Merge pull request #71 from NeuroML/development

For NML v2.1 release
NeuroML · Mar 22, 2021 · ce18e86 · ce18e86
2 parents daa29d9 + 6d509c5
commit ce18e86
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Showing 14 changed files with 709 additions and 344 deletions.
diff --git a/.gitignore b/.gitignore
@@ -6,6 +6,7 @@
 /src/test/resources/examples/ShapedCell.cell.png
 /src/test/resources/examples/TwoCell.net.png
 /src/test/resources/examples/*.svg
+runclass.sh
 
 /src/test/resources/*.svg
 
@@ -42,3 +43,4 @@ src/test/resources/examples/*nrn.py
 /libjhdf5.so
 /Test.gv
 /Test.png
+/src/test/resources/examples/report*.txt
diff --git a/.travis.yml b/.travis.yml
@@ -1,13 +1,13 @@
-dist: trusty
-sudo: false
+dist: xenial
 
 language: java
 
 jdk:
-  - openjdk7
+  - oraclejdk11
+
   - openjdk8
-  - oraclejdk8
-  # - oraclejdk9
+  #- openjdk10 # Some non deterministic recurring error in jlems with jdk10...?
+  - openjdk11
 
 
 install:
@@ -37,6 +37,7 @@ install:
     - cd jLEMS
     - git checkout $main_repo_branch
     - mvn install
+    - mvn dependency:tree
     - cd ..
 
 
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>1.6.1</version>
+    <version>1.7.2</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>1.6.1</version>
+            <version>1.7.2</version>
         </dependency>
         <dependency>
             <groupId>org.lemsml</groupId>
             <artifactId>jlems</artifactId>
-            <version>0.10.1</version>
+            <version>0.10.4</version>
         </dependency>
         <dependency>
             <groupId>org.apache.velocity</groupId>
@@ -33,11 +33,25 @@
         <dependency>
             <groupId>com.fasterxml.jackson.core</groupId>
             <artifactId>jackson-databind</artifactId>
-            <version>2.10.3</version>
+            <version>2.7.4</version>
         </dependency>
     </dependencies>
     <build>
         <plugins>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-javadoc-plugin</artifactId>
+                <version>3.2.0</version>
+                <configuration>
+                    <source>8</source>
+                    <top>
+                            &lt;br /&gt;&emsp;Learn more about NeuroML at &lt;a href=&quot;http://neuroml.org&quot; target=&quot;_blank&quot;&gt;NeuroML.org&lt;/a&gt;
+                            &lt;br /&gt;
+                            &lt;br /&gt;
+                    </top>
+                    <bottom>Copyright NeuroML Contributors 2021</bottom>
+                </configuration>
+            </plugin>
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-dependency-plugin</artifactId>
@@ -77,8 +91,8 @@
                 <artifactId>maven-compiler-plugin</artifactId>
                 <version>3.0</version>
                 <configuration>
-                    <source>1.6</source>
-                    <target>1.6</target>
+                    <source>1.7</source>
+                    <target>1.7</target>
                 </configuration>
             </plugin>
             <plugin>

diff --git a/rebuild_for_geppetto.sh b/rebuild_for_geppetto.sh
@@ -0,0 +1,26 @@
+set -e
+
+#### Script to rebuild libraries with modified dependencies required for use with Geppetto, e.g. https://github.com/openworm/org.geppetto.model.neuroml
+## See https://github.com/NeuroML/org.neuroml.model.injectingplugin/blob/172771ec4f528a740bf68f6443e8b47cdf25cd25/pom.xml#L15
+
+cd ../org.neuroml.model.injectingplugin/
+mvn clean install -Dgeppetto
+
+cd ../org.neuroml1.model
+mvn clean install -Dgeppetto
+
+cd ../NeuroML2
+mvn clean install -Dgeppetto
+
+cd ../org.neuroml.model
+mvn clean install -Dgeppetto
+
+cd ../jLEMS
+mvn clean install 
+
+cd ../org.neuroml.export
+mvn clean install -Dgeppetto
+
+
+
+
diff --git a/src/main/java/org/neuroml/export/graph/GraphWriter.java b/src/main/java/org/neuroml/export/graph/GraphWriter.java
@@ -117,7 +117,7 @@ public String getMainScript() throws GenerationException
 
 				addComment(main, "GraphViz compliant export for:" + tgtNet.summary() + "\n");
 
-				main.append("digraph " + simCpt.getID() + " {\n");
+				main.append("digraph " + simCpt.getID().replaceAll("-", "_") + " {\n");
 				main.append("fontsize=10;\n\n");
 				if(rankdirLR) main.append("rankdir=\"LR\"\n");