Merge pull request #26 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@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: 'temurin'
@@ -117,3 +122,14 @@ jobs:
         pwd
         mvn install
         mvn dependency:tree
+
+
+    - name: Run SBML test suite
+      if: ${{ matrix.runs-on == 'ubuntu-latest' }}
+      run: |
+        git clone https://github.com/sbmlteam/sbml-test-suite.git
+
+        mvn assembly:assembly -DdescriptorId=jar-with-dependencies
+
+        java -Xmx400M -classpath target/*jar-with-dependencies.jar org.neuroml.importer.sbml.SBMLImporter -runSBMLTestSuite
+        

.github/workflows/docs.yml

@@ -13,17 +13,18 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - uses: nelonoel/[email protected]
 
     - name: Set up JDK 11
-      uses: actions/setup-java@v1
+      uses: actions/setup-java@v4
       with:
         java-version: 11
         java-package: jdk
+        distribution: 'temurin'
 
     - name: Set up Python 3.9
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: 3.9
 
@@ -33,14 +34,14 @@ jobs:
         pip install ghp-import
 
     - name: Checkout NeuroML2
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
       with:
         repository: NeuroML/NeuroML2
         ref: development
         path: NeuroML2
 
     - name: Checkout org.lemsml
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
       with:
         repository: LEMS/jLEMS
         ref: development
@@ -54,14 +55,14 @@ jobs:
         path: org.neuroml.model.injectingplugin
 
     - name: Checkout org.neuroml.model
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
       with:
         repository: NeuroML/org.neuroml.model
         ref: development
         path: org.neuroml.model
 
     - name: Checkout org.neuroml.export
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
       with:
         repository: NeuroML/org.neuroml.export
         ref: development

.gitignore

@@ -32,3 +32,4 @@ src/test/resources/tmp
 
 biomodels
 Errors.txt
+/sbml-test-suite/

pom.xml

@@ -4,7 +4,7 @@
     <groupId>org.neuroml.import</groupId>
     <artifactId>org.neuroml.import</artifactId>
     <packaging>jar</packaging>
-    <version>1.9.1</version>
+    <version>1.10.1</version>
     <name>org.neuroml.import</name>
     <url>http://maven.apache.org</url>
     <repositories>
@@ -29,7 +29,7 @@
         <dependency>
             <groupId>org.neuroml.export</groupId>
             <artifactId>org.neuroml.export</artifactId>
-            <version>1.9.1</version>
+            <version>1.10.1</version>
         </dependency>
 
         <dependency>
@@ -71,15 +71,15 @@
                             &lt;br /&gt;
                             &lt;br /&gt;
                     </top>
-                    <bottom>Copyright NeuroML Contributors 2023</bottom>
+                    <bottom>Copyright NeuroML Contributors 2024</bottom>
                 </configuration>
             </plugin>
             <plugin>
                 <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>
         </plugins>

runSBMLTestSuite.sh

@@ -1,13 +1,12 @@
 #!/bin/bash
 
 
-if [ ! -d "sbmlTestSuite" ]; then
+if [ ! -d "sbml-test-suite" ]; then
 
     echo ""
-    echo "A copy of the SBML Test Suite needs to be checked out from Sourceforge. Try:"
+    echo "A copy of the SBML Test Suite needs to be checked out from GitHub. Try:"
     echo ""
-    echo "    mkdir sbmlTestSuite"
-    echo "    svn checkout https://svn.code.sf.net/p/sbml/code/trunk/test-suite/cases sbmlTestSuite/cases"
+    echo "    git clone https://github.com/sbmlteam/sbml-test-suite.git"
     echo ""
     exit 1
 

src/main/java/org/neuroml/importer/Main.java

@@ -4,5 +4,5 @@
 public class Main
 {
 
-    public static String ORG_NEUROML_IMPORT_VERSION = "1.9.1";
+    public static String ORG_NEUROML_IMPORT_VERSION = "1.10.1";
 }

src/main/java/org/neuroml/importer/sbml/SBMLImporter.java

@@ -314,6 +314,11 @@ public static Lems convertSBMLToLEMS(File sbmlFile, float simDuration, float sim
                         newDim.setN(newDim.getN() + exponent * 1);
                     } else if (kind.equals("second")) {
                         newDim.setT(newDim.getT() + exponent * 1);
+                    } else if (kind.equals("volt")) {
+                        newDim.setM(newDim.getM() + exponent * 1);
+                        newDim.setL(newDim.getL() + exponent * 2);
+                        newDim.setT(newDim.getT() + exponent * -3);
+                        newDim.setI(newDim.getI() + exponent * -1);
                     } else {
                         //TODO: Add all unit kinds from section 4.4.2 in SBML specs: http://sbml.org/Documents/Specifications
                         System.err.print("Add more unit definitions! Missing: "+kind);
@@ -831,7 +836,7 @@ else if (r.isAssignment()) {
             E.info(">>>> StateVariable "+sv);
             dyn.stateVariables.add(sv);
 
-            TimeDerivative td = new TimeDerivative(sv.getName(), "1");
+            TimeDerivative td = new TimeDerivative(sv.getName(), timeScale.getName() + "* 1");
             dyn.timeDerivatives.add(td);
         }
 
@@ -1209,7 +1214,7 @@ public static void main(String[] args) throws Exception
 
 
 
-        File sbmlTestSuiteDir = new File("sbmlTestSuite/cases/semantic/");
+        File sbmlTestSuiteDir = new File("sbml-test-suite/cases/semantic/");
 
         boolean useSbmlTestSuite = sbmlTestSuiteDir.exists() && forceSBMLTestSuite;
 
@@ -1292,7 +1297,7 @@ public static void main(String[] args) throws Exception
                     while(testCase.length()<5) testCase ="0"+testCase;
 
 
-                    sbmlFile = new File("sbmlTestSuite/cases/semantic/"+testCase+"/"+testCase+"-sbml-"+version+".xml");
+                    sbmlFile = new File("sbml-test-suite/cases/semantic/"+testCase+"/"+testCase+"-sbml-"+version+".xml");
                     if (!sbmlFile.exists()){
                         E.info("   ----  File not found: "+sbmlFile.getAbsolutePath()+"!!   ---- \n\n");
                         notFound++;