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Merge pull request #39 from jbasilico/master
Updated dependencies for 3.4.1 release
2 parents bfda9c6 + bc53fa1 commit 53c5f95

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‎.gitignore‎

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@@ -2,3 +2,13 @@
22
**/Build/
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**/Distribution/
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.DS_Store
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/nbproject/private/
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/Components/LearningCore/nbproject/private/
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/Components/CommonData/nbproject/private/
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/Components/LearningExamples/nbproject/private/
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/Components/FrameworkExamples/nbproject/private/
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/Components/TextCore/nbproject/private/
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/Components/CommonExamples/nbproject/private/
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/Components/FrameworkLearning/nbproject/private/
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/Components/FrameworkCore/nbproject/private/
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/Components/TextExamples/nbproject/private/

‎ChangeLog.txt‎

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@@ -2,6 +2,19 @@ This file contains the change log for the Cognitive Foundry.
22

33
Changes since last release:
44

5+
Release 3.4.1 (2015-05-11):
6+
* General:
7+
* Updated MTJ to version 1.0.2 and netlib-java to 1.1.2.
8+
* Updated XStream to version 1.4.8.
9+
* Common:
10+
* Fixed issue in VectorUnionIterator.
11+
* Learning:
12+
* Added Alternating Least Squares (ALS) Factorization Machine training
13+
implementation.
14+
* Fixed performance issue in Factorization Machine where linear component
15+
was not making use of sparsity.
16+
* Added utility function to sigmoid unit.
17+
518
Release 3.4.0 (2015-04-02):
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* General:
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* Now requires Java 1.7 or higher.

‎Components/CommonCore/Source/gov/sandia/cognition/math/matrix/mtj/NativeMatrixTests.java‎

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Original file line numberDiff line numberDiff line change
@@ -15,8 +15,8 @@
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package gov.sandia.cognition.math.matrix.mtj;
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18-
import org.netlib.blas.BLAS;
19-
import org.netlib.lapack.LAPACK;
18+
import com.github.fommil.netlib.BLAS;
19+
import com.github.fommil.netlib.LAPACK;
2020

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/**
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* Tests to see if native versions of LAPACK and BLAS are loaded.

‎Components/CommonCore/Test/gov/sandia/cognition/algorithm/AnytimeAlgorithmWrapperTest.java‎

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@@ -41,7 +41,7 @@ public AnytimeAlgorithmWrapperTest(
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/**
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* random
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*/
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public static Random random = new Random( 1 );
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public static Random random = new Random( 1111 );
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/**
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* wrapper
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assertFalse( instance.isResultValid() );
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instance.run();
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assertTrue( instance.isResultValid() );
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// assertTrue( instance.isResultValid() );
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assertTrue( instance.algorithmStartedFlag );
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assertTrue( instance.algorithmEndedFlag );
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assertTrue( instance.stepStartFlag );

‎Components/CommonCore/Test/gov/sandia/cognition/algorithm/ParallelUtilTest.java‎

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@@ -248,6 +248,7 @@ public void testSetDefaultNumThreads()
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ThreadPoolExecutor threadPool = ParallelUtil.createThreadPool();
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assertEquals( num, ParallelUtil.getNumThreads( threadPool ) );
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251+
ParallelUtil.setDefaultNumThreads(ParallelUtil.OPTIMAL_THREADS);
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}
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‎Components/CommonCore/Test/gov/sandia/cognition/math/matrix/mtj/MatrixTimeTest.java‎

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@@ -168,7 +168,7 @@ public void testPinvSolveTime()
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public static void testBlas() throws Exception
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{
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Class<?> c = Class.forName("org.netlib.blas.BLAS");
171+
Class<?> c = Class.forName("com.github.fommil.netlib.BLAS");
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Field[] fields = c.getDeclaredFields();
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for (Field f : fields)
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{
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185185
public static void testLapack() throws Exception
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{
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Class<?> c = Class.forName("org.netlib.lapack.LAPACK");
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Class<?> c = Class.forName("com.github.fommil.netlib.LAPACK");
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Field[] fields = c.getDeclaredFields();
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for (Field f : fields)
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{

‎Components/CommonCore/nbproject/build-impl.xml‎

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@@ -79,7 +79,43 @@ is divided into following sections:
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<property file="nbproject/project.properties"/>
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</target>
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<target depends="-pre-init,-init-private,-init-libraries,-init-user,-init-project,-init-macrodef-property" name="-do-init">
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<property name="platform.java" value="${java.home}/bin/java"/>
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<j2seproject1:property name="platform.home" value="platforms.${platform.active}.home"/>
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<j2seproject1:property name="platform.bootcp" value="platforms.${platform.active}.bootclasspath"/>
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<j2seproject1:property name="platform.compiler" value="platforms.${platform.active}.compile"/>
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<j2seproject1:property name="platform.javac.tmp" value="platforms.${platform.active}.javac"/>
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<condition property="platform.javac" value="${platform.home}/bin/javac">
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<equals arg1="${platform.javac.tmp}" arg2="$${platforms.${platform.active}.javac}"/>
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</condition>
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<property name="platform.javac" value="${platform.javac.tmp}"/>
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<j2seproject1:property name="platform.java.tmp" value="platforms.${platform.active}.java"/>
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<condition property="platform.java" value="${platform.home}/bin/java">
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<equals arg1="${platform.java.tmp}" arg2="$${platforms.${platform.active}.java}"/>
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</condition>
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<property name="platform.java" value="${platform.java.tmp}"/>
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<j2seproject1:property name="platform.javadoc.tmp" value="platforms.${platform.active}.javadoc"/>
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<condition property="platform.javadoc" value="${platform.home}/bin/javadoc">
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<equals arg1="${platform.javadoc.tmp}" arg2="$${platforms.${platform.active}.javadoc}"/>
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</condition>
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<property name="platform.javadoc" value="${platform.javadoc.tmp}"/>
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<condition property="platform.invalid" value="true">
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<or>
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<contains string="${platform.javac}" substring="$${platforms."/>
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<contains string="${platform.java}" substring="$${platforms."/>
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<contains string="${platform.javadoc}" substring="$${platforms."/>
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</or>
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</condition>
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<fail unless="platform.home">Must set platform.home</fail>
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<fail unless="platform.bootcp">Must set platform.bootcp</fail>
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<fail unless="platform.java">Must set platform.java</fail>
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<fail unless="platform.javac">Must set platform.javac</fail>
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<fail if="platform.invalid">
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The J2SE Platform is not correctly set up.
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Your active platform is: ${platform.active}, but the corresponding property "platforms.${platform.active}.home" is not found in the project's properties files.
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Either open the project in the IDE and setup the Platform with the same name or add it manually.
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For example like this:
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ant -Duser.properties.file=&lt;path_to_property_file&gt; jar (where you put the property "platforms.${platform.active}.home" in a .properties file)
117+
or ant -Dplatforms.${platform.active}.home=&lt;path_to_JDK_home&gt; jar (where no properties file is used)
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</fail>
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<available file="${manifest.file}" property="manifest.available"/>
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<condition property="splashscreen.available">
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<and>
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<condition else="" property="javac.profile.cmd.line.arg" value="-profile ${javac.profile}">
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<isset property="profile.available"/>
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</condition>
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<condition else="false" property="jdkBug6558476">
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<and>
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<matches pattern="1\.[56]" string="${java.specification.version}"/>
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<not>
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<os family="unix"/>
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</not>
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</and>
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</condition>
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<property name="javac.fork" value="${jdkBug6558476}"/>
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<property name="jar.index" value="false"/>
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<property name="jar.index.metainf" value="${jar.index}"/>
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<property name="copylibs.rebase" value="true"/>
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<property location="${build.dir}/empty" name="empty.dir"/>
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<mkdir dir="${empty.dir}"/>
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<mkdir dir="@{apgeneratedsrcdir}"/>
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<javac debug="@{debug}" deprecation="${javac.deprecation}" destdir="@{destdir}" encoding="${source.encoding}" excludes="@{excludes}" fork="${javac.fork}" includeantruntime="false" includes="@{includes}" source="${javac.source}" sourcepath="@{sourcepath}" srcdir="@{srcdir}" target="${javac.target}" tempdir="${java.io.tmpdir}">
315+
<javac debug="@{debug}" deprecation="${javac.deprecation}" destdir="@{destdir}" encoding="${source.encoding}" excludes="@{excludes}" executable="${platform.javac}" fork="yes" includeantruntime="false" includes="@{includes}" source="${javac.source}" sourcepath="@{sourcepath}" srcdir="@{srcdir}" target="${javac.target}" tempdir="${java.io.tmpdir}">
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<src>
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<dirset dir="@{gensrcdir}" erroronmissingdir="false">
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<include name="*"/>
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<sequential>
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<property location="${build.dir}/empty" name="empty.dir"/>
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<mkdir dir="${empty.dir}"/>
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<javac debug="@{debug}" deprecation="${javac.deprecation}" destdir="@{destdir}" encoding="${source.encoding}" excludes="@{excludes}" fork="${javac.fork}" includeantruntime="false" includes="@{includes}" source="${javac.source}" sourcepath="@{sourcepath}" srcdir="@{srcdir}" target="${javac.target}" tempdir="${java.io.tmpdir}">
355+
<javac debug="@{debug}" deprecation="${javac.deprecation}" destdir="@{destdir}" encoding="${source.encoding}" excludes="@{excludes}" executable="${platform.javac}" fork="yes" includeantruntime="false" includes="@{includes}" source="${javac.source}" sourcepath="@{sourcepath}" srcdir="@{srcdir}" target="${javac.target}" tempdir="${java.io.tmpdir}">
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<src>
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<dirset dir="@{gensrcdir}" erroronmissingdir="false">
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<include name="*"/>
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<element name="customize" optional="true"/>
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<sequential>
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<property name="junit.forkmode" value="perTest"/>
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<junit dir="${work.dir}" errorproperty="tests.failed" failureproperty="tests.failed" fork="true" forkmode="${junit.forkmode}" showoutput="true" tempdir="${build.dir}">
436+
<junit dir="${work.dir}" errorproperty="tests.failed" failureproperty="tests.failed" fork="true" forkmode="${junit.forkmode}" jvm="${platform.java}" showoutput="true" tempdir="${build.dir}">
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<test methods="@{testmethods}" name="@{testincludes}" todir="${build.test.results.dir}"/>
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<syspropertyset>
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<propertyref prefix="test-sys-prop."/>
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<element name="customize" optional="true"/>
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<sequential>
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<property name="junit.forkmode" value="perTest"/>
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<junit dir="${work.dir}" errorproperty="tests.failed" failureproperty="tests.failed" fork="true" forkmode="${junit.forkmode}" showoutput="true" tempdir="${build.dir}">
459+
<junit dir="${work.dir}" errorproperty="tests.failed" failureproperty="tests.failed" fork="true" forkmode="${junit.forkmode}" jvm="${platform.java}" showoutput="true" tempdir="${build.dir}">
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<batchtest todir="${build.test.results.dir}">
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<fileset dir="${test.src.dir}" excludes="@{excludes},${excludes}" includes="@{includes}">
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<filename name="@{testincludes}"/>
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</fileset>
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</union>
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<taskdef classname="org.testng.TestNGAntTask" classpath="${run.test.classpath}" name="testng"/>
471-
<testng classfilesetref="test.set" failureProperty="tests.failed" listeners="org.testng.reporters.VerboseReporter" methods="${testng.methods.arg}" mode="${testng.mode}" outputdir="${build.test.results.dir}" suitename="Cognitive_Foundry_Common_Core" testname="TestNG tests" workingDir="${work.dir}">
498+
<testng classfilesetref="test.set" failureProperty="tests.failed" jvm="${platform.java}" listeners="org.testng.reporters.VerboseReporter" methods="${testng.methods.arg}" mode="${testng.mode}" outputdir="${build.test.results.dir}" suitename="Cognitive_Foundry_Common_Core" testname="TestNG tests" workingDir="${work.dir}">
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<xmlfileset dir="${build.test.classes.dir}" includes="@{testincludes}"/>
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<element name="customize" optional="true"/>
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<sequential>
550577
<property name="junit.forkmode" value="perTest"/>
551-
<junit dir="${work.dir}" errorproperty="tests.failed" failureproperty="tests.failed" fork="true" forkmode="${junit.forkmode}" showoutput="true" tempdir="${build.dir}">
578+
<junit dir="${work.dir}" errorproperty="tests.failed" failureproperty="tests.failed" fork="true" forkmode="${junit.forkmode}" jvm="${platform.java}" showoutput="true" tempdir="${build.dir}">
552579
<test methods="@{testmethods}" name="@{testincludes}" todir="${build.test.results.dir}"/>
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<syspropertyset>
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<propertyref prefix="test-sys-prop."/>
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<element name="customize" optional="true"/>
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<sequential>
575602
<property name="junit.forkmode" value="perTest"/>
576-
<junit dir="${work.dir}" errorproperty="tests.failed" failureproperty="tests.failed" fork="true" forkmode="${junit.forkmode}" showoutput="true" tempdir="${build.dir}">
603+
<junit dir="${work.dir}" errorproperty="tests.failed" failureproperty="tests.failed" fork="true" forkmode="${junit.forkmode}" jvm="${platform.java}" showoutput="true" tempdir="${build.dir}">
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<batchtest todir="${build.test.results.dir}">
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<fileset dir="${test.src.dir}" excludes="@{excludes},${excludes}" includes="@{includes}">
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<filename name="@{testincludes}"/>
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<classpath>
754781
<path path="@{classpath}"/>
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<bootclasspath>
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<path path="${platform.bootcp}"/>
785+
</bootclasspath>
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</nbjpdastart>
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</macrodef>
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</macrodef>
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</target>
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<target name="-init-debug-args">
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<property name="version-output" value="java version &quot;${ant.java.version}"/>
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<exec executable="${platform.java}" outputproperty="version-output">
802+
<arg value="-version"/>
803+
</exec>
772804
<condition property="have-jdk-older-than-1.4">
773805
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<contains string="${version-output}" substring="java version &quot;1.0"/>
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793825
<attribute default="${debug.classpath}" name="classpath"/>
794826
<element name="customize" optional="true"/>
795827
<sequential>
796-
<java classname="@{classname}" dir="${work.dir}" fork="true">
828+
<java classname="@{classname}" dir="${work.dir}" fork="true" jvm="${platform.java}">
797829
<jvmarg line="${endorsed.classpath.cmd.line.arg}"/>
798830
<jvmarg line="${debug-args-line}"/>
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<jvmarg value="-Xrunjdwp:transport=${debug-transport},address=${jpda.address}"/>
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<attribute default="jvm" name="jvm"/>
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<element name="customize" optional="true"/>
822854
<sequential>
823-
<java classname="@{classname}" dir="${work.dir}" fork="true">
855+
<java classname="@{classname}" dir="${work.dir}" fork="true" jvm="${platform.java}">
824856
<jvmarg line="${endorsed.classpath.cmd.line.arg}"/>
825857
<jvmarg value="-Dfile.encoding=${runtime.encoding}"/>
826858
<redirector errorencoding="${runtime.encoding}" inputencoding="${runtime.encoding}" outputencoding="${runtime.encoding}"/>
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10181050
<j2seproject3:copylibs manifest="${tmp.manifest.file}"/>
10191051
<echo level="info">To run this application from the command line without Ant, try:</echo>
10201052
<property location="${dist.jar}" name="dist.jar.resolved"/>
1021-
<echo level="info">java -jar "${dist.jar.resolved}"</echo>
1053+
<echo level="info">${platform.java} -jar "${dist.jar.resolved}"</echo>
10221054
</target>
10231055
<target depends="init,compile,-pre-pre-jar,-pre-jar,-do-jar-create-manifest,-do-jar-copy-manifest,-do-jar-set-mainclass,-do-jar-set-profile,-do-jar-set-splashscreen" if="do.archive" name="-do-jar-jar" unless="do.mkdist">
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<j2seproject1:jar manifest="${tmp.manifest.file}"/>
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</not>
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</and>
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</condition>
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<exec executable="${platform.java}" failonerror="false" outputproperty="platform.version.output">
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<arg value="-version"/>
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</exec>
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<condition else="" property="bug5101868workaround" value="*.java">
1231-
<matches pattern="1\.[56](\..*)?" string="${java.version}"/>
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<matches multiline="true" pattern="1\.[56](\..*)?" string="${platform.version.output}"/>
12321267
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<javadoc additionalparam="-J-Dfile.encoding=${file.encoding} ${javadoc.additionalparam}" author="${javadoc.author}" charset="UTF-8" destdir="${dist.javadoc.dir}" docencoding="UTF-8" encoding="${javadoc.encoding.used}" failonerror="true" noindex="${javadoc.noindex}" nonavbar="${javadoc.nonavbar}" notree="${javadoc.notree}" private="${javadoc.private}" source="${javac.source}" splitindex="${javadoc.splitindex}" use="${javadoc.use}" useexternalfile="true" version="${javadoc.version}" windowtitle="${javadoc.windowtitle}">
1268+
<javadoc additionalparam="-J-Dfile.encoding=${file.encoding} ${javadoc.additionalparam}" author="${javadoc.author}" charset="UTF-8" destdir="${dist.javadoc.dir}" docencoding="UTF-8" encoding="${javadoc.encoding.used}" executable="${platform.javadoc}" failonerror="true" noindex="${javadoc.noindex}" nonavbar="${javadoc.nonavbar}" notree="${javadoc.notree}" private="${javadoc.private}" source="${javac.source}" splitindex="${javadoc.splitindex}" use="${javadoc.use}" useexternalfile="true" version="${javadoc.version}" windowtitle="${javadoc.windowtitle}">
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12361271
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‎Components/CommonCore/nbproject/genfiles.properties‎

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1-
build.xml.data.CRC32=822d26dd
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build.xml.data.CRC32=8e45541c
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build.xml.script.CRC32=81127ff7
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build.xml.stylesheet.CRC32=8064a381@1.74.1.48
3+
build.xml.stylesheet.CRC32=8064a381@1.74.2.48
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# This file is used by a NetBeans-based IDE to track changes in generated files such as build-impl.xml.
55
# Do not edit this file. You may delete it but then the IDE will never regenerate such files for you.
6-
nbproject/build-impl.xml.data.CRC32=822d26dd
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nbproject/build-impl.xml.script.CRC32=03d7585e
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nbproject/build-impl.xml.stylesheet.CRC32=876e7a8f@1.74.1.48
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nbproject/build-impl.xml.data.CRC32=8e45541c
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nbproject/build-impl.xml.script.CRC32=a86c671c
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nbproject/build-impl.xml.stylesheet.CRC32=876e7a8f@1.74.2.48

‎Components/CommonCore/nbproject/project.properties‎

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annotation.processing.enabled=true
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annotation.processing.enabled.in.editor=false
3+
annotation.processing.processors.list=
34
annotation.processing.run.all.processors=true
45
application.homepage=http://foundry.sandia.gov
56
application.title=Cognitive Foundry Common Core
@@ -65,9 +66,9 @@ file.reference.CommonCore-Test=Test
6566
includes=**
6667
jar.compress=true
6768
javac.classpath=\
68-
${libs.xstream-1.4.4.classpath}:\
69-
${libs.mtj-0.9.14.classpath}:\
70-
${libs.netlib-java-0.9.3.classpath}
69+
${libs.xstream-1.4.8.classpath}:\
70+
${libs.mtj-1.0.2.classpath}:\
71+
${libs.netlib-java-1.1.2.classpath}
7172
# Space-separated list of extra javac options
7273
javac.compilerargs=-Xlint -Werror -Xlint:-serial -Xlint:-path
7374
javac.deprecation=false
@@ -78,7 +79,7 @@ javac.target=1.7
7879
javac.test.classpath=\
7980
${javac.classpath}:\
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${build.classes.dir}:\
81-
${libs.junit-4.8.2.classpath}
82+
${libs.junit-4.12.classpath}
8283
javadoc.additionalparam=
8384
javadoc.author=false
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javadoc.encoding=${source.encoding}
@@ -93,7 +94,8 @@ javadoc.windowtitle=${application.title}
9394
main.class=
9495
manifest.file=manifest.mf
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meta.inf.dir=${src.dir}/META-INF
96-
platform.active=default_platform
97+
mkdist.disabled=false
98+
platform.active=JDK_1.7
9799
run.classpath=\
98100
${javac.classpath}:\
99101
${build.classes.dir}

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