Merge pull request #93 from NeuroML/development

Updates for NMLv2.3

Author: pgleeson

.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-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:
@@ -68,10 +68,12 @@ jobs:
         ./jnml ../NeuroML2/LEMSexamples/LEMS_NML2_Ex9_FN.xml -cvode
         ./jnml ../NeuroML2/LEMSexamples/LEMS_NML2_Ex9_FN.xml -matlab
         ./jnml ../NeuroML2/LEMSexamples/LEMS_NML2_Ex9_FN.xml -dlems
+        ./jnml ../NeuroML2/LEMSexamples/LEMS_NML2_Ex9_FN.xml -eden
         ./jnml ../NeuroML2/LEMSexamples/regression-tests/LEMS_NML2_Ex5_DetCell_unformatted.xml -nogui
         ./jnml ../NeuroML2/examples/NML2_SimpleMorphology.nml  -svg
         ls -alt ../NeuroML2/examples
         ls -alt ../NeuroML2/LEMSexamples
+        env
 
     - name: Further tests (Win)
       if: ${{ matrix.runs-on == 'windows-2019' }}
@@ -87,5 +89,6 @@ jobs:
         .\jnml.bat ..\NeuroML2\LEMSexamples\LEMS_NML2_Ex9_FN.xml -cvode
         .\jnml.bat ..\NeuroML2\LEMSexamples\LEMS_NML2_Ex9_FN.xml -matlab
         .\jnml.bat ..\NeuroML2\LEMSexamples\LEMS_NML2_Ex9_FN.xml -dlems
+        .\jnml.bat ..\NeuroML2\LEMSexamples\LEMS_NML2_Ex9_FN.xml -eden
         .\jnml.bat ..\NeuroML2\LEMSexamples\regression-tests\LEMS_NML2_Ex5_DetCell_unformatted.xml -nogui
         .\jnml.bat ..\NeuroML2\examples\NML2_SimpleMorphology.nml  -svg

.travis.yml

@@ -125,7 +125,8 @@ def main():
                 or ("jNeuroML" in repo)
             )
 
-            if (repo in java_repos or repo in neuroml2_spec_repo) and runMvnInstall:
+            if (repo in java_repos or repo in neuroml2_spec_repo) \
+                    and runMvnInstall:
                 command = "mvn install"
                 print("It's a Java repository, so installing using Maven...")
                 info = execute_command_in_dir(command, local_dir)
@@ -162,7 +163,8 @@ def execute_command_in_dir(command, directory, exit_on_fail=True):
         % (command, directory, os.path.abspath(directory))
     )
 
-    p = subprocess.Popen(command, cwd=directory, shell=True, stdout=subprocess.PIPE)
+    p = subprocess.Popen(command, cwd=directory, shell=True,
+                         stdout=subprocess.PIPE)
     return_str = p.communicate()
 
     if p.returncode != 0:

getNeuroML.py

@@ -5,7 +5,7 @@
 #   Type java -X for more info
 export JNML_MAX_MEMORY=400M
 
-export JNML_VERSION=0.11.1
+export JNML_VERSION=0.12.4
 
 
 export CLASSPATH=.:./target/jNeuroML-$JNML_VERSION-jar-with-dependencies.jar:$JNML_HOME/target/jNeuroML-$JNML_VERSION-jar-with-dependencies.jar

jnml

@@ -1,6 +1,6 @@
 @echo off
 
-set JNML_VERSION=0.11.1
+set JNML_VERSION=0.12.4
 
 set CLASSPATH=target\jNeuroML-%JNML_VERSION%-jar-with-dependencies.jar;%JNML_HOME%\jNeuroML-%JNML_VERSION%-jar-with-dependencies.jar
 

jnml.bat

@@ -4,7 +4,7 @@
 
     <groupId>org.neuroml</groupId>
     <artifactId>jNeuroML</artifactId>
-    <version>0.11.1</version>
+    <version>0.12.4</version>
     <packaging>jar</packaging>
 
     <name>jNeuroML</name>
@@ -24,26 +24,24 @@
         <dependency>
             <groupId>org.neuroml1.model</groupId>
             <artifactId>org.neuroml1.model</artifactId>
-            <version>1.8.1</version>
+            <version>1.9.1</version>
         </dependency>
         <dependency>
             <groupId>org.neuroml.import</groupId>
             <artifactId>org.neuroml.import</artifactId>
-            <version>1.8.1</version>
+            <version>1.9.1</version>
         </dependency>
 
         <!-- Dependencies to force use of log4j 2.17.1 -->
         <dependency>
             <groupId>org.apache.logging.log4j</groupId>
             <artifactId>log4j-1.2-api</artifactId>
             <version>2.17.1</version>
-            <scope>test</scope>
         </dependency>
         <dependency>
             <groupId>org.apache.logging.log4j</groupId>
             <artifactId>log4j-slf4j-impl</artifactId>
             <version>2.17.1</version>
-            <scope>test</scope>
         </dependency>
 
 
@@ -61,7 +59,7 @@
                             &lt;br /&gt;
                             &lt;br /&gt;
                     </top>
-                    <bottom>Copyright NeuroML Contributors 2021</bottom>
+                    <bottom>Copyright NeuroML Contributors 2023</bottom>
                 </configuration>
             </plugin>
             <plugin>