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joshuabmoorejoshuabmoore
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add infodynamics toolkit
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‎pyhctsa/Configurations/basic.yaml‎

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@@ -300,4 +300,15 @@ Correlation:
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hctsa_name: CO_CompareMinAMI
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ordered_args: ["binMethod", "numBins"]
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PeriodicityWang:
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base_name: PeriodicityWang
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labels:
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- periodicity
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- spline
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- C
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dependencies:
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configs:
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- zscore: True
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hctsa_name: PD_PeriodicityWang
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ordered_args:
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‎pyhctsa/FeatureCalculator/calculator.py‎

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from ..Utilities.utils import preprocess_decorator
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def range_constructor(loader, node):
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"""Construct a range from a YAML config"""
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start, end = loader.construct_sequence(node)
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return list(range(start, end + 1))
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yaml.SafeLoader.add_constructor("!range", range_constructor)

‎pyhctsa/Toolboxes/infodynamics-dist/build.xml‎

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<?xml version="1.0" encoding="UTF-8"?>
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<project basedir="." default="build" name="Java Information Dynamics Toolkit" xmlns:if="ant:if">
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<description>
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Build file for the Java Information Dynamics Toolkit
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</description>
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<!-- set global properties for this build -->
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<property name="version" value="1.6.1"/>
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<property name="mainfilename" value="infodynamics"/>
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<property name="jarplainname" value="${mainfilename}.jar" />
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<property name="jarversiondistnamezip" value="${mainfilename}-jar-${version}.zip" />
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<property name="distname" value="${mainfilename}-dist-${version}" />
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<property name="distnamezip" value="${distname}.zip" />
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<property name="distnametargz" value="${distname}.tar.gz" />
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<property name="src" location="java/source"/>
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<property name="cudasrc" location="cuda"/>
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<property name="bin" location="bin"/>
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<property name="unittestsouttoplevel" location="unittests"/>
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<property name="unittestssrc" location="java/unittests"/>
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<property name="unittestsbin" location="${unittestsouttoplevel}/bin"/>
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<property name="reports.tests" location="${unittestsouttoplevel}/reports"/>
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<property name="javadocsdir" location="javadocs"/>
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<property name="versionfile" value="version-${version}.txt"/>
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<!-- To enable GPU code, set the following variable to true -->
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<property name="enablegpu" value="false"/>
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<path id="project.classpath">
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<pathelement location="bin"/>
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</path>
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<path id="apache-classpath">
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<pathelement path="./share/commons-math3-3.5.jar"/>
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</path>
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<!-- Make required directories -->
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<target name="init" description="Create the compiled code directories">
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<mkdir dir="${bin}"/>
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<mkdir dir="${bin}/cuda"/>
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<mkdir dir="${unittestsbin}"/>
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<mkdir dir="${unittestsbin}/cuda"/>
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<mkdir dir="${reports.tests}"/>
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</target>
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<!-- Compile the java toolkit -->
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<target name="compile" depends="init" description="compile the source">
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<!-- Compile to Java 7 to provide compatibility for users with older JREs.
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Caveat: The flags here only check the language compatibility, but
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may still use newer libraries which may cause issues for users with JDK 7.
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Indeed, one gets the warning: "bootstrap class path not set in conjunction with -source 1.7"
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To fix this, one would use the bootstrap classpath to point our JDK to an rt.jar
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for Java 7.
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At this stage, I'm sure I'm not using new library calls from Java 8+, so we can
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ignore the warning, and I don't want to bother installing newer Java just to compile
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like this. I'll endeavour not to use JDK 8 libraries so as not to cause
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any issues here ... -->
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<javac srcdir="${src}" destdir="${bin}" includeAntRuntime="false" target="1.7" source="1.7" encoding="UTF8">
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<classpath refid="apache-classpath"/>
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</javac>
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<!-- Compiling Cpp code -->
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<antcall target="gpu" if:true="${enablegpu}">
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<param name="DEBUG" value="0"/>
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</antcall>
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</target>
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<!-- Jar the toolkit -->
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<target name="jar" depends="compile" description="Create the jar for distribution">
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<!-- Put everything in ${bin} into the infodynamics-${version}.jar file -->
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<jar jarfile="${jarplainname}" basedir="${bin}" excludes="cuda/*.o,cuda/*.a,cuda/findComputeCapability">
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<manifest>
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<attribute name="Main-Class" value="infodynamics.demos.autoanalysis.AutoAnalyserLauncher"/>
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</manifest>
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</jar>
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<!-- Set the jar to be runnable: (only has effect on unix/linux)
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so we can double click to run the AutoAnalyser -->
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<chmod file="${jarplainname}" perm="u+x"/>
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</target>
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<!-- Compile and run the JUnit tests -->
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<target name="junit" depends="compile" description="Run the junit tests and make sure they compile">
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<!-- Compile the junit tests first -->
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<javac destdir="${unittestsbin}" includeAntRuntime="true" debug="true">
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<!-- Need includeAntRuntime=true if you want to pick up junit.jar and ant-junit.jar in ANT_HOME/lib;
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Otherwise you will need to set the classpath to include these here. -->
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<src path="${unittestssrc}"/>
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<classpath refid="project.classpath"/>
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<classpath refid="apache-classpath"/>
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</javac>
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<!-- Run the junit tests and make sure they complete ok -->
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<junit printsummary="yes" showoutput="yes" fork="true" forkmode="once" haltonfailure="yes" haltonerror="yes" includeantruntime="true">
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<classpath>
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<path refid="project.classpath"/>
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<pathelement path="${unittestsbin}"/>
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<pathelement location="${basedir}/clover.jar"/>
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</classpath>
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<formatter type="plain"/>
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<batchtest todir="${reports.tests}"> <!-- Writes full reports with stdout and stderr to ${reports.tests} -->
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<fileset dir="${unittestsbin}">
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<include name="**/*.class"/>
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<exclude name="**/*AbstractTester.class"/>
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<exclude name="**/ActiveInfoStorageCalculatorCorrelationIntegrals.class"/>
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<exclude name="**/ActiveInfoStorageCalculatorKernelDirect.class"/>
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<exclude name="**/*GPU*.class"/>
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</fileset>
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</batchtest>
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</junit>
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<!-- If applicable, run also GPU tests -->
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<antcall target="gputest" if:true="${enablegpu}"/>
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</target>
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<!-- Make javadocs, excluding the AutoAnalyser and classes we've derived from Apache Commons Math -->
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<target name="javadocs" depends="compile" description="Make the javadocs for the toolkit">
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<delete dir="${javadocsdir}"/>
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<javadoc destdir="${javadocsdir}">
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<packageset dir="${src}">
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<include name="**"/>
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<exclude name="infodynamics/demos/**"/>
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<exclude name="**/commonsmath3/*"/>
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<exclude name="**/commonsmath3/**"/>
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</packageset>
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</javadoc>
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<!-- Change some of the style in the javadocs css for our lists: -->
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<concat destfile="${javadocsdir}/stylesheet.css" append="true">
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.block ul li {list-style:disc; margin-left: 20px;}
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.block ol li {list-style:decimal; margin-left: 40px;}
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.block ol li ol li {list-style:lower-alpha; margin-left: 40px;}
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.block ol li ul li {list-style:disc; margin-left: 40px;}
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.block ol li ul li ol li {list-style:lower-alpha; margin-left: 40px;}
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.block ol li ol li ol li {list-style:lower-roman; margin-left: 40px;}
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.block ul li ol li {list-style:decimal; margin-left: 20px;}
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</concat>
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</target>
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<!-- Clean up -->
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<target name="clean">
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<!-- Delete the compiled code directories -->
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<delete dir="${bin}"/>
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<delete dir="${unittestsbin}"/>
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<delete dir="${reports.tests}"/>
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<delete dir="${unittestsouttoplevel}"/>
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<delete dir="${javadocsdir}"/>
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<delete dir="demos/clojure/target"/>
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<delete file="demos/clojure/pom.xml"/>
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<delete file="demos/clojure/pom.xml.asc"/>
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<delete file="demos/clojure/project.clj"/>
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<delete file="${jarversiondistnamezip}"/>
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<delete file="${distnamezip}"/>
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<delete file="${distnametargz}"/>
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<delete file="${jarplainname}"/>
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<delete>
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<fileset dir="demos/AutoAnalyser" includes="GeneratedCalculator.*"/>
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</delete>
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<delete>
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<fileset dir="demos/java/infodynamics/demos/autoanalysis" includes="GeneratedCalculator.*"/>
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</delete>
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<antcall target="gpuclean"/>
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<!-- Don't delete the readme and version files - the user may not have the template to recreate them from -->
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</target>
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<!-- Build the project jar for users -->
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<target name="build" depends="jar" description="user: build the project jar file">
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<echo message="${ant.project.name}: ${ant.file}"/>
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</target>
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<!--
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***********************************
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Developer builds below here
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***********************************
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-->
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<!-- Compile and jar the toolkit with debug symbols -->
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<target name="debug" depends="init" description="compile and jar with debug symbols">
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<echo message="Compiling for debug"/>
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<javac srcdir="${src}" destdir="${bin}" includeAntRuntime="false" target="1.7" source="1.7" debug="true">
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<classpath refid="apache-classpath"/>
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</javac>
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<!-- Compiling Cpp code -->
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<antcall target="gpu" if:true="${enablegpu}">
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<param name="DEBUG" value="1"/>
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</antcall>
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<jar jarfile="${jarplainname}" basedir="${bin}"/>
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</target>
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<!-- Compile GPU code -->
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<target name="gpu" depends="init" description="compile only C/C++ GPU code">
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<exec executable="make" dir="${cudasrc}" failonerror="true" resultproperty="return.code">
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<env key="DEBUG" value="${DEBUG}"/>
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</exec>
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<fail>
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<condition>
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<isfailure code="${return.code}"/>
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</condition>
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</fail>
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</target>
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<!-- Clean GPU code -->
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<target name="gpuclean" description="clean only C/C++ GPU code">
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<exec executable="make" dir="${cudasrc}" failonerror="true">
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<arg value="clean"/>
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</exec>
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</target>
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<!-- Test GPU code -->
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<target name="gputest" depends="gpu, compile" description="compile and run C unit tests for GPU code">
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<!-- Compile and run the C-only GPU unit tests -->
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<exec executable="make" dir="${cudasrc}" failonerror="true" resultproperty="return.code">
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<arg value="test"/>
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</exec>
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<fail>
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<condition>
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<isfailure code="${return.code}"/>
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</condition>
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</fail>
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<exec executable="./unittest" dir="${unittestsbin}/cuda/" failonerror="true" resultproperty="return.code"/>
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<fail>
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<condition>
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<isfailure code="${return.code}"/>
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</condition>
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</fail>
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<!-- Compile and run the Java+C GPU tests -->
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<javac destdir="${unittestsbin}" includeAntRuntime="true" debug="true">
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<src path="${unittestssrc}"/>
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<classpath refid="project.classpath"/>
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<classpath refid="apache-classpath"/>
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</javac>
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<junit printsummary="yes" showoutput="yes" fork="true" forkmode="once" haltonfailure="yes" haltonerror="yes" includeantruntime="true">
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<classpath>
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<path refid="project.classpath"/>
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<pathelement path="${unittestsbin}"/>
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<pathelement location="${basedir}/clover.jar"/>
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</classpath>
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<formatter type="plain"/>
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<batchtest todir="${reports.tests}"> <!-- Writes full reports with stdout and stderr to ${reports.tests} -->
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<fileset dir="${unittestsbin}">
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<include name="**/*GPU*.class"/>
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</fileset>
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</batchtest>
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</junit>
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</target>
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<!-- Developer build - creates readme and version files -->
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<target name="readmefiles" description="developer: create the readme and version files from templates">
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<tstamp>
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<format property="TODAY_DATE" pattern="dd/MM/yyyy" locale="en,UK"/>
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<format property="TODAY_YEAR" pattern="yyyy" locale="en,UK"/>
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</tstamp>
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<copy file="readme-template.txt" toFile="readme.txt" failonerror="false" overwrite="true">
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<!-- The template file only exists in SVN - this won't crash ant
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if users try to run it though because failonerror="false" -->
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<filterset>
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<filter token="YEAR" value="${TODAY_YEAR}"/>
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<filter token="DATE" value="${TODAY_DATE}"/>
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<filter token="VERSION" value="${version}"/>
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</filterset>
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</copy>
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<copy file="version-template.txt" toFile="${versionfile}" failonerror="false">
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<!-- The template file only exists in SVN - this won't crash ant
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if users try to run it though because failonerror="false" -->
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<filterset>
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<filter token="YEAR" value="${TODAY_YEAR}"/>
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<filter token="DATE" value="${TODAY_DATE}"/>
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<filter token="VERSION" value="${version}"/>
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</filterset>
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</copy>
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<copy file="demos/clojure/deploy/project-template.clj" toFile="demos/clojure/deploy/project.clj" failonerror="false" overwrite="true">
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<!-- The template file only exists in SVN - this won't crash ant
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if users try to run it though because failonerror="false" -->
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<filterset>
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<filter token="VERSION" value="${version}"/>
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</filterset>
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</copy>
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</target>
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<!-- Developer build - builds everything and makes the jar only distribution file -->
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<target name="jardist" depends="build,readmefiles" description="developer: generate the jar distribution">
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<zip destfile="${jarversiondistnamezip}">
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<fileset file="${jarplainname}"/>
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<fileset file="license-gplv3.txt"/>
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<fileset file="readme.txt"/>
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<fileset file="${versionfile}"/>
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<zipfileset dir="notices" includes="**/*.*,**/*" prefix="notices"/>
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</zip>
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</target>
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<!-- Developer build - builds everything and makes the full distribution file in zip and tar.gz -->
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<target name="dist" depends="jar,junit,javadocs,readmefiles" description="developer: generate the full distribution">
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<echo message="${ant.project.name}: ${ant.file}"/>
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<zip destfile="${distnamezip}">
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<fileset file="build.xml"/>
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<zipfileset file="${jarplainname}" filemode="755"/>
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<fileset file="license-gplv3.txt"/>
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<fileset file="readme.txt"/>
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<fileset file="InfoDynamicsToolkit.pdf"/>
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<fileset file="JIDT-logo.png" erroronmissingdir="false"/> <!-- This file is missing in full repository versions -->
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<fileset file="${versionfile}"/>
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<zipfileset dir="java" includes="**/*.java" prefix="java"/>
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<zipfileset dir="demos" includes="**/*.*,**/*" excludes="clojure/deploy,clojure/deploy/*.*,python/*.pyc,**/*.sh,**/*.bat" prefix="demos"/>
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<zipfileset dir="demos" includes="**/*.sh,**/*.bat" prefix="demos" filemode="755"/> <!-- Do these separately to get executable permissions -->
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<zipfileset dir="javadocs" includes="**/*.*,**/*" prefix="javadocs"/>
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<zipfileset dir="notices" includes="**/*.*,**/*" prefix="notices"/>
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<zipfileset dir="cuda" prefix="cuda" excludes="benchmark.sh"/>
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<zipfileset dir="cuda" prefix="cuda" includes="benchmark.sh" filemode="755"/> <!-- Do this separately to get executable permissions -->
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<zipfileset dir="course" prefix="course"/>
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<zipfileset dir="tutorial" prefix="tutorial"/> <!-- Get rid of this when tutorial is subsumed in course... -->
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<zipfileset dir="web" includes="JIDT-logo.png" prefix="" erroronmissingdir="false"/> <!-- This file is missing in zip dist versions -->
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</zip>
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<tar destfile="${distnametargz}" compression="gzip" longfile="posix"> <!-- for longfiles could also use "gnu" but apparently is slightly less widely supported -->
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<zipfileset src="${distnamezip}"/>
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</tar>
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</target>
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</project>

‎pyhctsa/Toolboxes/infodynamics-dist/infodynamics.jar‎

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