build.xml

<project default="build" basedir=".">

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

  <property name="sourceVersion" value="1.8"/>
  <property name="targetVersion" value="1.8"/>
  <property name="beastSrcRevision" value="master"/>
  <!--*******************************************************************-->

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

  <!-- 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="build-beast" location="build-beast"/>
  <property name="test-reports" location="test-reports"/>
  <property name="dist" location="dist"/>


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

  <!-- Get beast -->
  <target name="get-beast" depends="init">
    <mkdir dir="${build-beast}"/>

    <get src="https://github.com/CompEvol/beast2/archive/${beastSrcRevision}.zip" dest="${build-beast}/beast.zip"/>
    <unzip src="${build-beast}/beast.zip" dest="${build-beast}"/>
    <mkdir dir="${build-beast}/beast2-${beastSrcRevision}/build"/>
    <javac target="${targetVersion}" source="${sourceVersion}"
           srcdir="${build-beast}/beast2-${beastSrcRevision}/src"
           destdir="${build-beast}/beast2-${beastSrcRevision}/build" includeantruntime="false">
      <classpath>
	<pathelement path="${classpath}"/>
	<fileset dir="${build-beast}/beast2-${beastSrcRevision}/lib" includes="*.jar"/>
      </classpath>
    </javac>
    <jar jarfile="${build-lib}/beast2.jar" basedir="${build-beast}/beast2-${beastSrcRevision}/build" />
    <copy todir="${build-lib}">
      <fileset dir="${build-beast}/beast2-${beastSrcRevision}/lib" includes="*.jar"/>
    </copy>

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

  <!-- Compile -->
  <target name="compile" depends="init, get-beast">
    <javac target="${targetVersion}" source="${sourceVersion}" srcdir="${src}" destdir="${build}" includeantruntime="false">
      <classpath>
	<pathelement path="${classpath}"/>
	<fileset dir="${build-lib}" includes="*.jar"/>
      </classpath>
    </javac>
  </target>

  
  <!-- Prepare for unit test compilation -->
  <target name="init-test" depends="init">
    <mkdir dir="${build-test}"/>
    <mkdir dir="${test-reports}"/>
      <!--
    <get src="http://search.maven.org/remotecontent?filepath=junit/junit/4.11/junit-4.11.jar"
	 dest="${build-lib}/junit-4.11.jar" />
    <get src="http://search.maven.org/remotecontent?filepath=org/hamcrest/hamcrest-core/1.3/hamcrest-core-1.3.jar"
	 dest="${build-lib}/hamcrest-core-1.3.jar" />
-->
  </target>


  <!-- Compile unit tests -->
  <target name="compile-test" depends="init-test,compile">
    <javac target="${targetVersion}" source="${sourceVersion}" srcdir="${test}" destdir="${build-test}" includeantruntime="false">
      <classpath>
	<pathelement path="${classpath}"/>
	<pathelement path="${build}" />
	<fileset dir="${build-lib}" includes="*.jar"/>
      </classpath>
    </javac>
  </target>


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

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


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

    <property name="pack" location="${dist}/package"/>
    <mkdir dir="${pack}"/>
    <mkdir dir="${pack}/examples"/>
    <mkdir dir="${pack}/templates"/>
    <mkdir dir="${pack}/lib"/>
    <mkdir dir="${pack}/doc"/>

    <jar jarfile="${pack}/${packageName}.src.jar" basedir="${src}" />

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

    <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="*.R" />
    </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="${dist}/${packageName}.zip" basedir="${pack}" />

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

    <echo/>
    <echo/>
    <echo>** Package ${dist}/${packageName}.zip created successfuly! **</echo>
  </target>

  <!-- Create stand-alone archive bundled with BEAST. -->
  <target name="build-standalone" depends="compile">
    <property name="archiveName" value="${projName}-${projVersion}"/>

    <property name="pack" location="${dist}/${archiveName}"/>
    <mkdir dir="${pack}"/>
    <mkdir dir="${pack}/examples"/>

    <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="*.R" />
    </copy>

    <copy file="master_linux.sh" todir="${pack}"/>
    <replace file="${pack}/master_linux.sh" token="_MASTERJAR_"
	     value="${archiveName}.jar"/>
    <chmod file="${pack}/master_linux.sh" perm="a+x"/>

    <jar jarfile="${pack}/${archiveName}.jar">
      <fileset dir="${build}"/>
      <restrict>
	<not>
	  <name name="META-INF/**"/>
	</not>
	<archives>
	  <zips>
	    <fileset dir="${build-lib}" includes="**/*.jar"/>
	  </zips>
	</archives>
      </restrict>
      <manifest>
	<attribute name="Main-Class" value="beast.app.beastapp.BeastMain"/>
      </manifest>
    </jar>

    <zip destfile="${dist}/${archiveName}.zip">
      <zipfileset dir="${pack}" prefix="${archiveName}" excludes="**/master_linux.sh"/>
      <zipfileset dir="${pack}" prefix="${archiveName}" includes="**/master_linux.sh"
		  filemode="755"/>
    </zip> 

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

    <echo/>
    <echo/>
    <echo>** Archive ${dist}/${archiveName}.zip created successfuly! **</echo>
  </target>

  <!-- Build EVERYTHING -->
  <target name="build" depends="build-package,build-standalone"/>

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