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build.xml
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build.xml
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<project default="build" basedir=".">
<!-- 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"/>
<property name="beastFX" location="../BeastFX" />
<property name="lib" location="lib" />
<!-- BEAST 2 currently uses Java 17 -->
<property name="sourceVersion" value="17"/>
<property name="targetVersion" value="17"/>
<!-- Directories necessary for all BEAST 2 packages -->
<property name="doc" location="doc"/>
<property name="examples" location="examples"/>
<property name="fxtemplates" location="fxtemplates"/>
<!-- 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"/>
<!-- 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"/>
<property name="pack" location="${dist}/package"/>
<!-- Prepare for compilation -->
<target name="init" depends="clean">
<available file="version.xml" property="versionAvailable"/>
<fail unless="versionAvailable">
** Required file version.xml does not exist. **
If this is a new project, run "ant skeleton" from
the command line to create the files required for
your BEAST 2 package.
</fail>
<!-- Read package name and version from xml file -->
<xmlproperty file="version.xml" prefix="fromVersionFile" />
<property name="projName" value="${fromVersionFile.package(name)}" />
<property name="projVersion" value="${fromVersionFile.package(version)}" />
<mkdir dir="${build}"/>
<mkdir dir="${build-lib}"/>
<mkdir dir="${dist}"/>
</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 ${beast-version} from GitHub.</echo>
<mkdir dir="${build-beast}"/>
<get src="https://github.com/CompEvol/beast2/archive/${beast-branch}.zip" dest="${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">
<classpath>
<pathelement path="${classpath}"/>
<fileset dir="${build-beast}/beast2-${beast-version}/lib" includes="*.jar"/>
</classpath>
</javac>
<jar jarfile="${build-lib}/beast2.jar" basedir="${build-beast}/beast2-${beast-version}/build" />
<copy todir="${build-lib}">
<fileset dir="${build-beast}/beast2-${beast-version}/lib" includes="*.jar"/>
<fileset dir="${build-beast}/beast2-${beast-version}/lib/junit" includes="junit-*.jar"/>
</copy>
<delete dir="${build-beast}" />
</target>
<target name="build-local-beast" depends="find-beast" if="localBeastAvailable">
<echo>Compiling against beast2 source found at ${beastDir}.</echo>
<!-- Read package name and version from xml file -->
<xmlproperty file="${beastDir}/version.xml" prefix="BeastVersionFile" />
<property name="beastName" value="${BeastVersionFile.package(name)}" />
<property name="beastVersion" value="${BeastVersionFile.package(version)}" />
<!-->
<mkdir dir="${build-beast}"/>
<javac target="${targetVersion}" source="${sourceVersion}"
srcdir="${beastDir}/src" destdir="${build-beast}"
includeantruntime="false">
<classpath>
<pathelement path="${classpath}"/>
<fileset dir="${beastDir}/lib" includes="*.jar"/>
</classpath>
</javac>
<jar jarfile="${build-lib}/beast.v${beastVersion}.jar" basedir="${build-beast}" />
<copy todir="${build-lib}">
<fileset dir="${beastDir}/lib" includes="*.jar"/>
<fileset dir="${beastDir}/lib/junit" includes="junit-*.jar"/>
</copy>
<delete dir="${build-beast}" />
-->
</target>
<target name="build-beast" depends="build-local-beast,build-remote-beast"/>
<target name="build-BeastFX" depends="build-beast">
<echo>Compiling BeastFX source found at ${beastFX}.</echo>
<!-- Read package name and version from xml file -->
<xmlproperty file="${beastFX}/version.xml" prefix="BeastFXVersionFile" />
<property name="beastFXName" value="${BeastFXVersionFile.package(name)}" />
<property name="beastFXVersion" value="${BeastFXVersionFile.package(version)}" />
<!-->
<mkdir dir="${build-beast}"/>
<javac target="${targetVersion}" source="${sourceVersion}"
srcdir="${beastFX}/src" destdir="${build-beast}"
fork="true" includeantruntime="false">
<classpath>
<pathelement path="${classpath}"/>
<fileset dir="${build-lib}" includes="*.jar"/>
</classpath>
<include name="beastfx/**/**" />
</javac>
<jar jarfile="${build-lib}/beastFX.v${beastFXVersion}.jar" basedir="${build-beast}" />
<copy todir="${build-lib}">
<fileset dir="${beastFX}/src" includes="**/*.png" />
<fileset dir="${beastFX}/src" includes="**/*.fxml" />
<fileset dir="${beastFX}/resources" includes="**/*.css" />
</copy>
<delete dir="${build-beast}" />
-->
<echo message="Successfully compiled beastFX v${beastFXVersion}." />
</target>
<!-- Compile -->
<target name="compile" depends="build-BeastFX">
<javac srcdir="${src}" destdir="${build}"
fork="true" includeantruntime="false">
<classpath>
<pathelement path="${classpath}"/>
<fileset dir="${build-lib}" includes="*.jar"/>
<fileset dir="../beast2/lib/junit/" includes="*.jar"/>
<fileset dir="../beast2/build"/>
<fileset dir="../BeastFX/build"/>
</classpath>
<include name="codonmodels/**/**" />
</javac>
</target>
<!-- <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,compile">
<javac target="${targetVersion}" source="${sourceVersion}" srcdir="${test}" destdir="${build-test}" includeantruntime="false">
<classpath>
<pathelement path="${classpath}"/>
<pathelement path="${build}" />
<fileset dir="${build-lib}" includes="*.jar"/>
</classpath>
</javac>
</target>
<!-- Run unit tests -->
<target name="test" depends="compile-test">
<junit printsummary="yes" failureproperty="testFailed" showoutput="true">
<classpath>
<pathelement path="${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"/>
<!--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="compile">
<property name="fullName" value="${projName}.v${projVersion}"/>
<mkdir dir="${pack}"/>
<mkdir dir="${pack}/examples"/>
<mkdir dir="${pack}/examples/data"/>
<mkdir dir="${pack}/fxtemplates"/>
<!--mkdir dir="${pack}/lib"/-->
<!-- <mkdir dir="${pack}/doc"/>-->
<jar jarfile="${pack}/${fullName}.src.jar" basedir="${src}" />
<!--
<copy todir="${pack}/lib">
<fileset dir="${lib}" includes="*.jar" />
</copy-->
<jar jarfile="${pack}/lib/${fullName}.jar" basedir="${build}" >
<include name="codonmodels/**/*"/>
</jar>
<copy file="README.md" tofile="${pack}/README" />
<copy file="LICENSE" tofile="${pack}/LICENSE" />
<copy todir="${pack}/examples">
<fileset dir="${examples}" includes="**/*.xml" />
</copy>
<copy todir="${pack}/examples/data">
<fileset dir="${examples}/data" includes="benchmarkData1024T1K.xml" />
<fileset dir="${examples}/data" includes="**/*.nex" />
</copy>
<copy todir="${pack}/fxtemplates">
<fileset dir="${fxtemplates}" includes="*.xml" />
</copy>
<!-- <copy todir="${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/>
<echo/>
<echo>** Package ${dist}/${fullName}.zip created successfuly! **</echo>
</target>
<!-- Revert to pristine state. -->
<target name="clean">
<delete dir="${build}" />
<delete dir="${build-lib}" />
<delete dir="${build-beast}"/>
<delete dir="${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="lgpl2.1" validargs="gpl3,lgpl3,lgpl2.1,apache2">Select open source software license</input>
<input addproperty="projVersion" defaultvalue="1.0.3">Enter package version</input>
<input addproperty="beastVersionReq" defaultvalue="2.5.0">Enter minimum required BEAST 2 version</input>
<echo>Assembling files and directory structure...</echo>
<echo file="version.xml"><addon name="${projName}" version="${projVersion}">
<depends on="beast2" atleast="${beastVersionReq}"/>
<!-- Add other dependencies as necessary. -->
</addon>
</echo>
<echo file="README.md" message="README for my package.${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>
<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="build" if="isLinux">
<mkdir dir="${user.home}/.beast/2.7/${projName}"/>
<unzip src="${dist}/${fullName}.zip" dest="${user.home}/.beast/2.7/${projName}"/>
</target>
<target name="installMac" depends="build" if="isMac">
<mkdir dir="${user.home}/.beast/2.7/${projName}"/>
<unzip src="${dist}/${fullName}.zip" dest="${user.home}/Library/Application Support/BEAST/2.7/${projName}"/>
</target>
<target name="installWindows" depends="build" if="isWindows">
<mkdir dir="${user.home}/BEAST/2.7/${projName}"/>
<unzip src="${dist}/${fullName}.zip" dest="${user.home}/BEAST/2.7/${projName}"/>
</target>
<target name="install" depends="installWindows,installMac,installLinux">
</target>
</project>