Merge pull request #96 from NeuroML/development

Updates for NMLv2.3
NeuroML · Sep 20, 2023 · 394dce4 · 394dce4
2 parents 88f87c1 + f7ec707
commit 394dce4
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Showing 25 changed files with 1,028 additions and 492 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -5,9 +5,9 @@ name: Java CI with Maven
 
 on:
   push:
-    branches:  [ master, development, experimental, osb* ]
+    branches:  [ master, development, experimental, osb*, test* ]
   pull_request:
-    branches:  [ master, development, experimental, osb* ]
+    branches:  [ master, development, experimental, osb*, test* ]
 
 jobs:
   build_and_test:
@@ -16,14 +16,14 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        java: [ '8', '11', '16', '17']
-        runs-on: [ubuntu-latest, macos-11, windows-2019 ]
+        java: [ '8', '11', '16', '17', '19']
+        runs-on: [ubuntu-latest, macos-latest, windows-2019 ]
 
     name: Test on Java ${{ matrix.Java }} on ${{ matrix.runs-on }}
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Set up JDK ${{ matrix.Java }}
-      uses: actions/setup-java@v2
+      uses: actions/setup-java@v3
       with:
         java-version: ${{ matrix.Java }}
         distribution: 'temurin'

diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
@@ -13,17 +13,18 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - uses: nelonoel/branch-name@v1.0.1
 
     - name: Set up JDK 11
-      uses: actions/setup-java@v1
+      uses: actions/setup-java@v3
       with:
         java-version: 11
+        distribution: 'temurin'
         java-package: jdk
 
     - name: Set up Python 3.9
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: 3.9
 
@@ -33,29 +34,29 @@ jobs:
         pip install ghp-import
 
     - name: Checkout NeuroML2
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
       with:
         repository: NeuroML/NeuroML2
         ref: development
         path: NeuroML2
 
     - name: Checkout org.lemsml
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
       with:
         repository: LEMS/jLEMS
         ref: development
         path: jLEMS
 
 
     - name: Checkout org.neuroml.model.injectingplugin
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
       with:
         repository: NeuroML/org.neuroml.model.injectingplugin
         ref: development
         path: org.neuroml.model.injectingplugin
 
     - name: Checkout org.neuroml.model
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
       with:
         repository: NeuroML/org.neuroml.model
         ref: development

diff --git a/.gitignore b/.gitignore
@@ -44,3 +44,6 @@ src/test/resources/examples/*nrn.py
 /Test.gv
 /Test.png
 /src/test/resources/examples/report*.txt
+/.classpath
+/.project
+/.settings
diff --git a/README.md b/README.md
@@ -1,7 +1,8 @@
 Export from NeuroML & LEMS
 ==========================
 
-[![Java CI with Maven](https://github.com/NeuroML/org.neuroml.export/actions/workflows/ci.yml/badge.svg)](https://github.com/NeuroML/org.neuroml.export/actions/workflows/ci.yml)
+[![Java CI with Maven](https://github.com/NeuroML/org.neuroml.export/actions/workflows/ci.yml/badge.svg)](https://github.com/NeuroML/org.neuroml.export/actions/workflows/ci.yml) [![Publish Javadocs](https://github.com/NeuroML/org.neuroml.export/actions/workflows/docs.yml/badge.svg)](https://github.com/NeuroML/org.neuroml.export/actions/workflows/docs.yml)
+
 [![GitHub](https://img.shields.io/github/license/NeuroML/org.neuroml.export)](https://github.com/NeuroML/org.neuroml.export/blob/master/LICENSE.lesser)
 [![GitHub pull requests](https://img.shields.io/github/issues-pr/NeuroML/org.neuroml.export)](https://github.com/NeuroML/org.neuroml.export/pulls)
 [![GitHub issues](https://img.shields.io/github/issues/NeuroML/org.neuroml.export)](https://github.com/NeuroML/org.neuroml.export/issues)

diff --git a/pom.xml b/pom.xml
@@ -4,7 +4,7 @@
     <groupId>org.neuroml.export</groupId>
     <artifactId>org.neuroml.export</artifactId>
     <packaging>bundle</packaging>
-    <version>1.8.1</version>
+    <version>1.9.1</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>1.8.1</version>
+            <version>1.9.1</version>
         </dependency>
         <dependency>
             <groupId>org.lemsml</groupId>
             <artifactId>jlems</artifactId>
-            <version>0.10.6</version>
+            <version>0.10.8</version>
         </dependency>
         <dependency>
             <groupId>org.apache.velocity</groupId>
@@ -49,7 +49,7 @@
                             &lt;br /&gt;
                             &lt;br /&gt;
                     </top>
-                    <bottom>Copyright NeuroML Contributors 2021</bottom>
+                    <bottom>Copyright NeuroML Contributors 2023</bottom>
                 </configuration>
             </plugin>
             <plugin>

diff --git a/src/main/java/org/lemsml/export/sedml/SEDMLWriter.java b/src/main/java/org/lemsml/export/sedml/SEDMLWriter.java
@@ -22,6 +22,7 @@
 import org.neuroml.export.utils.support.ModelFeature;
 import org.neuroml.model.util.NeuroMLException;
 import org.neuroml.export.utils.support.SupportLevelInfo;
+import org.neuroml.export.sbml.SBMLWriter;
 
 public class SEDMLWriter extends AXMLWriter
 {
@@ -274,24 +275,31 @@ public static void main(String[] args) throws Exception, ModelFeatureSupportExce
         ArrayList<File> lemsFiles = new ArrayList<File>();
 
 
-        lemsFiles.add(new File("../neuroConstruct/osb/cerebral_cortex/networks/ACnet2/neuroConstruct/generatedNeuroML2/LEMS_TwoCell.xml"));
+        //lemsFiles.add(new File("../neuroConstruct/osb/cerebral_cortex/networks/ACnet2/neuroConstruct/generatedNeuroML2/LEMS_TwoCell.xml"));
         //lemsFiles.add(new File("../OpenCortex/examples/LEMS_ACNet.xml"));
 
         //lemsFiles.add(new File("../OpenCortex/examples/LEMS_SpikingNet.xml"));
         //lemsFiles.add(new File("../OpenCortex/examples/LEMS_SimpleNet.xml"));
         lemsFiles.add(new File("../neuroConstruct/osb/showcase/SBMLShowcase/NeuroML2/LEMS_NML2_Ex9_FN.xml"));
+        lemsFiles.add(new File("../neuroConstruct/osb/generic/HindmarshRose1984/NeuroML2/LEMS_Regular_HindmarshRose.xml"));
 
 
         SEDMLWriter nw;
         for(File lemsFile : lemsFiles)
         {
             Lems lems = Utils.readLemsNeuroMLFile(lemsFile.getAbsoluteFile()).getLems();
-            nw = new SEDMLWriter(lems, lemsFile.getParentFile(), lemsFile.getName().replaceAll(".xml", ".sedml"), lemsFile.getName(), Format.SBML);
 
+            SBMLWriter sbmlw = new SBMLWriter(lems, lemsFile.getParentFile(), lemsFile.getName().replaceAll(".xml", ".sbml"));
+            for(File genFile : sbmlw.convert())
+            {
+                System.out.println("Generated SBML: " + genFile.getAbsolutePath());
+            }
+
+            nw = new SEDMLWriter(lems, lemsFile.getParentFile(), lemsFile.getName().replaceAll(".xml", ".sedml"), lemsFile.getName(), Format.SBML);
             List<File> ff = nw.convert();
             for(File f : ff)
             {
-                System.out.println("Generated sed-ml: " + f.getCanonicalPath());
+                System.out.println("Generated SED-ML: " + f.getCanonicalPath());
             }
 
         }