build.xml

<!--
This configuration document was modified based on the BEAST package setup blueprint by @Senbai Kang.
-->

<project default="" basedir="." xmlns:if="ant:if" xmlns:unless="ant:unless">

    <!-- Source, JUnit test code and jar library locations. -->
    <property name="src" location="src"/>
    <property name="test" location="test"/>
    <property name="lib" location="lib"/>

    <!-- Location to check for local copy of beast2 repository -->
    <property name="beastDir" location="../beast2"/>

    <!-- BEAST 2 currently uses Java 1.8 -->
    <property name="sourceVersion" value="1.8"/>
    <property name="targetVersion" value="1.8"/>

    <!-- Directories necessary for all BEAST 2 packages -->
    <property name="doc" location="doc"/>
    <property name="examples" location="examples"/>
    <property name="scripts" location="scripts"/>
    <property name="templates" location="templates"/>
    <property name="data" location="${examples}/data"/>

    <!-- BEAST branch and version to build against
         (only different for version tags because of
         a Github peculiarity) -->
    <!-- property name="beast-branch" value="master"/ -->
    <!-- property name="beast-version" value="master"/ -->
    <property name="beast-branch" value="v2.6.7"/>
    <property name="beast-version" value="2.6.7"/>

    <!-- Names of temporary build/test directories -->
    <property name="build" location="build"/>
    <property name="build-lib" location="build-lib"/>
    <property name="build-test" location="build-test"/>
    <property name="test-reports" location="test-reports"/>
    <property name="dist" location="dist"/>
    <property name="pack" location="${dist}/package"/>
    <property name="depends" location="depends"/>

    <!-- Names of resulting jars for different purposes -->
    <property name="standalone" value="standalone"/>

    <!-- related to one-jar -->
    <!-- refer to http://one-jar.sourceforge.net/index.php?page=getting-started&file=ant -->
    <property name="one-jar.dist.dir" value="../one_jar"/>
    <import file="${one-jar.dist.dir}/one-jar-ant-task.xml" optional="true"/>

    <!-- setup class path -->
    <path id="all-lib">
        <fileset dir="${build-lib}" includes="**/*.jar"/>
    </path>

    <!-- Prepare for compilation -->
    <target name="init">

        <available file="version.xml" property="versionAvailable"/>
        <fail unless="versionAvailable">
            ** Required file version.xml does not exist. **
            If this is a new project, run "ant skeleton" from
            the command line to create the files required for
            your BEAST 2 package.
        </fail>

        <!-- Read package name and version from xml file -->
        <xmlproperty file="version.xml" prefix="fromVersionFile" />
        <property name="projName" value="${fromVersionFile.addon(name)}" />
        <property name="projVersion" value="${fromVersionFile.addon(version)}" />

        <mkdir dir="${build}"/>
        <mkdir dir="${build-lib}"/>
        <mkdir dir="${depends}"/>
        <mkdir dir="${dist}"/>

        <mkdir dir="${lib}"/> <!-- build errors if this dir not present -->

        <copy todir="${build-lib}">
            <fileset dir="${lib}" includes="**/*.jar"/>
        </copy>
    </target>

    <!-- Get beast -->
    <target name="find-beast" depends="init">
        <available file="${beastDir}" property="localBeastAvailable"/>
    </target>

    <target name="build-remote-beast" depends="find-beast" unless="localBeastAvailable">
        <echo>No local copy of the beast2 source found at ${beastDir}.</echo>
        <echo>Compiling against version ${beast-version} from GitHub.</echo>

        <property name="build-beast" location="build-beast"/>
        <mkdir dir="${build-beast}"/>

        <path id="beast-remote-classpath">
            <fileset dir="${build-beast}/beast2-${beast-version}/lib" includes="**/*.jar"/>
        </path>

        <!--get src="https://github.com/CompEvol/beast2/archive/${beast-branch}.zip" dest="${build-beast}/beast.zip"/-->
        <get src="https://codeload.github.com/CompEvol/beast2/zip/refs/tags/${beast-branch}" dest="${build-beast}/beast.zip"/>
        <unzip src="${build-beast}/beast.zip" dest="${build-beast}"/>
        <mkdir dir="${build-beast}/beast2-${beast-version}/build"/>

        <javac target="${targetVersion}" source="${sourceVersion}"
               srcdir="${build-beast}/beast2-${beast-version}/src"
               destdir="${build-beast}/beast2-${beast-version}/build" includeantruntime="false"
               classpathref="beast-remote-classpath">

            <compilerarg line="-encoding utf-8"/>

        </javac>

        <jar jarfile="${build-lib}/beast2.jar" basedir="${build-beast}/beast2-${beast-version}/build"/>
        <copy todir="${build-lib}">
            <fileset dir="${build-beast}/beast2-${beast-version}/lib" includes="**/*.jar"/>
        </copy>

        <delete dir="${build-beast}"/>
    </target>

    <target name="build-local-beast" depends="find-beast" if="localBeastAvailable">
        <echo>Compiling against beast2 source found at ${beastDir}.</echo>

        <property name="build-beast" location="build-beast"/>
        <mkdir dir="${build-beast}"/>

        <path id="beast-local-classpath">
            <fileset dir="${beastDir}/lib" includes="**/*.jar"/>
        </path>

        <javac target="${targetVersion}" source="${sourceVersion}"
               srcdir="${beastDir}/src"
               destdir="${build-beast}" includeantruntime="false" classpathref="beast-local-classpath">

            <compilerarg line="-encoding utf-8"/>

        </javac>

        <jar jarfile="${build-lib}/beast2.jar" basedir="${build-beast}"/>
        <copy todir="${build-lib}">
            <fileset dir="${beastDir}/lib" includes="**/*.jar"/>
        </copy>

        <delete dir="${build-beast}"/>
    </target>

    <target name="build-beast" depends="build-local-beast,build-remote-beast"/>

    <!-- Light compile -->
    <target name="light-compile" depends="init">
        <echo>Compiling SIEVE without compiling BEAST2...</echo>

        <javac target="${targetVersion}" source="${sourceVersion}" srcdir="${src}" destdir="${build}"
               includeantruntime="false" classpathref="all-lib" failonerror="false"
               errorProperty="light-compile-failure" fork="true">

            <compilerarg line="-encoding utf-8"/>

        </javac>
    </target>

    <!-- Deep compile -->
    <target name="deep-compile" if="light-compile-failure">
        <echo>Compiling BEAST2 and SIEVE...</echo>

        <antcall target="build-beast"/>

        <javac target="${targetVersion}" source="${sourceVersion}" srcdir="${src}" destdir="${build}"
               includeantruntime="false" classpathref="all-lib" fork="true">

            <compilerarg line="-encoding utf-8"/>

        </javac>

    </target>

    <!-- Compile -->
    <target name="compile" depends="light-compile,deep-compile" description="compile beast2 package"/>


    <target name="copy-resources" depends="compile">
        <copy todir="${build}">
            <fileset dir="${src}"
                     includes="**/*.png"/>
        </copy>
    </target>

    <!-- Prepare for unit test compilation -->
    <target name="init-test" depends="init">
        <mkdir dir="${build-test}"/>
        <mkdir dir="${test-reports}"/>
    </target>

    <!-- Compile unit tests -->
    <target name="compile-test" depends="init-test,copy-resources">
        <javac target="${targetVersion}" source="${sourceVersion}" srcdir="${test}" destdir="${build-test}"
               includeantruntime="false">
            <classpath>
                <path refid="all-lib"/>
                <pathelement path="${build}"/>
            </classpath>

            <compilerarg line="-encoding utf-8"/>
        </javac>
    </target>

    <!-- Run unit tests -->
    <target name="test" depends="compile-test">
        <junit printsummary="yes" failureproperty="testFailed" showoutput="true">
            <classpath>
                <pathelement path="${build-test}"/>
                <path refid="all-lib"/>
                <pathelement path="${build}"/>
            </classpath>
            <batchtest fork="yes" todir="${test-reports}">
                <fileset dir="${test}">
                    <include name="**/*Test.java"/>
                </fileset>
                <formatter type="plain"/>
                <formatter type="plain" usefile="false"/> <!-- to screen -->
            </batchtest>
        </junit>

        <fail if="testFailed" status="1" message="Unit test failed."/>
    </target>


    <!-- Create BEAST 2 package -->
    <target name="build" depends="copy-resources">
        <property name="fullName" value="${projName}.v${projVersion}"/>

        <mkdir dir="${pack}"/>
        <!--mkdir dir="${pack}/examples"/-->
        <mkdir dir="${pack}/scripts"/>
        <mkdir dir="${pack}/templates"/>
        <mkdir dir="${pack}/lib"/>
        <mkdir dir="${pack}/doc"/>

        <jar jarfile="${pack}/${fullName}.src.jar" basedir="${src}"/>
        <copy todir="${build-lib}" file="${pack}/${fullName}.src.jar"/>

        <mkdir dir="${lib}"/>
        <copy todir="${pack}/lib">
            <fileset dir="${lib}" includes="**/*.jar"/>
        </copy>
        <jar jarfile="${pack}/lib/${fullName}.jar" basedir="${build}"/>
        <copy todir="${build-lib}" file="${pack}/lib/${fullName}.jar"/>

        <copy file="README.md" tofile="${pack}/README"/>
        <copy file="COPYING" todir="${pack}"/>
        <copy todir="${pack}">
            <fileset dir="${lib}" includes="LICENSE*"/>
        </copy>

        <!--mkdir dir="${examples}"/>
        <copy todir="${pack}/examples">
            <fileset dir="${examples}" includes="**/*.xml"/>
            <fileset dir="${examples}" includes="**/*.fasta" />
        </copy-->

        <mkdir dir="${scripts}" />
        <copy todir="${pack}/scripts">
            <fileset dir="${scripts}" includes="**/*" />
        </copy>


        <mkdir dir="${templates}" />
        <copy todir="${pack}/templates">
            <fileset dir="${templates}" includes="**/*.xml"/>
        </copy>

        <mkdir dir="${doc}" />
        <copy todir="${pack}/doc">
            <fileset dir="${doc}" includes="**/*.tex,**/*.doc,**/*.lyx,**/*.txt"/>
        </copy>

        <copy file="version.xml" todir="${pack}" />

        <zip destfile="${dist}/${fullName}.zip" basedir="${pack}" />

        <delete dir="${pack}"/>

        <echo>** Package ${dist}/${fullName}.zip created successfully! **</echo>
    </target>


    <!-- Revert to pristine state. -->
    <target name="clean">
        <delete dir="${build}" />
        <delete dir="${build-lib}" />
        <delete dir="${build-test}" />
        <delete dir="${test-reports}" />
        <delete dir="${depends}"/>
    </target>


    <!-- Create skeleton package layout in current directory -->
    <target name="skeleton">

        <fail>
            <condition>
                <or>
                    <resourcecount when="gt" count="1">
                        <fileset dir="${basedir}"/>
                    </resourcecount>
                    <resourcecount when="gt" count="1">
                        <dirset dir="${basedir}"/>
                    </resourcecount>
                </or>
            </condition>

            ** This directory contains files besides the build script. **
            You should run "ant skeleton" in a directory containing only the build script.
        </fail>

        <echo>===============================</echo>
        <echo>Create skeleton BEAST 2 package</echo>
        <echo>===============================</echo>
        <echo/>
        <echo>First, we need some information...</echo>
        <echo/>

        <basename property="defaultProjName" file="${basedir}"/>

        <input addproperty="projName" defaultvalue="${defaultProjName}">Enter package name</input>
        <input addproperty="license" defaultvalue="gpl3" validargs="gpl3,lgpl3,lgpl2.1,apache2">Select open source software license</input>
        <input addproperty="projVersion" defaultvalue="1.0.0">Enter package version</input>
        <input addproperty="beastVersionReq" defaultvalue="2.1.0">Enter minimum required BEAST 2 version</input>

        <echo>Assembling files and directory structure...</echo>

        <echo file="version.xml">&lt;addon name="${projName}" version="${projVersion}"&gt;
            &lt;depends on="beast2" atleast="${beastVersionReq}"/&gt;

            &lt;!-- Add other dependencies as necessary. --&gt;
            &lt;/addon&gt;
        </echo>

        <echo file="README.md" message="README for my package.${line.separator}"/>

        <condition property="licenseURL" value="https://www.gnu.org/licenses/gpl-3.0.txt">
            <equals arg1="${license}" arg2="gpl3"/>
        </condition>
        <condition property="licenseURL" value="https://www.gnu.org/licenses/lgpl-3.0.txt">
            <equals arg1="${license}" arg2="lgpl3"/>
        </condition>
        <condition property="licenseURL" value="https://www.gnu.org/licenses/lgpl-2.1.txt">
            <equals arg1="${license}" arg2="lgpl2.1"/>
        </condition>
        <condition property="licenseURL" value="http://www.apache.org/licenses/LICENSE-2.0.txt">
            <equals arg1="${license}" arg2="apache2"/>
        </condition>

        <get src="${licenseURL}" dest="COPYING"/>

        <mkdir dir="${src}"/>
        <mkdir dir="${test}"/>
        <mkdir dir="${lib}"/>
        <mkdir dir="${examples}"/>
        <mkdir dir="${templates}"/>
        <mkdir dir="${doc}"/>

        <echo/>
        <echo>Done.</echo>
        <echo/>
        <echo>The directory structure is as follows:</echo>
        <echo>${src} - your java source goes here</echo>
        <echo>${test} - your junit tests go here (You _are_ going to write, those, aren't you!)</echo>
        <echo>${doc} - your documentation goes here</echo>
        <echo>${examples} - your example XML scripts go here</echo>
        <echo>${templates} - your BEAUti templates go here</echo>
        <echo/>
        <echo>To build your package, just type "ant" at the command line.</echo>
        <echo/>
        <echo>To run unit tests, type "ant test".</echo>
        <echo/>
        <echo>That's it! Happy coding!</echo>

    </target>

</project>