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added empirival tree distribution and Beauti implementation
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Müller Nicola committed Jul 5, 2017
1 parent a18cc77 commit d2b9bb9
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4 changes: 4 additions & 0 deletions .gitignore
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.classpath
.project
/bin/
/build/
/build-lib
/dist/

674 changes: 674 additions & 0 deletions COPYING
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274 changes: 274 additions & 0 deletions build.xml
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<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="beastRev" value="master"/>
<property name="beastAr" value="beast2-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="test-reports" location="test-reports"/>
<property name="dist" location="dist"/>
<property name="pack" location="${dist}/package"/>

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

<get src="https://github.com/CompEvol/beast2/archive/${beastRev}.zip" dest="${build-beast}/beast.zip"/>
<unzip src="${build-beast}/beast.zip" dest="${build-beast}"/>
<mkdir dir="${build-beast}/${beastAr}/build"/>
<javac target="${targetVersion}" source="${sourceVersion}"
srcdir="${build-beast}/${beastAr}/src"
destdir="${build-beast}/${beastAr}/build" includeantruntime="false">
<classpath>
<pathelement path="${classpath}"/>
<fileset dir="${build-beast}/${beastAr}/lib" includes="*.jar"/>
</classpath>
</javac>
<jar jarfile="${build-lib}/beast2.jar" basedir="${build-beast}/${beastAr}/build" />
<copy todir="${build-lib}">
<fileset dir="${build-beast}/${beastAr}/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}"/>
</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" maxmemory="1g" 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"/> <!-- usefile="false" -->
</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="${pack}/templates"/>
<mkdir dir="${pack}/lib"/>
<mkdir dir="${pack}/doc"/>

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

<mkdir dir="${lib}" />
<copy todir="${pack}/lib">
<fileset dir="${lib}" includes="*.jar" />
</copy>
<jar jarfile="${pack}/lib/${fullName}.jar" basedir="${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="*.fna" />
</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/>
<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="${dist}" />
<delete dir="${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>

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