Merge pull request #101 from LEMS/development

NeuroML 2.2 release

.github/workflows/ci.yml

@@ -0,0 +1,71 @@
+# This workflow will build a Java project with Maven
+# For more information see: https://help.github.com/actions/language-and-framework-guides/building-and-testing-java-with-maven
+
+name: Java CI with Maven
+
+on:
+  push:
+    branches:  [ master, development, experimental, osb* ]
+  pull_request:
+    branches:  [ master, development, experimental, osb* ]
+
+jobs:
+  build_and_test:
+
+    runs-on: ${{ matrix.runs-on }}
+    strategy:
+      fail-fast: false
+      matrix:
+        java: [ '8', '11', '16', '17' ]
+        runs-on: [ubuntu-latest, macos-11, windows-latest]
+
+    name: Test on Java ${{ matrix.Java }} on ${{ matrix.runs-on }}
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up JDK ${{ matrix.Java }}
+      uses: actions/setup-java@v2
+      with:
+        java-version: ${{ matrix.Java }}
+        distribution: 'adopt'
+    - name: Test with Maven
+      run: mvn install
+    - name: Further tests, non Win
+      if: ${{ matrix.runs-on != 'windows-latest' }}
+      run: |
+        pwd
+        ls -alt
+        mvn dependency:tree
+        ./lems src/test/resources/example1.xml -nogui
+        ./lems src/test/resources/example2.xml -nogui
+        ./lems src/test/resources/example3.xml -nogui
+        ./lems src/test/resources/example4.xml -nogui
+        ./lems src/test/resources/example5.xml -nogui
+        ./lems src/test/resources/example6.xml -nogui
+        ./lems src/test/resources/example7.xml -nogui
+        ./lems src/test/resources/example8.xml -nogui
+        ./lems src/test/resources/bounce-conditional.xml -nogui
+        ./lems src/test/resources/bounce.xml -nogui
+        ./lems src/test/resources/ex-flat.xml -nogui
+        ./lems src/test/resources/test_regime_iaf.xml -nogui
+        ./lems src/test/resources/ex-properties.xml -nogui
+        
+    - name: Further tests, Windows
+      if: ${{ matrix.runs-on == 'windows-latest' }}
+      run: |
+        pwd
+        dir
+        mvn dependency:tree
+        
+        ./lems.bat src\test\resources\example1.xml -nogui
+        ./lems.bat src\test\resources\eexample2.xml -nogui
+        ./lems.bat src\test\resources\example3.xml -nogui
+        ./lems.bat src\test\resources\example4.xml -nogui
+        ./lems.bat src\test\resources\example5.xml -nogui
+        ./lems.bat src\test\resources\example6.xml -nogui
+        ./lems.bat src\test\resources\example7.xml -nogui
+        ./lems.bat src\test\resources\example8.xml -nogui
+        ./lems.bat src\test\resources\bounce-conditional.xml -nogui
+        ./lems.bat src\test\resources\bounce.xml -nogui
+        ./lems.bat src\test\resources\ex-flat.xml -nogui
+        ./lems.bat src\test\resources\test_regime_iaf.xml -nogui
+        ./lems.bat src\test\resources\ex-properties.xml -nogui

.github/workflows/examples.yml

@@ -0,0 +1,37 @@
+# Check that examples are same in LEMS and in jlems
+name: Check LEMS examples
+
+on:
+  push:
+    branches:  [ master, development, experimental ]
+
+jobs:
+  verify:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - uses: nelonoel/branch-name@v1.0.1
+
+    # https://stackoverflow.com/questions/58033366/how-to-get-current-branch-within-github-actions
+    - name: Extract branch name
+      shell: bash
+      run: echo "##[set-output name=branch;]$(echo ${GITHUB_REF#refs/heads/})"
+      id: extract_branch
+
+    - name: Checkout lems
+      uses: actions/checkout@v2
+      with:
+        repository: LEMS/LEMS
+        ref: ${{ steps.extract_branch.outputs.branch }}
+        path: LEMS
+
+    - name: check examples
+      run: |
+        for ex in "example1.xml" "example2.xml" "example3.xml" "example4.xml" "example5.xml" "example6.xml" "example7.xml" "example8.xml" "SimpleNetwork.xml" "SingleSimulation.xml" "elecdims.xml" "ex2dims.xml" "hhaltgate.xml" "hhcell.xml" "hhchannel.xml" "hhmodels.xml" "misciaf.xml" "spikegenerators.xml"; do
+
+          if ! diff -ur "LEMS/examples/$ex" "src/test/resources/$ex" ; then
+            echo "Example file $ex is not identical"
+            exit -1
+          fi
+        done

.gitignore

@@ -9,3 +9,6 @@ tst.txt
 .DS_Store
 src/main/java/META-INF
 /nb-configuration.xml
+.classpath
+.project
+.settings/

README.md

@@ -1,9 +1,12 @@
 jLEMS
 =====
 
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3550993.svg)](https://doi.org/10.5281/zenodo.3550993)
+[![Java CI with Maven](https://github.com/LEMS/jLEMS/actions/workflows/ci.yml/badge.svg)](https://github.com/LEMS/jLEMS/actions/workflows/ci.yml)
+
 Java Interpreter for the Low Entropy Model Specification language.
 
-See https://docs.neuroml.org/Userdocs/Software/jLEMS.html
+See https://docs.neuroml.org/Userdocs/Software/jLEMS.html.
 
 For more details on LEMS see: 
 
@@ -28,9 +31,4 @@ Run an example:
     ./lems src/test/resources/example1.xml        (Linux/Mac)
     lems.bat src\test\resources\example1.xml      (Windows)
 
-[![Build Status](https://travis-ci.com/LEMS/jLEMS.png?branch=master)](https://travis-ci.com/LEMS/jLEMS)
-[![DOI](https://www.zenodo.org/badge/4614078.svg)](https://www.zenodo.org/badge/latestdoi/4614078)
-
-
-
 This software is distributed under the terms of the MIT License.

lems

@@ -1,6 +1,6 @@
 #!/bin/sh
 
-export LEMS_VERSION=0.10.4
+export LEMS_VERSION=0.10.6
 
 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=0.10.4
+set LEMS_VERSION=0.10.6
 
 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>0.10.4</version>
+	<version>0.10.6</version>
 	<packaging>bundle</packaging>
 	<dependencies>
 		<dependency>

src/main/java/org/lemsml/jlems/core/reader/LemsFactory.java

@@ -626,6 +626,8 @@ private DerivedParameter buildDerivedParameter(XMLElement xel) {
                 ret.name = parseString(xv);
             } else if (xn.equals("dimension")) {
                 ret.dimension = parseString(xv);
+            } else if (xn.equals("description")) {
+                ret.description = parseString(xv);
             } else if (xn.equals("select")) {
                 ret.select = parseString(xv);
             } else if (xn.equals("value")) {
@@ -762,6 +764,8 @@ private Child buildChild(XMLElement xel) {
                 ret.name = parseString(xv);
             } else if (xn.equals("type")) {
                 ret.type = parseString(xv);
+            } else if (xn.equals("description")) {
+                ret.description = parseString(xv);
             } else if (xn.equals("substitute")) {
                 ret.substitute = parseString(xv);
             } else {
@@ -837,6 +841,8 @@ private ComponentReference buildComponentReference(XMLElement xel) {
                 ret.name = parseString(xv);
             } else if (xn.equals("type")) {
                 ret.type = parseString(xv);
+            } else if (xn.equals("description")) {
+                ret.description = parseString(xv);
             } else if (xn.equals("root")) {
                 ret.root = parseString(xv);
             } else if (xn.equals("isAny")) {
@@ -946,6 +952,8 @@ private Text buildText(XMLElement xel) {
             if (xn.equals("UNUSED")) {
             } else if (xn.equals("name")) {
                 ret.name = parseString(xv);
+            } else if (xn.equals("description")) {
+                ret.description = parseString(xv);
             } else {
                 E.warning("Unrecognized attribute " + xa + " " + xv);
             }
@@ -965,6 +973,8 @@ private Path buildPath(XMLElement xel) {
             if (xn.equals("UNUSED")) {
             } else if (xn.equals("name")) {
                 ret.name = parseString(xv);
+            } else if (xn.equals("description")) {
+                ret.description = parseString(xv);
             } else {
                 E.warning("Unrecognized attribute " + xa + " " + xv);
             }

src/main/java/org/lemsml/jlems/core/type/Child.java

@@ -20,6 +20,8 @@ public class Child implements Named {
 
     public String substitute;
 
+    public String description;
+
 
     public Child() {
     }

src/main/java/org/lemsml/jlems/core/type/ComponentReference.java

@@ -17,6 +17,7 @@ public class ComponentReference implements Named  {
 
 	@ModelProperty(info="Target type")
 	public String type;
+    public String description;
 	public ComponentType r_type;
 
 	public String root;

src/main/java/org/lemsml/jlems/core/type/DerivedParameter.java

@@ -17,6 +17,7 @@ public class DerivedParameter extends ExpressionValued implements Named {
 
 	public String name;
 	public String dimension;
+	public String description;
 	public Dimension r_dimension;
 
 	@ModelProperty(info="Path to the parameter that supplies the value. Exactly one of 'select' and 'value' is required.")

src/main/java/org/lemsml/jlems/core/type/Path.java

@@ -9,6 +9,8 @@ public class Path implements Named  {
 	@ModelProperty(info="")
 	public String name;
 
+    public String description;
+
     public Path() {
     	// TODO - only one
     }

src/main/java/org/lemsml/jlems/core/type/Text.java

@@ -10,6 +10,7 @@ public class Text implements Named  {
 	@ModelProperty(info="")
 	public String name;
 
+    public String description;
 
 	public Text() {
 		// empty