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‎README.md

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# Tempest
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# TempEst
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The source code is in https://github.com/beast-dev/tempest
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and is dependent on a library in https://github.com/beast-dev/beast-mcmc.
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## Citation
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Rambaut A, Lam TT, Carvalho LM & Pybus OG (2016) Exploring the temporal structure of heterochronous sequences using TempEst. *Virus Evolution* **2**: vew007 DOI: http://dx.doi.org/10.1093/ve/vew007
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## Documentation
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http://beast.community/tempest

‎build.xml

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<!--
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~ build_tempest.xml
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-->
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<project name="TempEst" default="build" basedir=".">
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<description>
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Build file for TempEst release versions.
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</description>
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<property name="JDK_SOURCE_VERSION" value="1.8"/>
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<property name="JDK_TARGET_VERSION" value="1.8"/>
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<!-- set global properties for this build -->
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<property name="src" location="src"/>
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<property name="build" location="build"/>
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<property name="lib" location="lib"/>
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<property name="dist" location="dist"/>
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<path id="classpath">
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<fileset dir="${lib}" includes="**/*.jar"/>
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</path>
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<property environment="env"/>
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<target name="init">
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<!-- Create the time stamp -->
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<echo message="${ant.project.name}: ${ant.file}" />
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<tstamp/>
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<!-- Create the build directory structure used by compile -->
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<mkdir dir="${build}"/>
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<mkdir dir="${dist}"/>
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</target>
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<target name="clean">
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<delete dir="${build}"/>
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</target>
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<target name="compile" depends="init">
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<!-- Compile the java code from ${src} into ${build} -->
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<javac source="${JDK_SOURCE_VERSION}" target="${JDK_TARGET_VERSION}" srcdir="${src}" destdir="${build}" classpathref="classpath">
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<include name="dr/app/tempest/**"/>
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<include name="dr/app/beauti/**"/>
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<include name="dr/app/tools/**"/>
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<include name="dr/app/util/**"/>
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<include name="dr/evolution/io/**"/>
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<include name="dr/evolution/datatype/**"/>
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<include name="dr/evolution/sequence/**"/>
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<include name="dr/evolution/alignment/**"/>
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<include name="dr/evolution/tree/**"/>
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<include name="dr/evolution/util/**"/>
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<include name="dr/app/gui/**"/>
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<include name="dr/matrix/**"/>
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<include name="dr/stats/**"/>
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<include name="dr/math/**"/>
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<include name="dr/util/**"/>
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<include name="org/virion/jam/**"/>
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</javac>
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</target>
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<target name="dist" depends="compile" description="generate the jar file">
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<!-- Create the distribution directory -->
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<mkdir dir="${dist}"/>
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<!-- Put everything in ${build} into the treestat.jar file -->
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<jar jarfile="${dist}/tempest.jar">
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<manifest>
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<attribute name="Built-By" value="${user.name}"/>
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<attribute name="Main-Class" value="dr.app.tempest.TempEstApp"/>
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</manifest>
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<fileset dir="${build}">
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<include name="dr/app/tempest/**/*.class"/>
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<include name="dr/app/beauti/**/*.class"/>
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<include name="dr/app/tools/**/*.class"/>
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<include name="dr/app/util/**/*.class"/>
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<include name="dr/evolution/io/**/*.class"/>
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<include name="dr/evolution/datatype/**/*.class"/>
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<include name="dr/evolution/sequence/**/*.class"/>
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<include name="dr/evolution/alignment/**/*.class"/>
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<include name="dr/evolution/tree/**/*.class"/>
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<include name="dr/evolution/util/**/*.class"/>
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<include name="dr/app/gui/**/*.class"/>
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<include name="dr/matrix/**/*.class"/>
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<include name="dr/stats/**/*.class"/>
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<include name="dr/math/**/*.class"/>
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<include name="dr/util/**/*.class"/>
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</fileset>
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<fileset dir="">
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<include name="images/*.png"/>
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</fileset>
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<fileset dir="${src}">
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<include name="dr/app/tempest/**/*.png"/>
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<include name="dr/app/gui/**/*.png"/>
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<include name="org/virion/jam/**/*.png"/>
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<include name="dr/gui/table/**/*.png"/>
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</fileset>
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<zipgroupfileset dir="${lib}" includes="**/jebl.jar"/>
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<zipgroupfileset dir="${lib}" includes="**/jam.jar"/>
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<zipgroupfileset dir="${lib}" includes="**/figtreepanel.jar"/>
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</jar>
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</target>
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<property name="version" value="1.5.3" />
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<property name="packaging_tools" value="packaging_tools" />
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<property name="release_dir" value="release_tempest" />
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<property name="name" value="TempEst" />
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<property name="common_dir" value="${release_dir}/common" />
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<property name="Mac_dir" value="${release_dir}/Mac" />
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<property name="Linux_dir" value="${release_dir}/Linux" />
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<property name="Windows_dir" value="${release_dir}/Windows" />
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<property name="Mac_package_dir" value="${Mac_dir}/${name} v${version}" />
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<property name="Linux_package_dir" value="${Linux_dir}/${name}_v${version}" />
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<property name="Windows_package_dir" value="${Windows_dir}/${name} v${version}" />
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<!-- Need to either install Launch4j under {BEAST workspace}/${release}
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or install it in the default directory and change the location of launch4j.dir -->
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<target name="windows" depends="dist" description="release Windows version of TempEst">
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<delete dir="${Windows_package_dir}" />
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<!-- Create the release directory -->
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<mkdir dir="${Windows_package_dir}" />
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<property name="launch4j.dir" location="${Windows_dir}/launch4j" />
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<taskdef name="launch4j" classname="net.sf.launch4j.ant.Launch4jTask"
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classpath="${launch4j.dir}/launch4j.jar :${launch4j.dir}/lib/xstream.jar" />
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<copy file="${dist}/tempest.jar" todir="${Windows_package_dir}/lib"/>
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<!--
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<copy todir="${Windows_package_dir}/lib">
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<fileset dir="${Windows_dir}/lib"/>
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</copy>
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-->
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<copy file="${common_dir}/README.txt" todir="${Windows_package_dir}"/>
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<launch4j configFile="${Windows_dir}/tempest_launch4j.xml"
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jar="${dist}/tempest.jar"
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outfile="${Windows_package_dir}/${name} v${version}.exe"
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fileVersion="${version}.0"
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txtFileVersion="${version}"
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productVersion="${version}.0"
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txtProductVersion="${version}"/>
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<zip destfile="${release_dir}/${name} v${version}.zip">
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<zipfileset dir="${Windows_package_dir}" prefix="${name} v${version}"/>
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</zip>
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<echo message="Windows version release is finished." />
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</target>
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<target name="linux" depends="dist" description="release Linux/Unix version of TempEst">
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<delete dir="${Linux_package_dir}" />
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<!-- Create the release directory -->
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<mkdir dir="${Linux_package_dir}" />
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<copy todir="${Linux_package_dir}/bin">
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<fileset dir="${Linux_dir}/scripts"/>
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</copy>
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<chmod dir="${Linux_package_dir}/bin" perm="755" includes="**/**"/>
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<copy file="${Linux_dir}/icons/tempest.png" todir="${Linux_package_dir}/images"/>
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<copy file="${dist}/tempest.jar" todir="${Linux_package_dir}/lib"/>
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<!-- no libraries to copy...
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<copy todir="${Linux_package_dir}/lib">
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<fileset dir="${Linux_dir}/lib"/>
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</copy>
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-->
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<copy file="${common_dir}/README.txt" todir="${Linux_package_dir}"/>
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<tar destfile="${release_dir}/${name}_v${version}.tgz" compression="gzip">
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<tarfileset dir="${Linux_package_dir}" prefix="${name}_v${version}"/>
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</tar>
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<echo message="Linux/Unix version release is finished." />
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</target>
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<!-- this will only work on Andrew's computer -->
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<property name="AppleSigner" value="Developer ID Application: Andrew Rambaut (9E4WXAQ6SE)" />
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<target name="mac" depends="dist" description="release Mac version of Tempest">
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<delete dir="${Mac_package_dir}" />
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<!-- Create the release directory -->
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<mkdir dir="${Mac_package_dir}" />
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<copy file="${common_dir}/README.txt" todir="${Mac_package_dir}"/>
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<taskdef name="jarbundler" classname="com.ultramixer.jarbundler.JarBundler" classpath="${packaging_tools}/mac/jarbundler-core-3.3.0.jar"/>
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<!-- create a jar bundle for the mac -->
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<jarbundler dir="${Mac_package_dir}"
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name="${name} v${version}"
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mainclass="dr.app.tempest.TempEstApp"
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stubfile="${packaging_tools}/mac/universalJavaApplicationStub"
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useJavaXKey="true"
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icon="${Mac_dir}/icons/TempEst.icns"
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jvmversion="1.6+"
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arguments=""
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vmoptions="-Xmx1024M"
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version="${version}"
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highresolutioncapable="true"
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copyright="${name} v${version}, Copyright 2006-2018, Andrew Rambaut"
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bundleid="tempest" >
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<javaproperty name="apple.laf.useScreenMenuBar" value="true"/>
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<jarfileset dir="${dist}">
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<include name="**/tempest.jar"/>
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</jarfileset>
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</jarbundler>
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<!-- code signing -->
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<exec executable="codesign">
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<arg value="--deep"/>
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<arg value="-s"/>
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<arg value="${AppleSigner}"/>
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<arg value="-v"/>
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<arg value="${Mac_package_dir}/${name} v${version}.app"/>
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</exec>
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<echo message="Building disk image." />
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<!-- create disk image -->
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<exec executable="/usr/bin/hdiutil">
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<arg value="create"/>
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<arg value="-ov"/>
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<arg value="-srcfolder"/>
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<arg value="${Mac_package_dir}"/>
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<arg value="-volname"/>
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<arg value="${name} v${version}"/>
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<arg value="-imagekey"/>
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<arg value="zlib-level=6"/>
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<arg value="${release_dir}/${name} v${version}.dmg"/>
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</exec>
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<exec executable="codesign">
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<arg value="-s"/>
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<arg value="${AppleSigner}"/>
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<arg value="-v"/>
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<arg value="${release_dir}/${name} v${version}.dmg"/>
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</exec>
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<echo message="Mac version release is finished." />
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</target>
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<target name="build" depends="mac, windows, linux" description="build all the executables" />
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</project>

‎lib/commons-math-2.2.jar

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‎lib/itext-1.4.5.jar

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‎lib/jam.jar

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‎lib/jebl.jar

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‎packaging_tools/mac/createdmg.sh

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#!/bin/sh
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cd release/Mac
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export title="Tracer"
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export version=`perl -e 'while($s=<>) {if ($s=~/"version"/) {$s =~ /value="([^"]*)"/; print $1;}}' < ../../build.xml`
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export applicationName="${title} v${version}"
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export size=1g
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export backgroundPictureName=install.png
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export finalDMGName="${title} v${version}"
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export source="${title} v${version}"
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echo ${version}
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hdiutil create -srcfolder "${source}" -volname "${title}" -fs HFS+ \
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-fsargs "-c c=64,a=16,e=16" -format UDRW -size ${size}k pack.temp.dmg
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export device=$(hdiutil attach -readwrite -noverify -noautoopen "pack.temp.dmg" | \
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egrep '^/dev/' | sed 1q | awk '{print $1}')
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echo '
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tell application "Finder"
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tell disk "'${title}'"
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open
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set current view of container window to icon view
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set toolbar visible of container window to false
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set statusbar visible of container window to false
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set the bounds of container window to {400, 100, 885, 430}
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set theViewOptions to the icon view options of container window
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set arrangement of theViewOptions to not arranged
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set background picture of theViewOptions to file "'${backgroundPictureName}'"
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set label position of theViewOptions to bottom
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set icon size of theViewOptions to 96
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make new alias file at container window to POSIX file "/Applications" with properties {name:"Applications"}
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set position of item "'${applicationName}'" of container window to {100, 120}
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set position of item "'${backgroundPictureName}'" of container window to {800, 120}
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set position of item "Applications" of container window to {375, 120}
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close
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open
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update without registering applications
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delay 5
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# eject
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end tell
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end tell
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' | osascript
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echo "OSASCRIPT DONE"
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chmod -Rf go-w /Volumes/"${title}"
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sync
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sync
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hdiutil detach ${device}
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hdiutil convert "pack.temp.dmg" -format UDZO -imagekey zlib-level=9 -o "../${finalDMGName}"
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rm -f /pack.temp.dmg

‎packaging_tools/mac/install.png

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‎packaging_tools/mac/jarbundler-core-3.3.0.jar

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