build.xml

<project basedir="." default="package" name="BUILD_CCD">
    <description>
        Build CCD.
        Also used by Hudson CCD project.
        JUnit test is available for this build.
        $Id: build_CCD.xml $
    </description>

    <!-- set global properties for this build -->
    <property name="CCDdir" location="../CCD/"/>
    <property name="srcCCD" location="${CCDdir}/src"/>
    <property name="buildCCD" location="${CCDdir}/build"/>
    <property name="libCCD" location="${CCDdir}/lib"/>
    <property name="release_dir" value="${CCDdir}/release"/>
    <property name="distCCD" location="${buildCCD}/dist"/>
    <property name="beast2path" location="../beast2"/>
    <property name="libBeast2" location="${beast2path}/lib"/>
    <property name="srcBeast2" location="${beast2path}/src"/>
    <property name="beast2classpath" location="${beast2path}/build"/>
    <property name="Add_on_dir" value="${release_dir}/add-on"/>
    <property name="beastapp2path" location="../BeastFX"/>
    <property name="beastapp2classpath" location="${beastapp2path}/build"/>
    <property name="asmclasspath" location="../asm/build"/>

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

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

    <path id="classpath">
        <pathelement path="${buildCCD}"/>
        <fileset dir="${libBeast2}" includes="antlr-runtime-4.10.1.jar"/>
        <fileset dir="${libBeast2}" includes="commons-math3-3.6.1.jar"/>
        <fileset dir="${libBeast2}" includes="fest.jar"/>
        <fileset dir="${libBeast2}" includes="beagle.jar"/>
        <fileset dir="${libBeast2}" includes="jam.jar"/>
        <fileset dir="${libBeast2}" includes="colt.jar"/>
        <pathelement path="${beast2classpath}"/>
        <pathelement path="${beastapp2classpath}"/>
        <pathelement path="${asmclasspath}"/>
        <fileset dir="${libBeast2}/junit" includes="junit-platform-console-standalone-1.8.2.jar"/>
    </path>

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

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

    <target name="cleanCCD">
        <delete dir="${buildCCD}"/>
    </target>

    <!-- clean previous build, and then compile Java source code, and Juint test -->
    <target name="build_all_CCD" depends="cleanCCD,compile-allCCD,junitCCD"
            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_CCD" depends="cleanCCD,compile-allCCD,junitCCD,dist_all_CCD"
            description="Clean and Build all run-time stuff">
    </target>


    <!-- No JUnit Test, clean previous build, compile Java source code, and make the CCD.jar and beauti.jar -->
    <target name="build_jar_all_CCD_NoJUnitTest" depends="cleanCCD,compile-allCCD,dist_all_CCD"
            description="Clean and Build all run-time stuff">
    </target>

    <!-- compile Java source code -->
    <target name="compile-allCCD" depends="initCCD,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="${buildCCD}"/>

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

    <!-- make the beast.jar and beauti.jar -->
    <target name="dist_all_CCD" depends="compile-allCCD" description="create CCD jar">
        <!-- Create the distribution directory -->
        <mkdir dir="${distCCD}"/>

        <jar jarfile="${distCCD}/CCD.src.jar">
            <fileset dir="${srcCCD}">
                <include name="**/*.java"/>
                <include name="**/*.css"/>
            </fileset>
        </jar>
        <jar jarfile="${distCCD}/CCD.package.jar">
            <manifest>
                <attribute name="Built-By" value="${user.name}"/>
            </manifest>
            <fileset dir="${buildCCD}">
                <include name="**/*.class"/>
                <include name="**/*.class"/>
                <include name="**/*.css"/>
            </fileset>
        </jar>
    </target>

    <!-- run beast.jar -->
    <target name="run_CCD">
        <java jar="${distCCD}/CCD.jar" fork="true"/>
    </target>

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

            <formatter type="xml"/>

            <batchtest fork="yes" todir="${report}">
                <fileset dir="${srcCCD}">
                    <include name="test/**/*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_CCD_NoJUnitTest"
            description="release BEAST 2 add-on version of CCD">

        <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"/>
        </copy>
        <copy todir="${Add_on_dir}/lib">
            <fileset dir="${distCCD}" includes="CCD.package.jar"/>
        </copy>
        <copy todir="${Add_on_dir}">
            <fileset dir="${distCCD}" includes="CCD.src.jar"/>
        </copy>
        <!-->
        <copy todir="${Add_on_dir}/fxtemplates">
            <fileset file="fxtemplates/CCD.xml" />
        </copy>
        -->
        <jar jarfile="${distCCD}/CCD.package.v${CCDversion}.zip">
            <fileset dir="${Add_on_dir}">
                <include name="**/*"/>
            </fileset>
        </jar>
        <echo message="Add-on version v${CCDversion} release is finished."/>
    </target>

    <condition property="isWindows">
        <os family="windows"/>
    </condition>
    <condition property="isLinux">
        <and>
            <os family="unix"/>
            <not>
                <os family="mac"/>
            </not>
        </and>
    </condition>
    <condition property="isMac">
        <os family="mac"/>
    </condition>

    <target name="installLinux" depends="package" if="isLinux">
        <mkdir dir="${user.home}/.beast/2.7/${projName}"/>
        <unzip src="${distCCD}/CCD.package.v${CCDversion}.zip" dest="${user.home}/.beast/2.7/${projName}"/>
    </target>

    <target name="installMac" depends="package" if="isMac">
        <mkdir dir="${user.home}/.beast/2.7/${projName}"/>
        <unzip src="${distCCD}/CCD.package.v${CCDversion}.zip" dest="${user.home}/Library/Application Support/BEAST/2.7/${projName}"/>
    </target>

    <target name="installWindows" depends="package" if="isWindows">
        <mkdir dir="${user.home}/BEAST/2.7/${projName}"/>
        <unzip src="${distCCD}/CCD.package.v${CCDversion}.zip" dest="${user.home}/BEAST/2.7/${projName}"/>
    </target>

    <target name="install" depends="installWindows,installMac,installLinux">
    </target>

</project>