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build.xml
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build.xml
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<!-- Build BEASTvntr. JUnit test is available for this build. -->
<project basedir="." default="build_jar_all_BEASTvntr" name="BUILD_BEAST_vntr">
<description>
Build BEASTvntr.
JUnit test is available for this build.
$Id: build_BEAST_II.xml $
</description>
<!-- set global properties for this build -->
<property name="srcvntr" location="../BEASTvntr/src" />
<property name="buildvntr" location="../BEASTvntr/build" />
<property name="libvntr" location="../BEASTvntr/lib" />
<property name="release_dir" value="release" />
<property name="distvntr" location="${buildvntr}/dist" />
<property name="beast2path" location="../beast2" />
<property name="srcBeast2" location="${beast2path}/src" />
<property name="beast2classpath" location="${beast2path}/build" />
<property name="Add_on_dir" value="${release_dir}/add-on" />
<property name="apppath" location="../BeastFX" />
<import file="${beast2path}/build.xml" />
<property name="main_class_BEAST" value="beast.app.BeastMCMC" />
<property name="report" value="${buildvntr}/junitreport"/>
<path id="classpath">
<pathelement path="${buildvntr}"/>
<fileset dir="${beast2path}/lib/junit/" includes="junit-platform-console-standalone-1.8.2.jar"/>
<fileset dir="${libvntr}" includes="EJML-core-0.29.jar"/>
<fileset dir="${libvntr}" includes="EJML-dense64-0.29.jar"/>
<fileset dir="${beast2path}/lib" includes="beagle.jar"/>
<fileset dir="${beast2path}/lib" includes="colt.jar"/>
<fileset dir="${beast2path}/lib" includes="antlr-runtime-4.10.1.jar"/>
<fileset dir="${beast2path}/lib" includes="commons-math3-3.6.1.jar"/>
<pathelement path="${beast2classpath}"/>
<pathelement path="${apppath}/build"/>
</path>
<!-- start -->
<target name="initBEASTvntr">
<echo message="${ant.project.name}: ${ant.file}" />
<available file="./version.xml" property="versionAvailable"/>
<fail unless="versionAvailable">
** Required file version.xml does not exist. **
</fail>
<!-- Read package name and version from xml file -->
<xmlproperty file="./version.xml" prefix="fromVersionFile" />
<property name="VNTRVersion" value="${fromVersionFile.package(version)}" />
</target>
<target name="cleanBEASTvntr">
<delete dir="${buildvntr}" />
</target>
<!-- clean previous build, and then compile Java source code, and Juint test -->
<target name="build_all_BEASTvntr" depends="cleanBEASTvntr,compile-allBEASTvntr,junitBEASTvntr"
description="Clean and Build all run-time stuff">
</target>
<!-- clean previous build, compile Java source code, and Junit test, and make the beast.jar and beauti.jar -->
<target name="build_jar_all_BEASTvntr" depends="cleanBEASTvntr,compile-allBEASTvntr,dist_all_BEASTvntr"
description="Clean and Build all run-time stuff">
</target>
<!-- No JUnit Test, clean previous build, compile Java source code, and make the BEASTvntr.jar and beauti.jar -->
<target name="build_jar_all_BEASTvntr_NoJUnitTest" depends="cleanBEASTvntr,compile-allBEASTvntr,dist_all_BEASTvntr"
description="Clean and Build all run-time stuff">
</target>
<!-- compile Java source code -->
<target name="compile-allBEASTvntr" depends="initBEASTvntr">
<!-- Capture the path as a delimited property using the refid attribute -->
<property name="myclasspath" refid="classpath"/>
<!-- Emit the property to the ant console -->
<echo message="Classpath = ${myclasspath}"/>
<mkdir dir="${buildvntr}" />
<!-- Compile the java code from ${srcvntr} into ${buildvntr} /bin -->
<javac srcdir="${srcvntr}" destdir="${buildvntr}" classpathref="classpath"
fork="true"
memoryinitialsize="256m"
memorymaximumsize="1024m"
source="1.8"
target="1.8">
<include name="vntr/**/**" />
<!-- compile JUnit test classes -->
<include name="test/beast/**" />
</javac>
<echo message="Successfully compiled." />
</target>
<!-- make the BEASTvntr.hjar and TreeAnnotator.jar -->
<target name="dist_all_BEASTvntr" depends="compile-allBEASTvntr" description="create BEASTvntr jar">
<!-- Create the distribution directory -->
<mkdir dir="${distvntr}" />
<jar jarfile="${distvntr}/BEASTvntr.src.jar">
<fileset dir="${srcvntr}">
<include name="vntr/**/*.java" />
<include name="test/**/*.java" />
<include name="beast/**/*.png" />
<include name="beast/**/*.xsl" />
</fileset>
</jar>
<jar jarfile="${distvntr}/BEASTvntr.addon.jar">
<manifest>
<attribute name="Built-By" value="${user.name}" />
</manifest>
<fileset dir="${buildvntr}">
<include name="vntr/**/*.class" />
<include name="**/*.properties" />
</fileset>
</jar>
</target>
<!-- run beast.jar -->
<target name="run_BEASTvntr">
<java jar="${distvntr}/BEASTvntr.jar" fork="true" />
</target>
<!-- JUnit test -->
<target name="junitBEASTvntr">
<mkdir dir="${report}" />
<junit printsummary="yes" haltonfailure="yes"> <!--showoutput='yes'-->
<classpath>
<path refid="classpath" />
<path location="${buildvntr}" />
</classpath>
<formatter type="xml" />
<batchtest fork="yes" todir="${report}">
<fileset dir="${srcvntr}">
<include name="test/**/*Test.java"/>
<exclude name="test/beast/integration/**/*Test.java"/>
</fileset>
<fileset dir="${srcBeast2}">
<include name="test/beast/integration/**/*Test.java"/>
<exclude name="test/beast/integration/**/ResumeTest.java"/>
<exclude name="test/beast/integration/**/ExampleXmlParsingTest.java"/>
</fileset>
</batchtest>
</junit>
<echo message="JUnit test finished." />
</target>
<target name="junitreport">
<junitreport todir="${report}">
<fileset dir="${report}" includes="*.xml"/>
<report format="frames" todir="${report}"/>
</junitreport>
<echo message="JUnit test report finished." />
</target>
<target name="addon"
depends="build_jar_all_BEASTvntr"
description="release BEAST 2 add-on version of BEASTvntr">
<delete dir="${Add_on_dir}" />
<!-- Create the release directory -->
<mkdir dir="${Add_on_dir}" />
<mkdir dir="${Add_on_dir}/lib" />
<mkdir dir="${Add_on_dir}/examples" />
<mkdir dir="${Add_on_dir}/fxtemplates" />
<copy todir="${Add_on_dir}">
<fileset file="version.xml"/>
</copy>
<copy todir="${Add_on_dir}/examples">
<fileset dir="examples" includes="*/*">
</fileset>
</copy>
<copy todir="${Add_on_dir}/lib">
<fileset file="${distvntr}/BEASTvntr.addon.jar" />
<fileset file="lib/EJML-core-0.29.jar" />
<fileset file="lib/EJML-dense64-0.29.jar" />
</copy>
<copy todir="${Add_on_dir}">
<fileset file="${distvntr}/BEASTvntr.src.jar" />
</copy>
<copy todir="${Add_on_dir}/fxtemplates">
<fileset file="fxtemplates/BEASTvntr-beauti-template.xml" />
</copy>
<jar jarfile="${distvntr}/BEASTvntr.addon.v${VNTRVersion}.zip">
<fileset dir="${Add_on_dir}">
<include name="**/*" />
</fileset>
</jar>
<echo message="Add-on version ${VNTRVersion} release is finished." />
</target>
</project>