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build.xml
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build.xml
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<!--
~ build.xml
~
~ Copyright (c) 2002-2017 Alexei Drummond, Andrew Rambaut and Marc Suchard
~
~ This file is part of BEAST.
~ See the NOTICE file distributed with this work for additional
~ information regarding copyright ownership and licensing.
~
~ BEAST is free software; you can redistribute it and/or modify
~ it under the terms of the GNU Lesser General Public License as
~ published by the Free Software Foundation; either version 2
~ of the License, or (at your option) any later version.
~
~ BEAST is distributed in the hope that it will be useful,
~ but WITHOUT ANY WARRANTY; without even the implied warranty of
~ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
~ GNU Lesser General Public License for more details.
~
~ You should have received a copy of the GNU Lesser General Public
~ License along with BEAST; if not, write to the
~ Free Software Foundation, Inc., 51 Franklin St, Fifth Floor,
~ Boston, MA 02110-1301 USA
-->
<!-- Build BEAST MCMC. It is also used by Hudson BEAST_MCMC project. JUnit test is available for this build. -->
<project basedir="." default="dist" name="BEAST">
<description>
Build BEAST MCMC. JUnit test is available for this build.
$Id$
</description>
<property name="JDK_SOURCE_VERSION" value="1.8"/>
<property name="JDK_TARGET_VERSION" value="1.8"/>
<!-- set global properties for this build -->
<property name="src" location="src"/>
<property name="build" location="build"/>
<property name="lib" location="lib"/>
<property name="dist" location="${build}/dist"/>
<property name="main_class_BEAST" value="dr.app.beast.BeastMain"/>
<property name="main_class_BEAUTI" value="dr.app.beauti.BeautiApp"/>
<property name="main_class_TRACER" value="dr.app.tracer.application.TracerApp"/>
<property name="main_class_Annotator" value="dr.app.tools.treeannotator.TreeAnnotator"/>
<property name="main_class_LogCombiner" value="dr.app.tools.logcombiner.LogCombiner"/>
<property name="report" value="${build}/junitreport"/>
<path id="classpath">
<fileset dir="${lib}" includes="**/*.jar"/>
</path>
<!-- start -->
<target name="init">
<echo message="${ant.project.name}: ${ant.file}"/>
</target>
<target name="clean">
<delete dir="${build}"/>
</target>
<!-- clean previous build, and then compile Java source code, and Juint test -->
<target name="test" depends="clean,compile-all,junit"
description="Clean and Build all run-time stuff with unit test">
</target>
<!-- https://stackoverflow.com/questions/2974106/how-to-lookup-the-latest-git-commit-hash-from-an-ant-build-script-->
<available file=".git" type="dir" property="git.present"/>
<target name="git.commit" description="Store git revision in ${repository.commit}" if="git.present">
<exec executable="git" outputproperty="git.commit" failifexecutionfails="true" errorproperty="">
<arg value="describe"/>
<arg value="--always"/>
<arg value="--dirty"/>
</exec>
<condition property="repository.commit" value="${git.commit}" else="git-commit-unavailable">
<and>
<isset property="git.commit"/>
<length string="${git.commit}" trim="yes" length="0" when="greater"/>
</and>
</condition>
</target>
<target name="revision" depends="git.commit" description="build revision.txt from template">
<copy file="revision.txt.template" tofile="src/revision.txt" overwrite="yes">
<filterchain>
<replacetokens>
<token key="repository.commit" value="${repository.commit}" />
</replacetokens>
</filterchain>
</copy>
</target>
<!-- compile Java source code -->
<target name="compile-all" depends="init,revision">
<mkdir dir="${build}"/>
<!-- Compile the java code from ${src} into ${build} /bin -->
<javac source="${JDK_SOURCE_VERSION}" target="${JDK_TARGET_VERSION}" srcdir="${src}" destdir="${build}"
classpathref="classpath"
fork="true"
includeantruntime="false"
memoryinitialsize="256m"
memorymaximumsize="1024m"
encoding="UTF-8">
<include name="dr/app/beast/**"/>
<include name="dr/app/beauti/**"/>
<include name="dr/app/bss/**"/>
<include name="dr/app/checkpoint/**"/>
<include name="dr/app/gui/**"/>
<include name="dr/app/oldbeauti/**"/>
<include name="dr/app/beagle/**"/>
<include name="dr/app/seqgen/**"/>
<include name="dr/app/plugin/**"/>
<include name="dr/app/realtime/**"/>
<include name="dr/app/tools/**"/>
<include name="dr/app/util/**"/>
<include name="dr/app/treestat/**"/>
<include name="dr/evolution/**"/>
<include name="dr/evomodel/**"/>
<include name="dr/evomodelxml/**"/>
<include name="dr/oldevomodel/**"/>
<include name="dr/oldevomodelxml/**"/>
<include name="dr/evoxml/**"/>
<include name="dr/exporters/**"/>
<include name="dr/gui/chart/**"/>
<include name="dr/gui/tree/**"/>
<include name="dr/inference/**"/>
<include name="dr/inferencexml/**"/>
<include name="dr/math/**"/>
<include name="dr/matrix/**"/>
<include name="dr/stats/**"/>
<include name="dr/util/**"/>
<include name="dr/xml/**"/>
<include name="dr/geo/**"/>
<!-- complie JUnit test classes -->
<include name="test/dr/**"/>
</javac>
<echo message="Successfully compiled."/>
</target>
<!-- make the beast.jar and beauti.jar -->
<target name="dist" depends="compile-all" description="create BEAST + BEAUTI jar">
<!-- Create the distribution directory -->
<mkdir dir="${dist}"/>
<!-- Put everything in ${build} into the beast.jar file -->
<jar jarfile="${dist}/beast.jar">
<manifest>
<attribute name="Built-By" value="${user.name}"/>
<attribute name="Main-Class" value="${main_class_BEAST}"/>
</manifest>
<fileset dir="${build}">
<include name="dr/app/beast/**/*.class"/>
<!--<include name="dr/app/beastdev/**/*.class"/>-->
<include name="dr/app/beauti/**/*.class"/>
<include name="dr/app/bss/**/*.class"/>
<include name="dr/app/checkpoint/**"/>
<include name="dr/app/gui/**/*.class"/>
<include name="dr/app/seqgen/**"/>
<include name="dr/app/plugin/**"/>
<include name="dr/app/realtime/**"/>
<include name="dr/app/util/**/*.class"/>
<include name="dr/app/tools/**/*.class"/>
<include name="dr/app/treestat/**/*.class"/>
<include name="dr/app/beagle/**/*.class"/>
<!-- include beagle -->
<include name="dr/evolution/**/*.class"/>
<include name="dr/evoxml/**/*.class"/>
<include name="dr/evomodel/**/*.class"/>
<include name="dr/evomodelxml/**/*.class"/>
<include name="dr/oldevomodel/**/*.class"/>
<include name="dr/oldevomodelxml/**/*.class"/>
<include name="dr/exporters/**/*.class"/>
<include name="dr/gui/tree/**/*.class"/>
<include name="dr/inference/**/*.class"/>
<include name="dr/inferencexml/**/*.class"/>
<include name="dr/math/**/*.class"/>
<include name="dr/matrix/**/*.class"/>
<include name="dr/stats/**/*.class"/>
<include name="dr/util/**/*.class"/>
<include name="dr/xml/**/*.class"/>
<include name="dr/geo/**/*.class"/>
</fileset>
<fileset dir="">
<include name="images/*.png"/>
</fileset>
<fileset dir="${src}">
<include name="dr/**/*.png"/>
<include name="revision.txt"/>
<include name="org/virion/jam/**/*.png"/>
<include name="dr/**/*.properties"/>
</fileset>
<zipgroupfileset dir="${lib}" includes="jebl.jar"/>
<zipgroupfileset dir="${lib}" includes="jam.jar"/>
<zipgroupfileset dir="${lib}" includes="jdom.jar"/>
<zipgroupfileset dir="${lib}" includes="commons-math-2.2.jar"/>
<zipgroupfileset dir="${lib}" includes="mtj.jar"/>
<zipgroupfileset dir="${lib}" includes="JRI.jar"/>
<zipgroupfileset dir="${lib}" includes="colt.jar"/>
<zipgroupfileset dir="${lib}" includes="beagle.jar"/>
<zipgroupfileset dir="${lib}" includes="beagle.jar"/>
<zipgroupfileset dir="${lib}" includes="EJML-core-0.30.jar"/>
<zipgroupfileset dir="${lib}" includes="lbfgs4j-0.2.1.jar"/>
<zipgroupfileset dir="${lib}" includes="EJML-dense64-0.30.jar"/>
</jar>
<!-- Put everything in ${build} into the beauti.jar file -->
<jar jarfile="${dist}/beauti.jar">
<manifest>
<attribute name="Built-By" value="${user.name}"/>
<attribute name="Main-Class" value="${main_class_BEAUTI}"/>
</manifest>
<fileset dir="${build}">
<include name="dr/app/beast/BeastVersion.class"/>
<include name="dr/app/beauti/**/*.class"/>
<include name="dr/app/oldbeauti/**/*.class"/>
<include name="dr/app/util/**/*.class"/>
<include name="dr/app/gui/**/*.class"/>
<include name="dr/app/java16compat/**/*.class"/>
<include name="dr/evolution/alignment/**/*.class"/>
<include name="dr/evolution/coalescent/**/*.class"/>
<include name="dr/evolution/colouring/**/*.class"/>
<include name="dr/evolution/datatype/**/*.class"/>
<include name="dr/evolution/distance/**/*.class"/>
<include name="dr/evolution/io/**/*.class"/>
<include name="dr/evolution/parsimony/**/*.class"/>
<include name="dr/evolution/sequence/**/*.class"/>
<include name="dr/evolution/tree/**/*.class"/>
<include name="dr/evolution/util/**/*.class"/>
<include name="dr/evomodel/branchratemodel/**/*.class"/>
<include name="dr/evomodel/clock/**/*.class"/>
<include name="dr/evomodel/coalescent/**/*.class"/>
<include name="dr/evomodel/continuous/**/*.class"/>
<include name="dr/evomodel/operators/**/*.class"/>
<include name="dr/evomodel/sitemodel/**/*.class"/>
<include name="dr/evomodel/speciation/**/*.class"/>
<include name="dr/evomodel/substmodel/**/*.class"/>
<include name="dr/evomodel/tree/**/*.class"/>
<include name="dr/evomodel/treelikelihood/**/*.class"/>
<include name="dr/evomodel/treedatalikelihood/**/*.class"/>
<include name="dr/evomodelxml/**/*.class"/>
<exclude name="dr/evomodelxml/treedatalikelihood/MultiPartitionDataLikelihoodDelegate*"/>
<include name="dr/evoxml/**/*.class"/>
<include name="dr/gui/chart/**"/>
<include name="dr/gui/table/**"/>
<include name="dr/gui/tree/**"/>
<include name="dr/inference/**/*.class"/>
<include name="dr/inferencexml/**/*.class"/>
<include name="dr/math/**/*.class"/>
<include name="dr/matrix/**/*.class"/>
<include name="dr/stats/**/*.class"/>
<include name="dr/util/**/*.class"/>
<include name="dr/xml/**/*.class"/>
<include name="dr/geo/**/*.class"/>
</fileset>
<fileset dir="">
<include name="images/*.png"/>
</fileset>
<fileset dir="${src}">
<include name="dr/**/*.png"/>
</fileset>
<zipgroupfileset dir="${lib}" includes="jam.jar"/>
<zipgroupfileset dir="${lib}" includes="jebl.jar"/>
<zipgroupfileset dir="${lib}" includes="jdom.jar"/>
<zipgroupfileset dir="${lib}" includes="commons-math-2.2.jar"/>
<zipgroupfileset dir="${lib}" includes="mtj.jar"/>
</jar>
<!-- Put everything in ${build} into the trace.jar file -->
<jar jarfile="${dist}/trace.jar">
<manifest>
<attribute name="Built-By" value="${user.name}"/>
</manifest>
<fileset dir="${build}">
<include name="dr/app/gui/**/*.class"/>
<include name="dr/app/util/*.class"/>
<include name="dr/evolution/coalescent/*.class"/>
<include name="dr/evolution/util/*.class"/>
<include name="dr/inference/trace/*.class"/>
<include name="dr/inference/model/**/*.class"/>
<include name="dr/math/**/*.class"/>
<include name="dr/stats/**/*.class"/>
<include name="dr/util/**/*.class"/>
</fileset>
</jar>
<!-- Put everything in ${build} into the tempest-lib.jar file -->
<jar jarfile="${dist}/tempest-lib.jar">
<manifest>
<attribute name="Built-By" value="${user.name}"/>
</manifest>
<fileset dir="${build}">
<include name="dr/app/beauti/tipdatepanel/**/*.class"/>
<include name="dr/app/beauti/util/**/*.class"/>
<include name="dr/app/beauti/options/**/*.class"/>
<include name="dr/app/gui/**/*.class"/>
<include name="dr/app/tools/*.class"/>
<include name="dr/app/util/*.class"/>
<include name="dr/evolution/tree/**/*.class"/>
<include name="dr/evolution/io/*.class"/>
<include name="dr/evolution/util/*.class"/>
<include name="dr/math/**/*.class"/>
<include name="dr/stats/**/*.class"/>
<include name="dr/util/**/*.class"/>
</fileset>
</jar>
</target>
<!-- used to copy the compiled trace.jar into place in the Tracer lib folder -->
<target name="copy_trace_jar" depends="dist" >
<copy file="${dist}/trace.jar" todir="../Tracer/lib"/>
</target>
<!-- used to copy the compiled tempest-lib.jar into place in the Tempest lib folder -->
<target name="copy_tempest-lib_jar" depends="dist" >
<copy file="${dist}/tempest-lib.jar" todir="../Tempest/lib"/>
</target>
<!-- run beast.jar -->
<target name="run_BEAST">
<java jar="${dist}/beast.jar" fork="true"/>
</target>
<!-- run beauti.jar -->
<target name="run_BEAUTI">
<java jar="${dist}/beauti.jar" fork="true"/>
</target>
<!-- run beast.jar -->
<target name="dist_test_jar" depends="dist">
<jar jarfile="${dist}/beastTest.jar">
<fileset dir="${build}">
<include name="test/dr/**/*.class"/>
</fileset>
<zipgroupfileset dir="${dist}" includes="beast.jar"/>
</jar>
</target>
<!-- JUnit test -->
<target name="junit">
<mkdir dir="${report}"/>
<junit printsummary="yes" haltonfailure="no" failureproperty="test.failed">
<classpath>
<path refid="classpath"/>
<path location="${build}"/>
</classpath>
<formatter type="xml"/>
<batchtest fork="yes" todir="${report}">
<fileset dir="${src}">
<include name="test/dr/**/*Test.java"/>
<!-- Broken JUnits -->
<exclude name="test/dr/app/beagle/AncestralStateBeagleTreeLikelihoodTest.java"/> <!-- doesn't always fail-->
<exclude name="test/dr/app/beagle/MarkovJumpsTest.java"/> <!-- doesn't always fail-->
<exclude name="test/dr/distibutions/InvGammaTest.java"/>
<exclude name="test/dr/evolution/TreeMetricsTest.java"/>
<exclude name="test/dr/evomodel/substmodel/CodonPartitionedRobustCountingTest.java"/>
<exclude name="test/dr/evomodel/operators/ExchangeOperatorTest.java"/> <!--too long-->
<exclude name="test/dr/evomodel/arg/operators/ARGAddRemoveOperatorTest.java"/>
<exclude name="test/dr/evomodel/branchratemodel/UncorrelatedRelaxedClockTest.java"/>
<exclude name="test/dr/evomodel/speciation/RLYModelTest.java"/>
<exclude name="test/dr/evomodel/substmodel/EigendecompositionTest.java"/>
<exclude name="test/dr/evomodel/substmodel/ProductChainSubstitutionModelTest.java"/>
<exclude name="test/dr/evomodel/substmodel/StateHistoryTest.java"/>
<exclude name="test/dr/evomodel/substmodel/TwoStateOccupancyMarkovRewardsTest.java"/>
<!-- <exclude name="test/dr/evomodel/treedatalikelihood/continuous/BranchSpecificGradientTest.java"/> -->
<!-- <exclude name="test/dr/evomodel/treedatalikelihood/continuous/ContinuousDataLikelihoodDelegateTest.java"/> -->
<!-- <exclude name="test/dr/evomodel/treedatalikelihood/hmc/PrecisionGradientTest.java"/> -->
<exclude name="test/dr/multidimensionalscaling/MDSRotationTest.java"/>
<exclude name="test/dr/evomodel/branchratemodel/StrictClockTest.java"/>
<!-- <exclude name="test/dr/evomodel/substmodel/TimeIrreversibleTest.java"/>--> <!--sometimes fails-->
<!-- <include name="test/dr/distibutions/**/*Test.java"/>-->
<!-- <include name="test/dr/evolution/**/*Test.java"/>-->
<!-- <!– <include name="test/dr/evomodel/**/*Test.java" /> –>-->
<!-- <!– <include name="test/dr/evomodel/arg/**/*Test.java" /> –>-->
<!-- <include name="test/dr/evomodel/branchratemodel/**/*Test.java"/>-->
<!-- <include name="test/dr/evomodel/coalescent/**/*Test.java"/>-->
<!-- <include name="test/dr/evomodel/operators/**/*Test.java"/>-->
<!-- <include name="test/dr/evomodel/speciation/**/*Test.java"/>-->
<!-- <include name="test/dr/evomodel/substmodel/**/*Test.java"/>-->
<!-- <include name="test/dr/evomodel/treelikelihood/**/*Test.java"/>-->
<!-- <include name="test/dr/inference/**/*Test.java"/>-->
<!-- <include name="test/dr/math/**/*Test.java"/>-->
</fileset>
</batchtest>
</junit>
<fail message="At least one of the JUnits failed the test. Check test results." if="test.failed"/>
<echo message="JUnit test finished."/>
</target>
<target name="junitreport">
<junitreport todir="${report}">
<fileset dir="${report}" includes="*.xml"/>
<report format="frames" todir="${report}"/>
</junitreport>
<echo message="JUnit test report finished."/>
</target>
<!--
<property name="version" value="1.9"/>
-->
<property name="version" value="10.5.0"/>
<property name="jvm_version" value="1.8+"/>
<property name="version_number" value="10.5.0"/>
<property name="copyright" value="Copyright 2002-2024"/>
<property name="release_dir" value="release"/>
<property name="BEAST_name" value="BEAST"/>
<property name="BEAST_package_name" value="BEAST X"/>
<property name="BEAST_package_name_linux" value="BEAST_X"/>
<property name="BEAUti_name" value="BEAUti"/>
<property name="TreeAnnotator_name" value="TreeAnnotator"/>
<property name="LogCombiner_name" value="LogCombiner"/>
<property name="LogAnalyser_name" value="LogAnalyser"/>
<property name="packaging_tools" value="packaging_tools" />
<property name="common_dir" value="${release_dir}/common"/>
<property name="Mac_dir" value="${release_dir}/Mac"/>
<property name="Linux_dir" value="${release_dir}/Linux"/>
<property name="Windows_dir" value="${release_dir}/Windows"/>
<property name="Windows_launchers_dir" value="${release_dir}/Windows_Launchers"/>
<property name="Packaging_dir" value="packaging_tools/windows"/>
<property name="Mac_package_dir" value="${Mac_dir}/${BEAST_package_name} v${version}"/>
<property name="Linux_package_dir" value="${Linux_dir}/${BEAST_package_name_linux}v${version}"/>
<property name="Windows_package_dir" value="${Windows_dir}/${BEAST_package_name} v${version}"/>
<property name="Windows_launchers_package_dir" value="${Windows_launchers_dir}/${BEAST_package_name} v${version}"/>
<!-- Need to either install Launch4j under {BEAST workspace}/${release}
or install it in the default directory and change the location of launch4j.dir -->
<target name="windows" depends="dist"
description="release Windows version of BEAST, BEAUTI, TreeAnnotator, LogCombiner">
<delete dir="${Windows_package_dir}"/>
<!-- Create the release directory -->
<mkdir dir="${Windows_package_dir}"/>
<property name="launch4j.dir" location="${Packaging_dir}/launch4j"/>
<taskdef name="launch4j" classname="net.sf.launch4j.ant.Launch4jTask"
classpath="${launch4j.dir}/launch4j.jar :${launch4j.dir}/lib/xstream.jar"/>
<copy todir="${Windows_package_dir}/doc">
<fileset dir="${common_dir}/doc"/>
</copy>
<copy todir="${Windows_package_dir}/examples">
<fileset dir="examples"/>
</copy>
<copy todir="${Windows_package_dir}/native">
<fileset dir="native">
<exclude name="deprecated/**"/>
</fileset>
</copy>
<copy todir="${Windows_package_dir}/bin">
<fileset dir="${Windows_dir}/scripts"/>
</copy>
<copy file="${dist}/beauti.jar" todir="${Windows_package_dir}/lib"/>
<copy file="${dist}/beast.jar" todir="${Windows_package_dir}/lib"/>
<!--
<copy todir="${Windows_package_dir}/lib">
<fileset dir="${Windows_dir}/lib"/>
</copy>
-->
<copy file="${common_dir}/VERSION HISTORY.txt" todir="${Windows_package_dir}"/>
<copy file="${common_dir}/README.txt" todir="${Windows_package_dir}"/>
<!-- BEAUTi v?.?.?.exe -->
<launch4j configFile="${Windows_dir}/BEAUti_launch4j.xml"
jar="${dist}/beauti.jar"
outfile="${Windows_package_dir}/${BEAUti_name} v${version}.exe"
fileVersion="${version_number}.0"
txtFileVersion="${version}"
productVersion="${version_number}.0"
txtProductVersion="${version}"/>
<!-- BEAST v?.?.?.exe -->
<launch4j configFile="${Windows_dir}/BEAST_launch4j.xml"
jar="${dist}/beast.jar"
outfile="${Windows_package_dir}/${BEAST_name} v${version}.exe"
fileVersion="${version_number}.0"
txtFileVersion="${version}"
productVersion="${version_number}.0"
txtProductVersion="${version}"/>
<!-- TreeAnnotator v?.?.?.exe -->
<launch4j configFile="${Windows_dir}/TreeAnnotator_launch4j.xml"
jar="${dist}/beast.jar"
outfile="${Windows_package_dir}/${TreeAnnotator_name} v${version}.exe"
fileVersion="${version_number}.0"
txtFileVersion="${version}"
productVersion="${version_number}.0"
txtProductVersion="${version}"/>
<!-- LogCombiner v?.?.?.exe -->
<launch4j configFile="${Windows_dir}/LogCombiner_launch4j.xml"
jar="${dist}/beast.jar"
outfile="${Windows_package_dir}/${LogCombiner_name} v${version}.exe"
fileVersion="${version_number}.0"
txtFileVersion="${version}"
productVersion="${version_number}.0"
txtProductVersion="${version}"/>
<!-- LogAnalyser v?.?.?.exe
<launch4j configFile="${Windows_dir}/LogAnalyser_launch4j.xml"
jar="${dist}/beast.jar"
outfile="${Windows_package_dir}/${LogAnalyser_name}v${version}.exe"
fileVersion="${version}.0"
txtFileVersion="${version}"
productVersion="${version}.0"
txtProductVersion="${version}"/> -->
<zip destfile="${release_dir}/${BEAST_package_name} v${version}.zip">
<zipfileset dir="${Windows_package_dir}" prefix="${BEAST_package_name} v${version}"/>
</zip>
<echo message="Windows version release is finished."/>
</target>
<target name="windows_launchers" depends="dist"
description="release Windows (launchers) version of BEAST, BEAUTI, TreeAnnotator, LogCombiner">
<delete dir="${Windows_launchers_package_dir}"/>
<!-- Create the release directory -->
<mkdir dir="${Windows_launchers_package_dir}"/>
<property name="launch4j.dir" location="${Packaging_dir}/launch4j"/>
<taskdef name="launch4j" classname="net.sf.launch4j.ant.Launch4jTask"
classpath="${launch4j.dir}/launch4j.jar :${launch4j.dir}/lib/xstream.jar"/>
<copy todir="${Windows_launchers_package_dir}/doc">
<fileset dir="${common_dir}/doc"/>
</copy>
<copy todir="${Windows_launchers_package_dir}/examples">
<fileset dir="examples"/>
</copy>
<copy todir="${Windows_launchers_package_dir}/native">
<fileset dir="native">
<exclude name="deprecated/**"/>
</fileset>
</copy>
<copy todir="${Windows_launchers_package_dir}/bin">
<fileset dir="${Windows_dir}/scripts"/>
</copy>
<copy file="${dist}/beauti.jar" todir="${Windows_launchers_package_dir}/lib"/>
<copy file="${dist}/beast.jar" todir="${Windows_launchers_package_dir}/lib"/>
<!--
<copy todir="${Windows_package_dir}/lib">
<fileset dir="${Windows_dir}/lib"/>
</copy>
-->
<copy file="${common_dir}/VERSION HISTORY.txt" todir="${Windows_launchers_package_dir}"/>
<copy file="${common_dir}/README.txt" todir="${Windows_launchers_package_dir}"/>
<!-- BEAUTi v?.?.?.exe -->
<launch4j configFile="${Windows_launchers_dir}/BEAUti_launch4j.xml"
outfile="${Windows_launchers_package_dir}/${BEAUti_name} v${version}.exe"
fileVersion="${version_number}.0"
txtFileVersion="${version}"
productVersion="${version_number}.0"
txtProductVersion="${version}"/>
<!-- BEAST v?.?.?.exe -->
<launch4j configFile="${Windows_launchers_dir}/BEAST_launch4j.xml"
outfile="${Windows_launchers_package_dir}/${BEAST_name} v${version}.exe"
fileVersion="${version_number}.0"
txtFileVersion="${version}"
productVersion="${version_number}.0"
txtProductVersion="${version}"/>
<!-- BEAST v?.?.?.exe -->
<launch4j configFile="${Windows_launchers_dir}/BEAST_launch4j.xml"
outfile="${Windows_launchers_package_dir}/${BEAST_name} v${version}.exe"
fileVersion="${version_number}.0"
txtFileVersion="${version}"
productVersion="${version_number}.0"
txtProductVersion="${version}"/>
<!-- TreeAnnotator v?.?.?.exe -->
<launch4j configFile="${Windows_launchers_dir}/TreeAnnotator_launch4j.xml"
outfile="${Windows_launchers_package_dir}/${TreeAnnotator_name} v${version}.exe"
fileVersion="${version_number}.0"
txtFileVersion="${version}"
productVersion="${version_number}.0"
txtProductVersion="${version}"/>
<!-- LogCombiner v?.?.?.exe -->
<launch4j configFile="${Windows_launchers_dir}/LogCombiner_launch4j.xml"
outfile="${Windows_launchers_package_dir}/${LogCombiner_name} v${version}.exe"
fileVersion="${version_number}.0"
txtFileVersion="${version}"
productVersion="${version_number}.0"
txtProductVersion="${version}"/>
<zip destfile="${release_dir}/${BEAST_package_name} v${version}_launchers.zip">
<zipfileset dir="${Windows_launchers_package_dir}" prefix="${BEAST_package_name} v${version}"/>
</zip>
<echo message="Windows launchers version release is finished."/>
</target>
<target name="linux" depends="dist"
description="release Linux/Unix version of BEAST, BEAUTI, TreeAnnotator, LogCombiner">
<delete dir="${Linux_package_dir}"/>
<!-- Create the release directory -->
<mkdir dir="${Linux_package_dir}"/>
<copy todir="${Linux_package_dir}/bin">
<fileset dir="${Linux_dir}/scripts"/>
</copy>
<chmod dir="${Linux_package_dir}/bin" perm="755" includes="**/**"/>
<copy todir="${Linux_package_dir}/doc">
<fileset dir="${common_dir}/doc"/>
</copy>
<copy todir="${Linux_package_dir}/examples">
<fileset dir="examples"/>
</copy>
<copy todir="${Linux_package_dir}/native">
<fileset dir="native">
<exclude name="deprecated/**"/>
</fileset>
</copy>
<copy file="${common_dir}/icons/beast.png" todir="${Linux_package_dir}/images"/>
<copy file="${common_dir}/icons/beauti.png" todir="${Linux_package_dir}/images"/>
<copy file="${common_dir}/icons/utility.png" todir="${Linux_package_dir}/images"/>
<copy file="${dist}/beauti.jar" todir="${Linux_package_dir}/lib"/>
<copy file="${dist}/beast.jar" todir="${Linux_package_dir}/lib"/>
<!-- <copy file="${dist}/beast-beagle.jar" todir="${Linux_package_dir}/lib"/> -->
<copy file="${common_dir}/VERSION HISTORY.txt" todir="${Linux_package_dir}"/>
<copy file="${common_dir}/README.txt" todir="${Linux_package_dir}"/>
<!-- Only works under Unix or NonStop Kernel (Tandem) -->
<!-- <chmod dir="${Linux_package_dir}/bin" perm="755" includes="**/**"/>
<tar destfile="${Linux_dir}/${BEAST_name}v${version}.tgz" compression="gzip">
<tarfileset dir="${Linux_package_dir}" prefix="${BEAST_name}v${version}"/>
</tar>-->
<!-- [ANT Bug 550] the tar task change the mode of the executables files, have to tar manaully -->
<echo message="Have to tar manaully, because [ANT Bug 550] the tar task change the mode of the executables files."/>
<!-- tar -cvzf BEASTv1.x.x.tgz BEASTv1.x.x/ -->
<!-- cksum BEASTv1.x.x.tgz -->
<!-- tar -xvzf BEASTv1.x.x.tgz -->
<echo message="Linux/Unix version release is finished."/>
</target>
<!-- this will only work on Andrew's computer -->
<property name="AppleSignerApplication" value="Developer ID Application: Andrew Rambaut (9E4WXAQ6SE)" />
<property name="AppleSignerInstaller" value="Developer ID Installer: Andrew Rambaut (9E4WXAQ6SE)" />
<!--
<property name="AppleSignerApplication" value="Developer ID Application: Marc Suchard (LC992Z5R7E)"/>
<property name="AppleSignerInstaller" value="Developer ID Application: Marc Suchard (LC992Z5R7E)"/>
-->
<!--
documentation on how to notarization for Apple: https://developer.apple.com/documentation/security/notarizing_macos_software_before_distribution/customizing_the_notarization_workflow
run once:
xcrun notarytool store-credentials "notarytool-password"
~~apple-id msuchard@mac.com
~~team-id LC992Z5R7E
~~password <secret_2FA_password> # from appleid.apple.com, app-specific password
to notarize:
xcrun notarytool submit release/BEAST\ X\ v10.5.0.dmg ~~keychain-profile "notarytool-password" ~~wait
xcrun stapler staple release/BEAST\ X\ v10.5.0.dmg
Note: change ~~ to double-dash
-->
<target name="mac" depends="dist"
description="release Mac version of BEAST, BEAUTI, TreeAnnotator, LogCombiner">
<delete dir="${Mac_package_dir}"/>
<!-- Create the release directory -->
<mkdir dir="${Mac_package_dir}"/>
<copy todir="${Mac_package_dir}/bin">
<fileset dir="${Mac_dir}/scripts"/>
</copy>
<chmod dir="${Mac_package_dir}/bin" perm="755" includes="**/**"/>
<copy todir="${Mac_package_dir}/doc">
<fileset dir="${common_dir}/doc"/>
</copy>
<copy todir="${Mac_package_dir}/examples">
<fileset dir="examples"/>
</copy>
<copy todir="${Mac_package_dir}/native">
<fileset dir="native">
<exclude name="deprecated/**"/>
</fileset>
</copy>
<copy file="${dist}/beauti.jar" todir="${Mac_package_dir}/lib"/>
<copy file="${dist}/beast.jar" todir="${Mac_package_dir}/lib"/>
<!-- <copy file="${dist}/beast-beagle.jar" todir="${Mac_package_dir}/lib"/> -->
<copy todir="${Mac_package_dir}/lib">
<!-- <fileset dir="${Mac_dir}/lib"/> -->
<fileset dir="lib"/>
</copy>
<copy file="${common_dir}/VERSION HISTORY.txt" todir="${Mac_package_dir}"/>
<copy file="${common_dir}/README.txt" todir="${Mac_package_dir}"/>
<taskdef name="jarbundler" classname="com.ultramixer.jarbundler.JarBundler" classpath="${packaging_tools}/mac/jarbundler-core-3.3.0.jar"/>
<!-- create a jar bundle for the mac -->
<jarbundler dir="${Mac_package_dir}"
name="${BEAST_name} v${version}"
mainclass="dr.app.beast.BeastMain"
stubfile="${packaging_tools}/mac/universalJavaApplicationStub"
useJavaXKey="true"
icon="${common_dir}/icons/beast.icns"
jvmversion="${jvm_version}"
vmoptions="-Xmx2048M -Djava.library.path=/usr/local/lib"
arguments="-window -working -options"
highresolutioncapable="true"
version="${version}"
copyright="${BEAST_name} v${version}, ${copyright}, Alexei J. Drummond, Andrew Rambaut and Marc A. Suchard"
bundleid="dr.app.beast">
<javaproperty name="apple.laf.useScreenMenuBar" value="true"/>
<!--<javaproperty name="java.library.path" value="$JAVAROOT:/usr/local/lib"/>-->
<jarfileset dir="${Mac_package_dir}/lib">
<include name="**/beast.jar"/>
<include name="**/beast-beagle.jar"/>
</jarfileset>
<jarfileset dir="${Mac_package_dir}/lib">
<include name="libNucleotideLikelihoodCore.jnilib"/>
</jarfileset>
</jarbundler>
<!-- code signing -->
<exec executable="codesign">
<arg value="--deep"/>
<arg value="-s"/>
<arg value="${AppleSignerApplication}"/>
<arg value="-v"/>
<arg value="${Mac_package_dir}/${BEAST_name} v${version}.app"/>
</exec>
<jarbundler dir="${Mac_package_dir}"
name="${BEAUti_name} v${version}"
mainclass="dr.app.beauti.BeautiApp"
stubfile="${packaging_tools}/mac/universalJavaApplicationStub"
useJavaXKey="true"
icon="${common_dir}/icons/beauti.icns"
jvmversion="${jvm_version}"
vmoptions="-Xmx2048M"
arguments=""
version="${version}"
highresolutioncapable="true"
copyright="${BEAUti_name} v${version}, ${copyright}, Alexei J. Drummond, Andrew Rambaut and Marc A. Suchard"
bundleid="dr.app.beauti">
<documenttype name="BEAUti document"
extensions="beauti bti"
iconFile="beautidoc.icns"
role="Editor"/>
<jarfileset dir="${Mac_package_dir}/lib">
<include name="**/beauti.jar"/>
</jarfileset>
<jarfileset dir="${Mac_package_dir}/lib">
<include name="**/quaqua.jar"/>
</jarfileset>
<jarfileset dir="${Mac_package_dir}/lib">
<include name="libquaqua*.*"/>
</jarfileset>
<javaproperty name="apple.laf.useScreenMenuBar" value="true"/>
<!--<javaproperty name="java.library.path" value="$JAVAROOT"/>-->
</jarbundler>
<!-- code signing -->
<exec executable="codesign">
<arg value="--deep"/>
<arg value="-s"/>
<arg value="${AppleSignerApplication}"/>
<arg value="-v"/>
<arg value="${Mac_package_dir}/${BEAUti_name} v${version}.app"/>
</exec>
<jarbundler dir="${Mac_package_dir}"
name="${LogCombiner_name} v${version}"
mainclass="dr.app.tools.logcombiner.LogCombiner"
stubfile="${packaging_tools}/mac/universalJavaApplicationStub"
useJavaXKey="true"
icon="${common_dir}/icons/utility.icns"
jvmversion="${jvm_version}"
vmoptions="-Xmx2048M"
highresolutioncapable="true"
arguments=""
version="${version}"
copyright="${LogCombiner_name} v${version}, ${copyright}, Alexei J. Drummond, Andrew Rambaut and Marc A. Suchard"
bundleid="dr.app.tools.logcombiner">
<jarfileset dir="${Mac_package_dir}/lib">
<include name="**/beast.jar"/>
</jarfileset>
<javaproperty name="apple.laf.useScreenMenuBar" value="true"/>
<!--<javaproperty name="java.library.path" value="$JAVAROOT"/>-->
</jarbundler>
<!-- code signing -->
<exec executable="codesign">
<arg value="--deep"/>
<arg value="-s"/>
<arg value="${AppleSignerApplication}"/>
<arg value="-v"/>
<arg value="${Mac_package_dir}/${LogCombiner_name} v${version}.app"/>
</exec>
<jarbundler dir="${Mac_package_dir}"
name="${TreeAnnotator_name} v${version}"
mainclass="dr.app.tools.treeannotator.TreeAnnotator"
stubfile="${packaging_tools}/mac/universalJavaApplicationStub"
useJavaXKey="true"
icon="${common_dir}/icons/utility.icns"
jvmversion="${jvm_version}"
vmoptions="-Xmx4096M"
highresolutioncapable="true"
arguments=""
version="${version}"
copyright="${TreeAnnotator_name} v${version}, ${copyright}, Alexei J. Drummond, Andrew Rambaut and Marc A. Suchard"
bundleid="dr.app.tools.treeannotator">
<jarfileset dir="${Mac_package_dir}/lib">
<include name="**/beast.jar"/>
</jarfileset>
<javaproperty name="apple.laf.useScreenMenuBar" value="true"/>
<!--<javaproperty name="java.library.path" value="$JAVAROOT"/>-->
</jarbundler>
<!-- code signing -->
<exec executable="codesign">
<arg value="--deep"/>
<arg value="-s"/>
<arg value="${AppleSignerApplication}"/>
<arg value="-v"/>
<arg value="${Mac_package_dir}/${TreeAnnotator_name} v${version}.app"/>
</exec>
<echo message="Building disk image."/>
<!-- create disk image -->
<exec executable="/usr/bin/hdiutil">
<arg value="create"/>
<arg value="-ov"/>
<arg value="-srcfolder"/>
<arg value="${Mac_package_dir}"/>
<arg value="-volname"/>
<arg value="${BEAST_name} v${version}"/>
<arg value="${release_dir}/${BEAST_package_name} v${version}.dmg"/>
</exec>
<exec executable="codesign">
<arg value="-s"/>
<arg value="${AppleSignerInstaller}"/>
<arg value="-v"/>
<arg value="${release_dir}/${BEAST_package_name} v${version}.dmg"/>
</exec>
<echo message="Mac version release is finished."/>
</target>
<target name="build" depends="mac, windows, linux" description="build all the executables" />
</project>