Merge pull request #124 from LEMS/development

Changes for NeuroML v2.3.1 release

Author: pgleeson

.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/branch-name@v1.0.1
 
     # 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 }}

.travis.yml

@@ -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"/>

build.xml

@@ -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

@@ -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
 

lems.bat

@@ -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>

pom.xml

@@ -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/run/StateInstance.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/AbstractStateChange.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);
 			}
 		}