From 9a71e6a0791ad56161127d410d6ccdb04efcf11c Mon Sep 17 00:00:00 2001
From: Remco Bouckaert <higgs.ml@gmail.com>
Date: Thu, 12 Jul 2018 13:26:15 +1200
Subject: [PATCH] release for BEAST v2.5.0

---
 build.xml                                | 467 +++++++++++------------
 src/modeladequacy/TreeModelAdequacy.java |   3 +
 version.xml                              |   4 +-
 3 files changed, 234 insertions(+), 240 deletions(-)

diff --git a/build.xml b/build.xml
index 2192fc2..a8ccc4a 100644
--- a/build.xml
+++ b/build.xml
@@ -1,240 +1,231 @@
-<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"/>
-
-    <!-- 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="templates" location="templates"/>
-    <property name="master" location="master"/>
-
-    <!-- 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="${dist}/package"/>
-
-    <!-- Prepare for compilation -->
-    <target name="init">
-
-        <available file="version.xml" property="versionAvailable"/>
-        <fail unless="versionAvailable">
-            ** Required file version.xml does not exist. **
-            If this is a new project, run "ant skeleton" from
-            the command line to create the files required for
-            your BEAST 2 package.
-        </fail>
-
-        <!-- Read package name and version from xml file -->
-        <xmlproperty file="version.xml" prefix="fromVersionFile" />
-        <property name="projName" value="${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="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-${beast-version}/lib" includes="*.jar"/>
-        </copy>
-
-        <delete dir="${build-beast}" />
-    </target>
-
-    <target name="build-local-beast" depends="find-beast" if="localBeastAvailable">
-        <echo>Compiling against beast2 source found at ${beastDir}.</echo>
-
-        <mkdir dir="${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="${build-lib}/beast2.jar" basedir="${build-beast}" />
-        <copy todir="${build-lib}">
-            <fileset dir="${beastDir}/lib" includes="*.jar"/>
-        </copy>
-
-        <delete dir="${build-beast}" />
-    </target>
-
-    <target name="build-beast" depends="build-local-beast,build-remote-beast"/>
-
-    <!-- Compile -->
-    <target name="compile" depends="build-beast">
-        <javac target="${targetVersion}" source="${sourceVersion}" srcdir="${src}" destdir="${build}" includeantruntime="false">
-            <classpath>
-                <pathelement path="${classpath}"/>
-                <fileset dir="${build-lib}" includes="*.jar"/>
-            </classpath>
-        </javac>
-    </target>
-
-    <target name="copy-resources" depends="compile">
-        <copy todir="${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="${test-reports}"/>
-    </target>
-
-
-    <!-- Compile unit tests -->
-    <target name="compile-test" depends="init-test,compile,copy-resources">
-        <javac target="${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="${classpath}"/>
-                <pathelement path="${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,copy-resources">
-        <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="**/*.fasta" />
-        </copy>
-
-        <mkdir dir="${templates}" />
-        <copy todir="${pack}/templates">
-            <fileset dir="${templates}" includes="*.xml" />
-        </copy>
-
-        <mkdir dir="${master}" />
-        <copy todir="${pack}/master">
-            <fileset dir="${master}" 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="${build-beast}"/>
-        <delete dir="${dist}" />
-        <delete dir="${build-test}" />
-        <delete dir="${test-reports}" />
-    </target>
+<!-- Build TMA. It is also used by Hudson TMA project. JUnit test is available for this build. -->
+<project basedir="." default="addon" name="BUILD_TMA">
+	<description>
+	    Build TMA. 
+            Also used by Hudson TMA project. 
+	    JUnit test is available for this build.
+	    $Id: build_TMA.xml $
+	</description>
+
+	<!-- set global properties for this build -->
+	<property name="srcTMA" location="src" />
+	<property name="buildTMA" location="build" />
+	<property name="libTMA" location="lib" />
+	<property name="release_dir" value="release" />
+	<property name="distTMA" location="${buildTMA}/dist" />
+	<property name="beast2path" location="../beast2" />
+	<property name="libBeast2" location="${beast2path}/lib" />
+	<property name="srcBeast2" location="${beast2path}/src" />
+	<property name="beast2classpath" location="${beast2path}/build" />
+	<property name="Add_on_dir" value="${release_dir}/add-on" />
+	<property name="version" value="1.0.0" />
+	
+	<property name="buildMODEL_SELECTION" location="../model-selection/build"/>
+	<property name="buildBEAST_LABS" location="../BEASTLabs/build"/>
+
+
+    <import file="${beast2path}/build.xml" />
+
+	<property name="main_class_BEAST" value="beast.app.BeastMCMC" />
+	<property name="report" value="${buildTMA}/junitreport"/>
+
+	<path id="classpath">
+        <pathelement path="${buildTMA}"/>
+		<fileset dir="${libBeast2}" includes="antlr-runtime-4.7.jar"/>
+		<fileset dir="${libBeast2}" includes="junit-4.8.2.jar"/>
+		<fileset dir="${libBeast2}" includes="beagle.jar"/>
+        <fileset dir="${libBeast2}" includes="jam.jar"/>
+        <fileset dir="${libBeast2}" includes="ntlr-runtime-4.5.jar"/>
+        <fileset dir="${libBeast2}" includes="commons-math3-3.1.1.jar"/>
+        <fileset dir="${libBeast2}" includes="colt.jar"/>
+        <fileset dir="${libBeast2}" includes="debug-1.0.jar"/>
+        <pathelement path="../beast2/build"/>
+        <pathelement path="../BEASTLabs/build"/>
+        <pathelement path="../TreeStat2/build"/>
+        <pathelement path="${buildBEAST_LABS}"/>
+        <pathelement path="${beast2classpath}"/>
+	</path>
+
+	<!-- start -->
+	<target name="initTMA">
+		<echo message="${ant.project.name}: ${ant.file}" />
+	</target>
+
+	<target name="cleanTMA">
+    	<delete dir="${buildTMA}" />
+	</target>
+
+	<!-- clean previous build, and then compile Java source code, and Juint test -->
+	<target name="build_all_TMA" depends="cleanTMA,compile-allTMA,junitTMA"
+        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_TMA" depends="cleanTMA,compile-allTMA,junitTMA,dist_all_TMA"
+        description="Clean and Build all run-time stuff">
+	</target>
+
+
+	<!-- No JUnit Test, clean previous build, compile Java source code, and make the TMA.jar and beauti.jar -->
+	<target name="build_jar_all_TMA_NoJUnitTest" depends="cleanTMA,compile-allTMA,dist_all_TMA"
+        description="Clean and Build all run-time stuff">
+	</target>
+
+	<!-- compile Java source code -->
+	<target name="compile-allTMA" depends="initTMA,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 = ${myclasspath}"/>
+
+		<mkdir dir="${buildTMA}" />
+
+		<!-- Compile the java code from ${srcTMA} into ${buildTMA} /bin -->
+		<javac srcdir="${srcTMA}" destdir="${buildTMA}" classpathref="classpath" 
+		       fork="true"
+		       memoryinitialsize="256m"
+		       memorymaximumsize="256m">
+			   <!--source="1.6"
+		       target="1.6"-->
+			<include name="beast/**/**" />
+			<!-- compile JUnit test classes -->
+			<include name="test/beast/**" />
+		</javac>
+		<echo message="Successfully compiled." />
+	</target>
+
+	<!-- make the beast.jar and beauti.jar -->
+	<target name="dist_all_TMA" depends="compile-allTMA" description="create TMA jar">
+		<!-- Create the distribution directory -->
+		<mkdir dir="${distTMA}" />
+
+		<!-- Put everything in ${buildTMA} into the beast.jar file -->
+		<jar jarfile="${distTMA}/TMA.jar">
+			<manifest>
+				<attribute name="Built-By" value="${user.name}" />
+				<attribute name="Main-Class" value="${main_class_BEAST}" />
+			</manifest>
+			<fileset dir="${buildTMA}">
+				<include name="**/*.class" />
+			</fileset>
+			<fileset dir="${buildMODEL_SELECTION}">
+				<include name="**/*.class" />
+			</fileset>
+			<fileset dir="${buildBEAST_LABS}">
+				<include name="**/*.class" />
+			</fileset>
+			<fileset dir="${beast2classpath}">
+				<include name="**/*.class" />
+				<include name="**/*.properties" />
+				<include name="**/*.png" />
+			</fileset>
+            <zipgroupfileset dir="${lib}" includes="jam.jar" />
+            <zipgroupfileset dir="${lib}" includes="beagle.jar" />
+            <zipgroupfileset dir="${lib}" includes="colt.jar" />
+            <zipgroupfileset dir="${lib}" includes="commons-math3-3.1.1.jar" />
+            <zipgroupfileset dir="${lib}" includes="antlr-runtime-4.7.jar"/>
+		</jar>
+		<jar jarfile="${distTMA}/TMA.src.jar">
+			<fileset dir="${srcTMA}">
+				<include name="beast/**/*.java" />
+				<include name="beast/**/*.png" />
+				<include name="beast/**/*.xsl" />
+			</fileset>
+        </jar>
+		<jar jarfile="${distTMA}/TMA.addon.jar">
+			<manifest>
+				<attribute name="Built-By" value="${user.name}" />
+			</manifest>
+			<fileset dir="${buildTMA}">
+				<include name="beast/**/*.class" />
+				<include name="util/**/*.class" />
+				<include name="**/*.properties" />
+			</fileset>
+		</jar>
+	</target>
+
+	<!-- run beast.jar -->
+	<target name="run_TMA">
+		<java jar="${distTMA}/TMA.jar" fork="true" />
+	</target>
+
+	
+	<!-- JUnit test -->
+	<target name="junitTMA">
+		<mkdir dir="${report}" />
+		<junit printsummary="yes"> <!--showoutput='yes'-->
+			<classpath>
+				<path refid="classpath" />
+				<path location="${buildTMA}" />
+			</classpath>
+
+			<formatter type="xml" />
+
+			<batchtest fork="yes" todir="${report}">
+				<fileset dir="${srcTMA}">
+                    <include name="test/**/*Test.java"/>                                         
+				</fileset>
+				<fileset dir="${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="${report}"/>
+		</junitreport>
+		<echo message="JUnit test report finished." />
+	</target>
+
+
+	<target name="addon"
+	        depends="build_jar_all_TMA_NoJUnitTest"
+	        description="release BEAST 2 add-on version of TMA">
+
+		<delete dir="${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}/templates" />
+		<mkdir dir="${Add_on_dir}/master" />
+
+		<copy todir="${Add_on_dir}">
+			<fileset file="version.xml"/>
+		</copy>
+		<copy todir="${Add_on_dir}">
+			<fileset file="README"/>
+		</copy>
+		<copy todir="${Add_on_dir}/examples">
+			<fileset dir="examples" />
+		</copy>
+		<copy todir="${Add_on_dir}/lib">
+			<fileset dir="${distTMA}" includes="TMA.addon.jar" />
+		</copy>
+		<copy todir="${Add_on_dir}">
+			<fileset dir="${distTMA}" includes="TMA.src.jar" />
+		</copy>
+		<copy todir="${Add_on_dir}/master">
+			<fileset dir="master" />
+		</copy>
+		<copy todir="${Add_on_dir}/templates">
+			<fileset file="templates/TreeModelAdequacy.xml" />
+			<fileset file="templates/TreePriorsMA.xml" />
+		</copy>
+
+		<jar jarfile="${distTMA}/TMA.addon.v${version}.zip">
+			<fileset dir="${Add_on_dir}">
+				<include name="**/*" />
+			</fileset>
+        </jar>
+		<echo message="Add-on version v${version} release is finished." />
+	</target>
 
 </project>
diff --git a/src/modeladequacy/TreeModelAdequacy.java b/src/modeladequacy/TreeModelAdequacy.java
index 07c0bcb..661d713 100644
--- a/src/modeladequacy/TreeModelAdequacy.java
+++ b/src/modeladequacy/TreeModelAdequacy.java
@@ -23,6 +23,7 @@
 import beast.app.util.OutFile;
 import beast.app.util.Utils;
 import beast.app.util.XMLFile;
+import beast.core.Citation;
 import beast.core.Description;
 import beast.core.Distribution;
 import beast.core.Input;
@@ -39,6 +40,8 @@
 import modeladequacy.util.TreeModelAdequacyAnalyser;
 
 @Description("Run a complete tree model adequacy analysis")
+@Citation(value="Maturana R, P., Brewer, B. J., Klaere, S., & Bouckaert, R. (2018). Model selection and parameter inference in phylogenetics using Nested Sampling. Systematic Biology, syy050. doi:10.1093/sysbio/syy050", 
+	year=2018, DOI="doi:10.1093/sysbio/syy050", firstAuthorSurname="Duchene")
 public class TreeModelAdequacy extends MCMC {
 	public Input<Integer> treeCountInput = new Input<>("nrOfTrees", "the number of trees to use, default 100", 100);
 	public Input<String> rootDirInput = new Input<>("rootdir", "root directory for storing individual tree files (default /tmp)", "/tmp");
diff --git a/version.xml b/version.xml
index 25cdddd..631a638 100644
--- a/version.xml
+++ b/version.xml
@@ -1,5 +1,5 @@
-<addon name='TMA' version='0.0.1'>
-	<depends on='beast2' atleast='2.4.6'/>
+<addon name='TMA' version='1.0.0'>
+	<depends on='beast2' atleast='2.5.0'/>
 	<depends on='MASTER' atleast='5.1.1'/>
 	<depends on='BEASTLabs' atleast='1.7.1'/>
 	<depends on='phylodynamics' atleast='1.2.1'/>