build.xml

<!-- Build BEAST_CLASSIC. It is also used by Hudson BEAST_CLASSIC project. JUnit test is available for this build. -->
<project basedir="." default="build_jar_all_BEAST_CLASSIC" name="BUILD_BEAST_CLASSIC">
	<description>
	    Build BEAST_CLASSIC. 
            Also used by Hudson BEAST_CLASSIC project. 
	    JUnit test is available for this build.
	    $Id: build_BEAST_CLASSIC.xml $
	</description>

	<!-- set global properties for this build -->
	<property name="BEAST_CLASSICdir" location="../beast-classic/" />
	<property name="srcBEAST_CLASSIC" location="${BEAST_CLASSICdir}/src" />
	<property name="buildBEAST_CLASSIC" location="${BEAST_CLASSICdir}/build" />
	<property name="libBEAST_CLASSIC" location="${BEAST_CLASSICdir}/lib" />
	<property name="release_dir" value="${BEAST_CLASSICdir}/release" />
	<property name="distBEAST_CLASSIC" location="${buildBEAST_CLASSIC}/dist" />
	<property name="beast2path" location="../beast2" />
	<property name="libBeast2" location="${beast2path}/lib" />
	<property name="srcBeast2" location="${beast2path}/src" />
	<property name="beast2classpath" location="${beast2path}/build" />
    <property name="beastappdir" location="../BeastFX/" />
    <property name="beastappclasspath" location="${beastappdir}/build" />
    <property name="beastapplib" location="${beastappdir}/locallib" />
	<property name="Add_on_dir" value="${release_dir}/add-on" />

    <import file="${beast2path}/build.xml" />

	<property name="main_class_BEAST" value="beast.app.BeastMCMC" />
	<property name="report" value="${buildBEAST_CLASSIC}/junitreport"/>

	<path id="classpath">
        <pathelement path="${buildBEAST_CLASSIC}"/>
        <fileset dir="${libBeast2}/junit" includes="junit-platform-console-standalone-1.8.2.jar"/>
        <fileset dir="${libBEAST_CLASSIC}" includes="mtj.jar"/>
        <fileset dir="${libBeast2}" includes="beagle.jar"/>
        <fileset dir="${libBeast2}" includes="antlr-runtime-4.10.1.jar"/>
        <fileset dir="${libBeast2}" includes="beagle.jar"/> 
        <fileset dir="${libBeast2}" includes="colt.jar"/> 
		<fileset dir="${libBeast2}" includes="commons-math3-3.6.1.jar"/>
		<fileset dir="${beastapplib}" includes="testfx.jar"/>
        <pathelement path="${beast2classpath}"/>
        <pathelement path="${beastappclasspath}"/>
	</path>

	<!-- start -->
	<target name="initBEAST_CLASSIC">
		<echo message="${ant.project.name}: ${ant.file}" />

        <available file="${BEAST_CLASSICdir}/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="${BEAST_CLASSICdir}/version.xml" prefix="fromVersionFile" />
        <property name="BEAST_CLASSICversion" value="${fromVersionFile.package(version)}" />
	</target>

	<target name="cleanBEAST_CLASSIC">
    	<delete dir="${buildBEAST_CLASSIC}" />
	</target>

	<!-- clean previous build, and then compile Java source code, and Juint test -->
	<target name="build_all_BEAST_CLASSIC" depends="cleanBEAST_CLASSIC,compile-allBEAST_CLASSIC,junitBEAST_CLASSIC"
        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_BEAST_CLASSIC" depends="cleanBEAST_CLASSIC,compile-allBEAST_CLASSIC,junitBEAST_CLASSIC,dist_all_BEAST_CLASSIC"
        description="Clean and Build all run-time stuff">
	</target>


	<!-- No JUnit Test, clean previous build, compile Java source code, and make the BEAST_CLASSIC.jar and beauti.jar -->
	<target name="build_jar_all_BEAST_CLASSIC_NoJUnitTest" depends="cleanBEAST_CLASSIC,compile-allBEAST_CLASSIC,dist_all_BEAST_CLASSIC"
        description="Clean and Build all run-time stuff">
	</target>

	<!-- compile Java source code -->
	<target name="compile-allBEAST_CLASSIC" depends="initBEAST_CLASSIC,compile-all">


	    <!-- 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="${buildBEAST_CLASSIC}" />

		<!-- Compile the java code from ${srcBEAST_CLASSIC} into ${buildBEAST_CLASSIC} /bin -->
		<javac srcdir="${srcBEAST_CLASSIC}" destdir="${buildBEAST_CLASSIC}" classpathref="classpath" 
		       fork="true"
		       memoryinitialsize="256m"
		       memorymaximumsize="256m"
		       >
			<include name="beastclassic/**/**" />
			<!-- compile JUnit test classes -->
			<!--
			<include name="test/**" />
			-->
		</javac>
		<echo message="Successfully compiled." />
	</target>

	<!-- make the beast.jar and beauti.jar -->
	<target name="dist_all_BEAST_CLASSIC" depends="compile-allBEAST_CLASSIC" description="create BEAST_CLASSIC jar">
		<!-- Create the distribution directory -->
		<mkdir dir="${distBEAST_CLASSIC}" />

		<!-- Put everything in ${buildBEAST_CLASSIC} into the beast.jar file -->
		<jar jarfile="${distBEAST_CLASSIC}/BEAST_CLASSIC.jar">
			<manifest>
				<attribute name="Built-By" value="${user.name}" />
				<attribute name="Main-Class" value="${main_class_BEAST}" />
			</manifest>
			<fileset dir="${buildBEAST_CLASSIC}">
				<include name="**/*.class" />
			</fileset>
			<fileset dir="${beast2classpath}">
				<include name="beast/**/*.class" />
				<include name="beast/**/*.properties" />
				<include name="beast/**/*.png" />
				<include name="beagle/**/*.class" />
				<include name="org/**/*.class" />
			</fileset>
			<zipgroupfileset dir="${libBeast2}" includes="jam.jar" />
			<zipgroupfileset dir="${libBeast2}" includes="beagle.jar" />
			<zipgroupfileset dir="${libBeast2}" includes="colt.jar" />
			<zipgroupfileset dir="${libBeast2}" includes="commons-math3-3.1.1.jar" />
			<zipgroupfileset dir="${libBEAST_CLASSIC}" includes="mtj.jar"/>
		</jar>
		<jar jarfile="${distBEAST_CLASSIC}/BEAST_CLASSIC.src.jar">
			<fileset dir="${srcBEAST_CLASSIC}">
				<include name="beastclassic/**/*.java" />
				<include name="test/**/*.java" />
				<include name="beast/**/*.png" />
				<include name="beast/**/*.xsl" />
			</fileset>
        </jar>
		<jar jarfile="${distBEAST_CLASSIC}/BEAST_CLASSIC.package.jar">
			<manifest>
				<attribute name="Built-By" value="${user.name}" />
			</manifest>
			<fileset dir="${buildBEAST_CLASSIC}">
				<include name="beastclassic/**/*.class" />
				<include name="test/**/*.class" />
				<include name="**/*.properties" />
			</fileset>
		</jar>
	</target>

	<!-- run beast.jar -->
	<target name="run_BEAST_CLASSIC">
		<java jar="${distBEAST_CLASSIC}/BEAST_CLASSIC.jar" fork="true" />
	</target>

	
	<!-- JUnit test -->
	<target name="junitBEAST_CLASSIC">
		<mkdir dir="${report}" />
		<junit printsummary="yes"> <!--showoutput='yes'-->
			<classpath>
				<path refid="classpath" />
				<path location="${buildBEAST_CLASSIC}" />
			</classpath>

			<formatter type="xml" />

			<batchtest fork="yes" todir="${report}">
				<fileset dir="${srcBEAST_CLASSIC}">
                    <include name="test/**/*Test.java"/>                                         
                    <!--exclude name="test/**/beauti/*Test.java"/-->
				</fileset>
<!--
				<fileset dir="${srcBeast2}">
                    <include name="test/beast/integration/**/*Test.java"/>                                         
                    <exclude name="test/beast/integration/**/ResumeTest.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="package"/>

	<target name="package"
	        depends="build_jar_all_BEAST_CLASSIC_NoJUnitTest"
	        description="release BEAST 2 add-on version of BEAST_CLASSIC">

		<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="${Add_on_dir}/examples/nexus" />
		<mkdir dir="${Add_on_dir}/fxtemplates" />

		<copy todir="${Add_on_dir}">
			<fileset file="version.xml"/>
		</copy>
		<copy todir="${Add_on_dir}/examples">
			<fileset dir="examples" includes="*.xml"/>
		</copy>
		<copy todir="${Add_on_dir}/examples/nexus">
			<fileset dir="examples/nexus" includes="*"/>
		</copy>
		<copy todir="${Add_on_dir}/lib">
			<fileset dir="${libBEAST_CLASSIC}" includes="mtj.jar"/>
			<fileset dir="${distBEAST_CLASSIC}" includes="BEAST_CLASSIC.package.jar" />
		</copy>
		<copy todir="${Add_on_dir}">
			<fileset dir="${distBEAST_CLASSIC}" includes="BEAST_CLASSIC.src.jar" />
		</copy>
		<copy todir="${Add_on_dir}/fxtemplates">
			<fileset file="fxtemplates/discrete-trait.xml" />
			<fileset file="fxtemplates/ClassicSubtseModels.xml" />
			<fileset file="fxtemplates/ClassicTreePriors.xml" />
			<fileset file="fxtemplates/RelaxedClockModels.xml" />
			<fileset file="fxtemplates/StarBeast.xml" />
		</copy>
		<jar jarfile="${distBEAST_CLASSIC}/BEAST_CLASSIC.package.v${BEAST_CLASSICversion}.zip">
			<fileset dir="${Add_on_dir}">
				<include name="**/*" />
			</fileset>
        </jar>
		<echo message="Add-on version v${BEAST_CLASSICversion} release is finished." />
	</target>

	<target name="tutorial">
		<!-- generate images -->
		<junit printsummary="yes"> 
			<classpath>
				<path refid="classpath" />
				<path location="${buildBEAST_CLASSIC}" />
			</classpath>

			<formatter type="xml" />

			<batchtest fork="yes" todir="${report}">
				<fileset dir="${srcBEAST_CLASSIC}">
                    <include name="test/**/beauti/*Test.java"/>                                         
				</fileset>
			</batchtest>
		</junit>
	</target>

	<target name="tutorial2">
		<!-- generate discrete phylogeography AR.pdf -->
		<exec executable="sh" dir="doc/tutorial/phylogeography_discrete">
			<arg value='-c'/>
			<arg value='pdflatex AR.tex'/>
		</exec>
		<exec executable="sh" dir="doc/tutorial/phylogeography_discrete">
			<arg value='-c'/>
			<arg value='bibtex AR.aux'/>
		</exec>
		<exec executable="sh" dir="doc/tutorial/phylogeography_discrete">
			<arg value='-c'/>
			<arg value='pdflatex AR.tex'/>
		</exec>
		<exec executable="sh" dir="doc/tutorial/phylogeography_discrete">
			<arg value='-c'/>
			<arg value='pdflatex AR.tex'/>
		</exec>

		<!-- generate continuous phylogeography phylogeography_s.pdf -->
		<exec executable="sh" dir="doc/tutorial/phylogeography_continuous">
			<arg value='-c'/>
			<arg value='pdflatex phylogeography_c.tex'/>
		</exec>
		<exec executable="sh" dir="doc/tutorial/phylogeography_continuous">
			<arg value='-c'/>
			<arg value='bibtex phylogeography_c.aux'/>
		</exec>
		<exec executable="sh" dir="doc/tutorial/phylogeography_continuous">
			<arg value='-c'/>
			<arg value='pdflatex phylogeography_c.tex'/>
		</exec>
		<exec executable="sh" dir="doc/tutorial/phylogeography_continuous">
			<arg value='-c'/>
			<arg value='pdflatex phylogeography_c.tex'/>
		</exec>
	</target>


</project>