ -16,17 +16,23 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        java: [ '8', '11', '16', '17', '19' ]
+        java: [ '8', '11', '16', '17', '19', '21' ]
         runs-on: [ubuntu-latest, macos-latest, windows-latest]
+        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@v2
+    - uses: actions/checkout@v4
     - name: Set up JDK ${{ matrix.Java }}
-      uses: actions/setup-java@v2
+      uses: actions/setup-java@v4
       with:
         java-version: ${{ matrix.Java }}
-        distribution: 'adopt'
+        distribution: 'temurin'
     - name: Test with Maven
       run: mvn install
     - name: Further tests, non Win

.github/workflows/examples.yml

@@ -10,7 +10,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - uses: nelonoel/[email protected]
 
     # https://stackoverflow.com/questions/58033366/how-to-get-current-branch-within-github-actions
@@ -20,7 +20,7 @@ jobs:
       id: extract_branch
 
     - name: Checkout lems
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
       with:
         repository: LEMS/LEMS
         ref: ${{ steps.extract_branch.outputs.branch }}

build.xml

@@ -42,8 +42,8 @@
         <javac srcdir="src"
                destdir="build"
                debug="true"
-               source="1.6"
-               target="1.6"
+               source="1.8"
+               target="1.8"
                includeantruntime="false"
                classpathref="junit.classpath">
             <include name="**/*.java"/>

lems

@@ -1,6 +1,6 @@
 #!/bin/sh
 
-export LEMS_VERSION=0.10.8
+export LEMS_VERSION=0.11.1
 
 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=0.10.8
+set LEMS_VERSION=0.11.1
 
 set CLASSPATH=target\jlems-%LEMS_VERSION%.jar;%LEMS_HOME%\target\jlems-%LEMS_VERSION%.jar
 

pom.xml

@@ -3,7 +3,7 @@
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>org.lemsml</groupId>
 	<artifactId>jlems</artifactId>
-	<version>0.10.8</version>
+	<version>0.11.1</version>
 	<packaging>bundle</packaging>  
 	<properties>
     	<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
@@ -29,8 +29,8 @@
 				<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/jlems/core/run/StateInstance.java

@@ -300,6 +300,9 @@ public void advance(StateRunnable parent, double t, double dt) throws RuntimeErr
 
 
 	public void transitionTo(String rnm) throws RuntimeError {
+		if (regimeHM == null) {
+			throw new IllegalStateException("No Regimes.");
+		}
 		activeRegime = regimeHM.get(rnm);
 		activeRegime.enter();
 	}
@@ -314,6 +317,9 @@ public void doneInit() {
 
 	public void initRegime() throws RuntimeError {
 		if (activeRegime == null) {
+			if (regimeHM == null || regimeHM.isEmpty()) {
+				throw new IllegalStateException("No Regimes.");
+			}
 			activeRegime = regimeHM.get(regimeHM.keySet().iterator().next());
 			// TODO just picks random regime
 		}

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

@@ -90,9 +90,12 @@ public void checkDimensions(HashMap<String, Dimensional> dimHM) throws ContentEr
                 if (dres.isDimensionless()) {
                     // OK
                 } else {
-                    E.oneLineError("Dimension mismatch in equation: " + variable + " = " + value + ". Residual dimension: " + dres);
-                    E.info("Dimension of " + variable + ": " + dsv + ", multiplier=" + dlf + ", left=" + dl + ", rhs=" + drhs);
-                    E.info("All:" + dimHM);
+
+					String errmsg = ("Dimension mismatch in the equation: " + variable + " = " + value + ". Residual dimension: " + dres + 
+                        "\nDimension of " + variable + ": " + dsv + ", multiplier=" + dlf + ", left=" + dl + ", rhs=" + drhs +
+                        "\nAll:" + dimHM);
+					E.info(errmsg);
+                	throw new ContentError(errmsg);
                 }
             }
 

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

@@ -525,7 +525,7 @@ public Valued getValued(String select) throws ContentError {
 
 
 
-	public void checkEquations(HashMap<String, Dimensional> cdimHM) throws ContentError {
+	public void checkEquations(HashMap<String, Dimensional> cdimHM) throws ContentError{
 
 		HashMap<String, Dimensional> dimHM = new HashMap<String, Dimensional>();
 
@@ -559,15 +559,18 @@ public void checkEquations(HashMap<String, Dimensional> cdimHM) throws ContentEr
 			try {
 				dimHM.put(dv.getName(), dv.getDimensionality(dimHM));
 			} catch (ContentError ce) {
-				E.error("Checking " + dv + " in " + r_type + " " + ce.getMessage());
+				String errmsg = ("Checking derived variable: " + dv + " in " + r_type + "\nError here: " + ce.getMessage());
+                E.error(errmsg+"\n**************\n* Note: this may not be a serious error, in the case that the derived variables are all present, just have been specified out of order, e.g. b = f(a) is defined in the xML file before a is defined. ");
+
 			}
 		}
 
 		for (ConditionalDerivedVariable cdv : conditionalDerivedVariables) {
 			try {
 				dimHM.put(cdv.getName(), cdv.getDimensionality(dimHM));
 			} catch (ContentError ce) {
-				E.error("Checking " + cdv + " in " + r_type + " " + ce.getMessage());
+				String errmsg = "Checking " + cdv + " in " + r_type + " " + ce.getMessage();
+                throw new ContentError(errmsg);
 			}
 		}
 

src/main/java/org/lemsml/jlems/io/Main.java

@@ -19,7 +19,7 @@
 
 public final class Main {
 
-	 public static final String VERSION = "0.10.8";
+	 public static final String VERSION = "0.11.1";
 
 	 static String usage = "USAGE: java -jar target/jlems-"+VERSION+".jar [-cp folderpaths] model-file [-nogui]\n";
 

src/test/java/org/lemsml/jlems/test/ExamplesTest.java

@@ -85,6 +85,7 @@ public void testExample10() throws ContentError, ConnectionError, RuntimeError,
 
     public boolean executeExample(String filename) throws ContentError, ConnectionError, RuntimeError, ParseError, IOException, ParseException, BuildException,  XMLException {
 		URL url = this.getClass().getResource("/"+filename);
+        System.out.println(" - Testing: "+url);
 		File f = new File(url.getFile());
 
     	FileInclusionReader fir = new FileInclusionReader(f);

src/test/java/org/lemsml/jlems/test/XMLExamplesReaderTest.java

@@ -29,7 +29,7 @@ public void testReadFromString() throws ParseException, BuildException,
 		File fdir = new File(url.getFile());
 
 		for (File fx : fdir.listFiles()) {
-			E.info("Testing: " + fx);
+			E.info("   >>>  Testing: " + fx);
 			if (fx.isFile() && fx.getName().endsWith(".xml")) {
 				String stxt = FileUtil.readStringFromFile(fx);
 				XMLElementReader xmlReader = new XMLElementReader(stxt);
@@ -53,7 +53,7 @@ public void testReadFromString() throws ParseException, BuildException,
 							+ "'<Element a=\"val\"/>' and not '<Element a=\"val\"></Element>'");
 				}
 
-				assertEquals("Rewrite matches", sns.length(), tns.length());
+				assertEquals("Rewrite matches ("+fx+")", sns.length(), tns.length());
 			}
 		}
 	}

src/test/resources/SimpleNetwork.xml

@@ -4,7 +4,6 @@
         <Children name="connectivities" type="EventConnectivity"/>
     </ComponentType>
 
-
     <ComponentType name="Population">
         <ComponentReference name="component" type="Component"/>
         <Parameter name="size" dimension="none"/>
@@ -13,8 +12,6 @@
         </Structure>
     </ComponentType>
 
-
-
     <ComponentType name="EventConnectivity">
         <Link name="source" type="Population"/>
         <Link name="target" type="Population"/>
@@ -23,17 +20,13 @@
 
     <ComponentType name="ConnectionPattern"/>
 
-
-
     <ComponentType name="AllAll" extends="ConnectionPattern">
         <Structure>
             <ForEach instances="../source" as="a">
                 <ForEach instances="../target" as="b">
                     <EventConnection from="a" to="b"/>
                 </ForEach>
-            </ForEach>    
+            </ForEach>
         </Structure>
-
     </ComponentType>
-
 </Lems>

src/test/resources/SingleSimulation.xml

@@ -1,22 +1,17 @@
 <Lems>
-
-
     <ComponentType name="Display">
-        <Text name="title"/>   
+        <Text name="title"/>
         <Parameter name="xmin" dimension="none"/>
         <Parameter name="xmax" dimension="none"/>
         <Parameter name="ymin" dimension="none"/>
         <Parameter name="ymax" dimension="none"/>
-
         <Parameter name="timeScale" dimension="time"/>
         <Children name="lines" type="Line"/>
-
         <Simulation>
             <DataDisplay title="title" dataRegion="xmin,xmax,ymin,ymax"/>
         </Simulation>
     </ComponentType>
 
-
     <ComponentType name="Line">
         <Parameter name="scale" dimension="*"/>
         <Parameter name="timeScale" dimension="*"/>
@@ -27,49 +22,33 @@
         </Simulation>
     </ComponentType>
 
-
     <ComponentType name="OutputFile">
         <Text name="path"/>
         <Text name="fileName"/>
-
         <Children name="outputColumn" type="OutputColumn"/>
-
         <Simulation>
             <DataWriter path="path" fileName="fileName"/>
         </Simulation>
-
     </ComponentType>
 
-
     <ComponentType name="OutputColumn">
         <Path name="quantity"/>
         <Simulation>
             <Record quantity="quantity"/>
         </Simulation>
     </ComponentType>
 
-
-
     <ComponentType name="Simulation">
         <Parameter name="length" dimension="time"/>
         <Parameter name="step" dimension="time"/>
-
         <ComponentReference name="target" type="Component"/>
-
-
         <Children name="displays" type="Display"/>
-
         <Children name="outputs" type="OutputFile"/>
-
         <Dynamics>
             <StateVariable name="t" dimension="time"/>
         </Dynamics>
-
         <Simulation>
             <Run component="target" variable="t" increment="step" total="length"/>
         </Simulation>
     </ComponentType>
-
-
-
-</Lems>
+</Lems>

src/test/resources/elecdims.xml

@@ -4,5 +4,4 @@
     <Dimension name="conductance" m="-1" l="-2" t="3" i="2"/>
     <Dimension name="capacitance" m="-1" l="-2" t="4" i="2"/>
     <Dimension name="current" i="1"/>
-
-</Lems>
+</Lems>

src/test/resources/ex2dims.xml

@@ -1,5 +1,4 @@
-<Lems> 
-
+<Lems>
     <Dimension name="voltage" m="1" l="2" t="-3" i="-1"/>
     <Dimension name="time" t="1"/>
     <Dimension name="per_time" t="-1"/>
@@ -8,8 +7,8 @@
     <Dimension name="current" i="1"/>
     <Dimension name="temperature" k="1"/>
 
-    <Unit symbol="mV" dimension="voltage" power="-3"/> 
-    <Unit symbol="ms" dimension="time" power="-3"/> 
+    <Unit symbol="mV" dimension="voltage" power="-3"/>
+    <Unit symbol="ms" dimension="time" power="-3"/>
     <Unit symbol="pS" dimension="conductance" power="-12"/>
     <Unit symbol="nS" dimension="conductance" power="-9"/>
     <Unit symbol="uF" dimension="capacitance" power="-6"/>
@@ -19,5 +18,4 @@
     <Unit symbol="pA" dimension="current" power="-12"/>
     <Unit symbol="nA" dimension="current" power="-9"/>
     <Unit symbol="degC" dimension="temperature" offset="273.15"/>
-
-</Lems>
+</Lems>