Merge branch 'development'

Repast · Oct 21, 2021 · d924281 · d924281
2 parents c2314e7 + e77bc72
commit d924281
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diff --git a/libs.bsf/META-INF/MANIFEST.MF b/libs.bsf/META-INF/MANIFEST.MF
@@ -2,7 +2,7 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: Repast libs bsf
 Bundle-SymbolicName: libs.bsf
-Bundle-Version: 2.8.0
+Bundle-Version: 2.9.0
 Bundle-ClassPath: lib/bsf.jar,
  lib/bsh-2.0b4.jar
 Export-Package: bsh,

diff --git a/libs.bsf/plugin_jpf.xml b/libs.bsf/plugin_jpf.xml
@@ -2,7 +2,7 @@
 <!DOCTYPE plugin PUBLIC "-//JPF//Java Plug-in Manifest 0.6" "http://jpf.sourceforge.net/plugin_0_6.dtd">
 <plugin id="libs.bsf" version="">
 	<attributes>
-         <attribute id="simphony" value="2.8.0"/>
+         <attribute id="simphony" value="2.9.0"/>
      </attributes>
 
 	<runtime>

diff --git a/libs.ext/META-INF/MANIFEST.MF b/libs.ext/META-INF/MANIFEST.MF
@@ -2,7 +2,7 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: Repast libs ext
 Bundle-SymbolicName: libs.ext
-Bundle-Version: 2.8.0
+Bundle-Version: 2.9.0
 Bundle-ClassPath: lib/clibwrapper_jiio.jar,
  lib/gluegen-rt.jar,
  lib/jai_codec.jar,

diff --git a/libs.ext/plugin_jpf.xml b/libs.ext/plugin_jpf.xml
@@ -2,7 +2,7 @@
 <!DOCTYPE plugin PUBLIC "-//JPF//Java Plug-in Manifest 0.6" "http://jpf.sourceforge.net/plugin_0_6.dtd">
 <plugin id="libs.ext" version="">
 	<attributes>
-		<attribute id="simphony" value="2.8.0"/>
+		<attribute id="simphony" value="2.9.0"/>
 	</attributes>
 
 	<runtime>

diff --git a/libs.piccolo/META-INF/MANIFEST.MF b/libs.piccolo/META-INF/MANIFEST.MF
@@ -2,7 +2,7 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: Repast libs piccolo
 Bundle-SymbolicName: libs.piccolo
-Bundle-Version: 2.8.0
+Bundle-Version: 2.9.0
 Bundle-ClassPath: lib/piccolo2d-core-3.0.jar,
  lib/piccolo2d-extras-3.0.jar
 Export-Package: org.piccolo2d,

diff --git a/libs.piccolo/plugin_jpf.xml b/libs.piccolo/plugin_jpf.xml
@@ -2,7 +2,7 @@
 <!DOCTYPE plugin PUBLIC "-//JPF//Java Plug-in Manifest 0.6" "http://jpf.sourceforge.net/plugin_0_6.dtd">
 <plugin id="libs.piccolo" version="">
 	<attributes>
-         <attribute id="simphony" value="2.8.0"/>
+         <attribute id="simphony" value="2.9.0"/>
      </attributes>
 
 	<runtime>

diff --git a/repast.simphony.R/META-INF/MANIFEST.MF b/repast.simphony.R/META-INF/MANIFEST.MF
@@ -2,7 +2,7 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: Repast R
 Bundle-SymbolicName: repast.simphony.R
-Bundle-Version: 2.8.0
+Bundle-Version: 2.9.0
 Require-Bundle: repast.simphony.gui,
  repast.simphony.data,
  repast.simphony.core,

diff --git a/repast.simphony.R/licenses/repast-license.txt b/repast.simphony.R/licenses/repast-license.txt
@@ -1,6 +1,6 @@
 Repast Simphony
 
-   Copyright (c) 2020 Argonne National Laboratory
+   Copyright (c) 2021 Argonne National Laboratory
    All rights reserved.
 
    Redistribution and use in source and binary forms, with 

diff --git a/repast.simphony.R/plugin_jpf.xml b/repast.simphony.R/plugin_jpf.xml
@@ -3,7 +3,7 @@
 <plugin id="repast.simphony.R" version="">
 
 	<attributes>
-         <attribute id="simphony" value="2.8.0"/>
+         <attribute id="simphony" value="2.9.0"/>
      </attributes>
 
 	<requires>

diff --git a/repast.simphony.batch/META-INF/MANIFEST.MF b/repast.simphony.batch/META-INF/MANIFEST.MF
@@ -2,7 +2,7 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: Repast batch
 Bundle-SymbolicName: repast.simphony.batch;singleton:=true
-Bundle-Version: 2.8.0
+Bundle-Version: 2.9.0
 Require-Bundle: libs.bsf,
  repast.simphony.dataLoader,
  repast.simphony.data,

diff --git a/repast.simphony.batch/licenses/repast-license.txt b/repast.simphony.batch/licenses/repast-license.txt
@@ -1,6 +1,6 @@
 Repast Simphony
 
-   Copyright (c) 2020 Argonne National Laboratory
+   Copyright (c) 2021 Argonne National Laboratory
    All rights reserved.
 
    Redistribution and use in source and binary forms, with 

diff --git a/repast.simphony.batch/plugin_jpf.xml b/repast.simphony.batch/plugin_jpf.xml
@@ -2,7 +2,7 @@
 <!DOCTYPE plugin PUBLIC "-//JPF//Java Plug-in Manifest 0.6" "http://jpf.sourceforge.net/plugin_0_6.dtd">
 <plugin id="repast.simphony.batch" version="">
 	<attributes>
-         <attribute id="simphony" value="2.8.0"/>
+         <attribute id="simphony" value="2.9.0"/>
      </attributes>
 
 	<requires>

diff --git a/repast.simphony.bin_and_src/META-INF/MANIFEST.MF b/repast.simphony.bin_and_src/META-INF/MANIFEST.MF
@@ -2,6 +2,6 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: Repast bin and src
 Bundle-SymbolicName: repast.simphony.bin_and_src
-Bundle-Version: 2.8.0
+Bundle-Version: 2.9.0
 Bundle-Vendor: Argonne National Laboratory
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8
diff --git a/repast.simphony.chart/META-INF/MANIFEST.MF b/repast.simphony.chart/META-INF/MANIFEST.MF
@@ -2,7 +2,7 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: Repast chart
 Bundle-SymbolicName: repast.simphony.chart
-Bundle-Version: 2.8.0
+Bundle-Version: 2.9.0
 Bundle-ClassPath: lib/jcommon-1.0.23.jar,
  lib/jfreechart-1.0.19.jar
 Export-Package: com.keypoint,

diff --git a/repast.simphony.chart/licenses/repast-license.txt b/repast.simphony.chart/licenses/repast-license.txt
@@ -1,6 +1,6 @@
 Repast Simphony
 
-   Copyright (c) 2020 Argonne National Laboratory
+   Copyright (c) 2021 Argonne National Laboratory
    All rights reserved.
 
    Redistribution and use in source and binary forms, with 

diff --git a/repast.simphony.chart/plugin_jpf.xml b/repast.simphony.chart/plugin_jpf.xml
@@ -2,7 +2,7 @@
 <!DOCTYPE plugin PUBLIC "-//JPF//Java Plug-in Manifest 0.6" "http://jpf.sourceforge.net/plugin_0_6.dtd">
 <plugin id="repast.simphony.chart" version="">
 	<attributes>
-         <attribute id="simphony" value="2.8.0"/>
+         <attribute id="simphony" value="2.9.0"/>
      </attributes>
 
 	<requires>

diff --git a/repast.simphony.core/META-INF/MANIFEST.MF b/repast.simphony.core/META-INF/MANIFEST.MF
@@ -2,7 +2,7 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: Repast core
 Bundle-SymbolicName: repast.simphony.core
-Bundle-Version: 2.8.0
+Bundle-Version: 2.9.0
 Bundle-ClassPath: lib/jsr108-0.01.jar,
  lib/concurrent-1.3.4.jar,
  lib/collections-generic-4.01.jar,

diff --git a/repast.simphony.core/licenses/repast-license.txt b/repast.simphony.core/licenses/repast-license.txt
@@ -1,6 +1,6 @@
 Repast Simphony
 
-   Copyright (c) 2020 Argonne National Laboratory
+   Copyright (c) 2021 Argonne National Laboratory
    All rights reserved.
 
    Redistribution and use in source and binary forms, with 

diff --git a/repast.simphony.core/plugin_jpf.xml b/repast.simphony.core/plugin_jpf.xml
@@ -2,7 +2,7 @@
 <!DOCTYPE plugin PUBLIC "-//JPF//Java Plug-in Manifest 0.6" "http://jpf.sourceforge.net/plugin_0_6.dtd">
 <plugin id="repast.simphony.core" version="">
 	<attributes>
-		<attribute id="simphony" value="2.8.0"/>
+		<attribute id="simphony" value="2.9.0"/>
 	</attributes>
 
 	<requires>

diff --git a/repast.simphony.data.ui/META-INF/MANIFEST.MF b/repast.simphony.data.ui/META-INF/MANIFEST.MF
@@ -2,15 +2,15 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: Repast ui
 Bundle-SymbolicName: repast.simphony.data.ui
-Bundle-Version: 2.8.0
+Bundle-Version: 2.9.0
 Require-Bundle: saf.core.ui,
  repast.simphony.data,
  repast.simphony.gui,
  repast.simphony.plugin.util,
  repast.simphony.core,
  repast.simphony.runtime,
  repast.simphony.scenario,
- repast.simphony.eclipse;bundle-version="2.8.0"
+ repast.simphony.eclipse;bundle-version="2.9.0"
 Export-Package: repast.simphony.data.analysis,
  repast.simphony.data2.gui,
  repast.simphony.data2.wizard

diff --git a/repast.simphony.data.ui/licenses/repast-license.txt b/repast.simphony.data.ui/licenses/repast-license.txt
@@ -1,6 +1,6 @@
 Repast Simphony
 
-   Copyright (c) 2020 Argonne National Laboratory
+   Copyright (c) 2021 Argonne National Laboratory
    All rights reserved.
 
    Redistribution and use in source and binary forms, with 

diff --git a/repast.simphony.data.ui/plugin_jpf.xml b/repast.simphony.data.ui/plugin_jpf.xml
@@ -3,7 +3,7 @@
 <plugin id="repast.simphony.data.ui" version="">
 
 	<attributes>
-         <attribute id="simphony" value="2.8.0"/>
+         <attribute id="simphony" value="2.9.0"/>
      </attributes>
 
 	<requires>

diff --git a/repast.simphony.data/META-INF/MANIFEST.MF b/repast.simphony.data/META-INF/MANIFEST.MF
@@ -2,7 +2,7 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: Repast data
 Bundle-SymbolicName: repast.simphony.data
-Bundle-Version: 2.8.0
+Bundle-Version: 2.9.0
 Bundle-ClassPath: bin/
 Export-Package: repast.simphony.data2,
  repast.simphony.data2.builder,

diff --git a/repast.simphony.data/licenses/repast-license.txt b/repast.simphony.data/licenses/repast-license.txt
@@ -1,6 +1,6 @@
 Repast Simphony
 
-   Copyright (c) 2020 Argonne National Laboratory
+   Copyright (c) 2021 Argonne National Laboratory
    All rights reserved.
 
    Redistribution and use in source and binary forms, with 

diff --git a/repast.simphony.data/plugin_jpf.xml b/repast.simphony.data/plugin_jpf.xml
@@ -2,7 +2,7 @@
 <!DOCTYPE plugin PUBLIC "-//JPF//Java Plug-in Manifest 0.6" "http://jpf.sourceforge.net/plugin_0_6.dtd">
 <plugin id="repast.simphony.data" version="">
 	<attributes>
-         <attribute id="simphony" value="2.8.0"/>
+         <attribute id="simphony" value="2.9.0"/>
      </attributes>
 
 	<requires>

diff --git a/repast.simphony.data/src/repast/simphony/data2/AbstractDataSetManager.java b/repast.simphony.data/src/repast/simphony/data2/AbstractDataSetManager.java
@@ -32,7 +32,8 @@
  */
 public abstract class AbstractDataSetManager implements DataSetManager, RunListener {
 
-  @SuppressWarnings("rawtypes")
+
+@SuppressWarnings("rawtypes")
   protected static class ObjList implements ContextListener, SizedIterable<Object> {
 
     Class<?> targetType;
@@ -143,6 +144,16 @@ public AbstractDataSetManager() {
     rndSeedDataSource = new RandomSeedDataSource();
     batchRunDataSource = new BatchRunDataSource();
   }
+
+  @Override
+	public void removeDataSetbuilder(String id) {
+	  builders.remove(id);
+	}
+
+	@Override
+	public void clearDataSetBuilders() {
+		builders.clear();
+	}
 
   /**
    * Gets the BatchRunDataSource that this manager will auto update with the
@@ -261,6 +272,7 @@ public void addDataSetBuilder(DataSetBuilder<?> builder) {
   public DataSetBuilder<?> getDataSetBuilder(String id) {
     return builders.get(id);
   }
+
 
   /* (non-Javadoc)
    * @see repast.simphony.engine.environment.RunListener#stopped()

diff --git a/repast.simphony.data/src/repast/simphony/data2/DataSetManager.java b/repast.simphony.data/src/repast/simphony/data2/DataSetManager.java
@@ -97,6 +97,20 @@ public interface DataSetManager {
    */
   void addDataSetBuilder(DataSetBuilder<?> builder);
 
+
+  /**
+   * Removes the specified DataSetBuilder.
+   * 
+   * @param id the id of the DataSetBuilder to remove.
+   */
+  void removeDataSetbuilder(String id);
+
+
+  /**
+   * Clears all the DataSetBuilder-s from this DataSetManager.
+   */
+  void clearDataSetBuilders();
+
   /**
    * Gets the named DataSetBuilder.
    * 

diff --git a/repast.simphony.dataLoader.ui/META-INF/MANIFEST.MF b/repast.simphony.dataLoader.ui/META-INF/MANIFEST.MF
@@ -2,7 +2,7 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: Repast dataloader ui
 Bundle-SymbolicName: repast.simphony.dataLoader.ui
-Bundle-Version: 2.8.0
+Bundle-Version: 2.9.0
 Export-Package: repast.simphony.dataLoader.ui,
  repast.simphony.dataLoader.ui.wizard,
  repast.simphony.dataLoader.ui.wizard.builder

diff --git a/repast.simphony.dataLoader.ui/licenses/repast-license.txt b/repast.simphony.dataLoader.ui/licenses/repast-license.txt
@@ -1,6 +1,6 @@
 Repast Simphony
 
-   Copyright (c) 2020 Argonne National Laboratory
+   Copyright (c) 2021 Argonne National Laboratory
    All rights reserved.
 
    Redistribution and use in source and binary forms, with 

diff --git a/repast.simphony.dataLoader.ui/plugin_jpf.xml b/repast.simphony.dataLoader.ui/plugin_jpf.xml
@@ -3,7 +3,7 @@
 <plugin id="repast.simphony.dataloader.ui" version="">
 
 	<attributes>
-         <attribute id="simphony" value="2.8.0"/>
+         <attribute id="simphony" value="2.9.0"/>
      </attributes>
 
   <requires>

diff --git a/repast.simphony.dataLoader/META-INF/MANIFEST.MF b/repast.simphony.dataLoader/META-INF/MANIFEST.MF
@@ -2,7 +2,7 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: Repast dataloader
 Bundle-SymbolicName: repast.simphony.dataLoader
-Bundle-Version: 2.8.0
+Bundle-Version: 2.9.0
 Require-Bundle: repast.simphony.core,
  repast.simphony.plugin.util,
  repast.simphony.scenario,

diff --git a/repast.simphony.dataLoader/licenses/repast-license.txt b/repast.simphony.dataLoader/licenses/repast-license.txt
@@ -1,6 +1,6 @@
 Repast Simphony
 
-   Copyright (c) 2020 Argonne National Laboratory
+   Copyright (c) 2021 Argonne National Laboratory
    All rights reserved.
 
    Redistribution and use in source and binary forms, with 

diff --git a/repast.simphony.dataLoader/plugin_jpf.xml b/repast.simphony.dataLoader/plugin_jpf.xml
@@ -3,7 +3,7 @@
 <plugin id="repast.simphony.dataloader" version="">
 
 	<attributes>
-         <attribute id="simphony" value="2.8.0"/>
+         <attribute id="simphony" value="2.9.0"/>
      </attributes>
 
   <requires>

diff --git a/repast.simphony.deployment/Building Javadoc.txt b/repast.simphony.deployment/Building Javadoc.txt
@@ -19,6 +19,11 @@ Building Repast Javadoc
       These will be the "groovy-...jar" files and one or two of the other jars
       in the groovy /lib folder (see existing launch config).
 
+        * Note that building groovy docs with Groovy 3.x fails and we have used 2.5 to
+          build the docs for RS release 2.9 (Oct 2021).  Using the Groovy 2.5 SDK for
+          groovy doc building does not interfere with the groovy 3.x distributed with
+          Repast.
+
     - The buildGroovyDocs.xml launch configuration JRE settings should be 
        "Separate JRE" not "Run in same JRE as workspace" since using the later
        causes issues (on Windows) even though they are the same JRE!

diff --git a/repast.simphony.deployment/Generate javadoc Win.launch b/repast.simphony.deployment/Generate javadoc Win.launch
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <launchConfiguration type="org.eclipse.ant.AntLaunchConfigurationType">
-    <booleanAttribute key="org.eclipse.ant.ui.DEFAULT_VM_INSTALL" value="true"/>
+    <booleanAttribute key="org.eclipse.ant.ui.DEFAULT_VM_INSTALL" value="false"/>
     <listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_PATHS">
         <listEntry value="/repast.simphony.deployment/javadoc.xml"/>
     </listAttribute>
@@ -16,8 +16,6 @@
     </listAttribute>
     <booleanAttribute key="org.eclipse.jdt.launching.ATTR_USE_CLASSPATH_ONLY_JAR" value="false"/>
     <stringAttribute key="org.eclipse.jdt.launching.CLASSPATH_PROVIDER" value="org.eclipse.ant.ui.AntClasspathProvider"/>
-    <stringAttribute key="org.eclipse.jdt.launching.JRE_CONTAINER" value="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/jdk-11.0.8+10"/>
-    <stringAttribute key="org.eclipse.jdt.launching.MAIN_TYPE" value="org.eclipse.ant.internal.launching.remote.InternalAntRunner"/>
     <stringAttribute key="org.eclipse.jdt.launching.PROJECT_ATTR" value="repast.simphony.deployment"/>
     <stringAttribute key="org.eclipse.jdt.launching.SOURCE_PATH_PROVIDER" value="org.eclipse.ant.ui.AntClasspathProvider"/>
     <stringAttribute key="org.eclipse.ui.externaltools.ATTR_LOCATION" value="${workspace_loc:/repast.simphony.deployment/javadoc.xml}"/>

diff --git a/repast.simphony.deployment/installer_scripts/RepastInstallerScript.nsi b/repast.simphony.deployment/installer_scripts/RepastInstallerScript.nsi
@@ -10,7 +10,7 @@
 !include "StrFunc.nsh"    ; String functions
 !include "x64.nsh"        ; Macros for x64 machines
 
-!define VERSION "2.7"     ; Repast Version
+!define VERSION "2.9"     ; Repast Version
 
 !define JAVA_HOME "jdk11"                          ; The included Java root dir
 !define JAVA_BIN "eclipse\${JAVA_HOME}\bin\javaw"  ; path to bundled VM

diff --git a/repast.simphony.deployment/installer_scripts/repast-license.txt b/repast.simphony.deployment/installer_scripts/repast-license.txt
@@ -1,6 +1,6 @@
 Repast Simphony
 
-   Copyright (c) 2020 Argonne National Laboratory
+   Copyright (c) 2021 Argonne National Laboratory
    All rights reserved.
 
    Redistribution and use in source and binary forms, with