.gitignore

+# IntelliJ ignores
+/.idea
+/beast2.iml
+/META-INF
+/out
+
+# OS X ignores
+.DS_Store

.travis.yml

+sudo: require
+
+services:
+    - docker
+
+before_install:
+    - docker build -t docker-image .
+
+script:
+    - docker run docker-image

Dockerfile

+# Dockerfile to build container for unit testing.
+#
+# To build the image, run the following from this directory:
+#   docker build -t beast_testing .
+#
+# To run the tests, use
+#   docker run beast_testing
+#
+# To run the tests interactively, use
+#   docker run -it -p 5900:5900 beast_testing /bin/bash
+# This will give you a shell in the container. From this
+# shell, run
+#   vncserver $DISPLAY -geometry 1920x1080; ant travis
+#
+# The previous command exposes the VNC session, so while the
+# BEAUti test suite is running you can run a VNC viewer and
+# connect it to localhost (password: password) to observe
+# the graphical output of these tests.
+
+FROM openjdk:8
+
+# Install Apache Ant
+RUN apt-get update && apt-get install -y ant
+
+# Install and configure VNC server
+RUN apt-get update && apt-get install -y tightvncserver twm
+ENV DISPLAY :0
+ENV USER root
+RUN mkdir /root/.vnc
+RUN echo password | vncpasswd -f > /root/.vnc/passwd
+RUN chmod 600 /root/.vnc/passwd
+
+# Install BEAGLE
+RUN apt-get update && apt-get install -y build-essential autoconf automake libtool pkg-config
+RUN cd /root && git clone --depth=1 https://github.com/beagle-dev/beagle-lib.git
+RUN cd /root/beagle-lib && ./autogen.sh && ./configure --prefix=/usr/local && make install
+ENV LD_LIBRARY_PATH=/lib:/usr/lib:/usr/local/lib
+RUN ldconfig
+
+# Ant build fails if the repo dir isn't named beast2
+RUN mkdir /root/beast2
+WORKDIR /root/beast2
+
+ADD . ./
+
+CMD vncserver $DISPLAY -geometry 1920x1080; ant travis

README.md

 BEAST 2
 =======
 
+[![Build Status](https://travis-ci.org/CompEvol/beast2.svg?branch=master)](https://travis-ci.org/CompEvol/beast2)
+
 BEAST is a cross-platform program for Bayesian inference using MCMC of
 molecular sequences. It is entirely orientated towards rooted,
 time-measured phylogenies inferred using strict or relaxed molecular

build.xml

@@ -24,7 +24,7 @@
         <fileset dir="${lib}" includes="colt.jar"/>
         <fileset dir="${lib}" includes="fest.jar"/>
         <fileset dir="${lib}" includes="junit-4.8.2.jar"/>
-        <fileset dir="${lib}" includes="antlr-runtime-4.5.jar"/>
+        <fileset dir="${lib}" includes="antlr-runtime-4.7.jar"/>
     </path>
 
     <!--
@@ -135,7 +135,7 @@
             <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-4.5.jar"/>
+            <zipgroupfileset dir="${lib}" includes="antlr-runtime-4.7.jar"/>
         </jar>
         <jar jarfile="${dist}/launcher.jar">
             <fileset dir="${build}">
@@ -215,14 +215,15 @@
     </target>
 
     <!-- Target for Travis-CI with non-zero exit status on test failure. -->
-    <target name="travis" depends="clean, compile-all, junit">
-        <fail if="junitfailed" message="One or more unit tests failed."/>
+    <target name="travis" depends="clean, compile-all, junit, junitb">
+        <fail if="junitfailed" message="One or more CORE BEAST tests failed."/>
+        <fail if="junitbfailed" message="One or more BEAUTI tests failed."/>
     </target>
 
     <!-- testing beauti gui-->
     <target name="junitb">
         <mkdir dir="${report}" />
-        <junit printsummary="yes">
+        <junit printsummary="yes" failureproperty="junitbfailed">
             <!--showoutput='yes'-->
             <classpath>
                 <path refid="classpath" />
@@ -242,10 +243,10 @@
 
 
     <!-- Release -->
-    <property name="version" value="2.4.4" />
-    <property name="version_number" value="2.4.4" />
+    <property name="version" value="2.4.7" />
+    <property name="version_number" value="2.4.7" />
     <property name="release_dir" value="release" />
-    <property name="copyright" value="Beast 2 development team 2011-2016" />
+    <property name="copyright" value="Beast 2 development team 2011-2017" />
 
     <property name="BEAST_name" value="BEAST" />
     <property name="beast_name" value="beast" />
@@ -532,6 +533,7 @@
             <option value="-Xmx4g"/>
             <option value="-Dapple.laf.useScreenMenuBar=true"/>
             <option value="-Djava.library.path=$JAVAROOT:/usr/local/lib"/>
+            <option value="-Duser.language=en"/>            
             <argument value="-window"/>
             <argument value="-working"/>
             <argument value="-options"/>
@@ -561,6 +563,7 @@
             <option value="-Xdock:name=&quot;BEAUti&quot;"/>
             <option value="-Dapple.laf.useScreenMenuBar=true"/>
             <option value="-Djava.library.path=$JAVAROOT:/usr/local/lib"/>
+            <option value="-Duser.language=en"/>            
             <argument value="-capture"/>
         </bundleapp>
 
@@ -587,6 +590,7 @@
             <option value="-Xmx4g"/>
             <option value="-Dapple.laf.useScreenMenuBar=true"/>
             <option value="-Djava.library.path=$JAVAROOT:/usr/local/lib"/>
+            <option value="-Duser.language=en"/>            
         </bundleapp>
 
         <exec executable="codesign">
@@ -612,6 +616,7 @@
             <option value="-Xmx4g"/>
             <option value="-Dapple.laf.useScreenMenuBar=true"/>
             <option value="-Djava.library.path=$JAVAROOT:/usr/local/lib"/>
+            <option value="-Duser.language=en"/>            
         </bundleapp>
 
         <exec executable="codesign">
@@ -636,6 +641,7 @@
             <option value="-Xmx4g"/>
             <option value="-Dapple.laf.useScreenMenuBar=true"/>
             <option value="-Djava.library.path=$JAVAROOT:/usr/local/lib"/>
+            <option value="-Duser.language=en"/>            
         </bundleapp>
 
         <exec executable="codesign">
@@ -660,6 +666,7 @@
             <option value="-Xmx1024M"/>
             <option value="-Dapple.laf.useScreenMenuBar=true"/>
             <option value="-Djava.library.path=$JAVAROOT:/usr/local/lib"/>
+            <option value="-Duser.language=en"/>            
         </bundleapp>
 
         <exec executable="codesign">

debian/changelog

-beast2-mcmc (2.4.4+dfsg-2) UNRELEASED; urgency=medium
+beast2-mcmc (2.4.8+dfsg-1) UNRELEASED; urgency=medium
 
+  [ Steffen Moeller ]
   * d/control: Standards-Version: 4.1.3 (no changes required)
   * d/u/metadata:
     - added RRIDs
     - yamllint cleanliness 
 
- -- Steffen Moeller <moeller@debian.org>  Thu, 29 Mar 2018 20:26:22 +0200
+  [ Andreas Tille ]
+  * New upstream version
+  * Point Vcs fields to salsa.debian.org
+  * debhelper 11
+  * Build-Depends: s/openjdk-8-jdk/default-jdk/
+    Closes: #894359
+  * Depends: s/openjdk-8-jre | java8-runtime/default-jre | java9-runtime/
+
+ -- Andreas Tille <tille@debian.org>  Fri, 06 Apr 2018 09:03:13 +0200
 
 beast2-mcmc (2.4.4+dfsg-1) unstable; urgency=medium
 

debian/compat

-10
+11

debian/control

@@ -4,11 +4,11 @@ Uploaders: Andreas Tille <tille@debian.org>,
            Olivier Sallou <osallou@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 10),
+Build-Depends: debhelper (>= 11~),
                javahelper,
                ant,
                ant-optional,
-               openjdk-8-jdk,
+               default-jdk,
                libjam-java,
                libhmsbeagle-java,
                libcolt-free-java,
@@ -18,8 +18,8 @@ Build-Depends: debhelper (>= 10),
                texlive-latex-base,
                texlive-latex-extra
 Standards-Version: 4.1.3
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/beast2-mcmc.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/beast2-mcmc.git
+Vcs-Browser: https://salsa.debian.org/med-team/beast2-mcmc
+Vcs-Git: https://salsa.debian.org/med-team/beast2-mcmc.git
 Homepage: http://www.beast2.org
 
 Package: beast2-mcmc
@@ -28,7 +28,7 @@ Depends: ${shlibs:Depends},
          ${misc:Depends},
          libhmsbeagle-java (>= 1.1r1092),
          ${java:Depends},
-         openjdk-8-jre | java8-runtime
+         default-jre | java9-runtime
 Suggests: beast2-mcmc-doc
 Description: Bayesian MCMC phylogenetic inference
  BEAST is a cross-platform program for Bayesian MCMC analysis of molecular 

debian/patches/fix_classpath_in_build_xml.patch

@@ -6,7 +6,7 @@ Forwarded: no
 
 --- a/build.xml
 +++ b/build.xml
-@@ -8,23 +8,24 @@
+@@ -8,12 +8,12 @@
      </description>
  
      <!-- set global properties for this build -->
@@ -18,32 +18,25 @@ Forwarded: no
 -    <property name="test" location="../beast2/test" />
 +    <property name="src" location="src" />
 +    <property name="build" location="build" />
-+    <property name="lib" location="lib" />
-+    <property name="deblib" location="/usr/share/java" />
++    <property name="lib" location="/usr/share/java" />
 +    <property name="doc" location="doc" />
 +    <property name="dist" location="build/dist" />
 +    <property name="test" location="test" />
  
      <property name="main_class_BEAST" value="beast.app.beastapp.BeastMain" />
      <property name="report" value="build/junitreport" />
- 
-     <path id="classpath">
--        <fileset dir="${lib}" includes="beagle.jar"/>
--        <fileset dir="${lib}" includes="jam.jar"/>
--        <fileset dir="${lib}" includes="colt.jar"/>
--        <fileset dir="${lib}" includes="fest.jar"/>
+@@ -23,8 +23,8 @@
+         <fileset dir="${lib}" includes="jam.jar"/>
+         <fileset dir="${lib}" includes="colt.jar"/>
+         <fileset dir="${lib}" includes="fest.jar"/>
 -        <fileset dir="${lib}" includes="junit-4.8.2.jar"/>
--        <fileset dir="${lib}" includes="antlr-runtime-4.5.jar"/>
-+        <fileset dir="${deblib}" includes="beagle.jar"/>
-+        <fileset dir="${deblib}" includes="jam.jar"/>
-+        <fileset dir="${deblib}" includes="colt.jar"/>
-+        <fileset dir="${deblib}" includes="fest-util.jar"/>
-+        <fileset dir="${deblib}" includes="junit4.jar"/>
-+        <fileset dir="${deblib}" includes="antlr4-runtime.jar"/>
+-        <fileset dir="${lib}" includes="antlr-runtime-4.7.jar"/>
++        <fileset dir="${lib}" includes="junit4.jar"/>
++        <fileset dir="${lib}" includes="antlr-runtime.jar"/>
      </path>
  
      <!--
-@@ -161,7 +162,7 @@
+@@ -161,7 +161,7 @@
          <mkdir dir="${release_dir}/package/lib" />
          <copy file="${dist}/beast.src.jar" todir="${release_dir}/package/"/>
          <copy file="${dist}/beast.jar" todir="${release_dir}/package/lib/"/>

examples/nexus/maddison.nex

+#NEXUS
+
+[
+	Example from Nexus: An Extensible File Format for Systematic Information
+	David R. Maddison David L. Swofford Wayne P. Maddison David Cannatella
+	Syst Biol (1997) 46 (4): 590-621.
+]
+
+
+BEGIN TAXA;
+  DIMENSIONS NTAX=4;
+  TAXLABELS fish frog snake mouse;
+END;
+
+BEGIN CHARACTERS;
+  DIMENSIONS NCHAR=20;
+  FORMAT DATATYPE=DNA;
+  MATRIX
+    fish ACATAGAGGGTACCTCTAAG
+    frog ACTTAGAGGCTACCTCTACG
+    snake ACTCACTGGGTACCTTTGCG
+    mouse ACTCAGACGGTACCTTTGCG;
+END;
+
+BEGIN TREES;
+  TREE best = (fish,(frog,(snake,mouse)));
+END;

examples/testDirectSimulator.xml

+<beast version="2.0" namespace="beast.core
+                              :beast.evolution.alignment
+                              :beast.evolution.tree
+                              :beast.math.distributions
+                              :beast.evolution.speciation
+                              :beast.core.util
+                              :beast.core.parameter">
+
+
+
+    <run spec="DirectSimulator" nSamples="2">
+
+        <distribution spec="CompoundDistribution" id="fullModel">
+            <distribution spec="YuleModel" id="yuleModel">
+                <tree spec="Tree" id="tree">
+                    <taxonset spec="TaxonSet">
+                        <taxon spec="Taxon" id="t1"/>
+                        <taxon spec="Taxon" id="t2"/>
+                        <taxon spec="Taxon" id="t3"/>
+                        <taxon spec="Taxon" id="t4"/>
+                        <taxon spec="Taxon" id="t5"/>
+                    </taxonset>
+                </tree>
+                <birthDiffRate spec="RealParameter" id="birthDiffRateParam" value="1.0"/>
+            </distribution>
+
+            <distribution spec="beast.math.distributions.Prior" id="birthDiffRatePrior">
+                <distr spec="Exponential" id="xExpParamDist" mean="1"/>
+                <x spec="RealParameter" idref="birthDiffRateParam"/>
+            </distribution>
+
+        </distribution>
+
+        <logger logEvery="1" fileName="$(filebase).trees">
+            <log idref="tree"/>
+        </logger>
+    </run>
+</beast>

examples/testDirectSimulator2.xml

+<beast version="2.0" namespace="beast.core
+                              :beast.evolution.alignment
+                              :beast.evolution.tree
+                              :beast.math.distributions
+                              :beast.core.util
+                              :beast.core.parameter">
+
+
+
+    <run spec="DirectSimulator" nSamples="10000">
+
+        <distribution spec="CompoundDistribution">
+            <distribution spec="beast.math.distributions.Prior">
+                <distr spec="Exponential" mean="1"/>
+                <x spec="RealParameter" id="x" value="1.0"/>
+            </distribution>
+        </distribution>
+
+        <logger logEvery="1" fileName="$(filebase).log">
+            <log idref="x"/>
+        </logger>
+    </run>
+</beast>

examples/testDirectSimulatorHierarchical.xml

+<beast version="2.0" namespace="beast.core
+                              :beast.evolution.alignment
+                              :beast.evolution.tree
+                              :beast.math.distributions
+                              :beast.core.util
+                              :beast.core.parameter">
+
+
+    <parameter spec="RealParameter" id="meanParam" value="1.0"/>
+
+
+    <run spec="DirectSimulator" nSamples="1">
+
+        <distribution spec="CompoundDistribution">
+
+            <distribution spec="beast.math.distributions.Prior" id="xPriorDist">
+                <distr spec="Exponential" id="meanExpParamDist" mean="@meanParam"/>
+                <x spec="RealParameter" id="x" value="1.0"/>
+            </distribution>
+
+            <distribution spec="beast.math.distributions.Prior" id="meanPriorDist">
+                <distr spec="Exponential" id="xExpParamDist" mean="1"/>
+                <x spec="RealParameter" idref="meanParam"/>
+            </distribution>
+
+        </distribution>
+
+        <logger logEvery="1" fileName="$(filebase).log">
+            <log idref="x"/>
+            <log idref="meanParam"/>
+        </logger>
+    </run>
+</beast>

release/Linux/bin/addonmanager

@@ -29,5 +29,5 @@ if [ -z "$JAVA_HOME" ]; then
 else
   JAVA=$JAVA_HOME/bin/java
 fi
-$JAVA -Xms256m -Xmx1024m -Djava.library.path="$BEAST_LIB" -cp "$BEAST_LIB/beast.jar" beast.util.AddOnManager $*
+$JAVA -Xms256m -Xmx1024m -Djava.library.path="$BEAST_LIB" -Duser.language=en -cp "$BEAST_LIB/beast.jar" beast.util.AddOnManager $*
 

release/Linux/bin/appstore

@@ -29,5 +29,5 @@ if [ -z "$JAVA_HOME" ]; then
 else
   JAVA=$JAVA_HOME/bin/java
 fi
-$JAVA -Xms256m -Xmx1024m -Djava.library.path="$BEAST_LIB" -cp "$BEAST_LIB/launcher.jar" beast.app.tools.AppStoreLauncher $*
+$JAVA -Xms256m -Xmx1024m -Djava.library.path="$BEAST_LIB" -Duser.language=en -cp "$BEAST_LIB/launcher.jar" beast.app.tools.AppStoreLauncher $*
 

release/Linux/bin/beast

@@ -52,7 +52,7 @@ fi
 # use BEAST_EXTRA_LIBS variable to load BEAGLE and other libraries from non-default locations 
 # this assumes that the library path contains all these libraries (or are set through LD_LIBRARY_PATH)
 if [ -n "$BEAST_EXTRA_LIBS" ]; then 
-  $JAVA -Xms64m -Xmx4g -Djava.library.path=$BEAST_EXTRA_LIBS -cp "$BEAST_LIB/launcher.jar" beast.app.beastapp.BeastLauncher $*
+  $JAVA -Xms64m -Xmx4g -Djava.library.path=$BEAST_EXTRA_LIBS -Duser.language=en -cp "$BEAST_LIB/launcher.jar" beast.app.beastapp.BeastLauncher $*
 else	
-  $JAVA -Xms64m -Xmx4g -cp "$BEAST_LIB/launcher.jar" beast.app.beastapp.BeastLauncher $*
+  $JAVA -Xms64m -Xmx4g -Duser.language=en -cp "$BEAST_LIB/launcher.jar" beast.app.beastapp.BeastLauncher $*
 fi

release/Linux/bin/beauti

@@ -29,5 +29,5 @@ if [ -z "$JAVA_HOME" ]; then
 else
   JAVA=$JAVA_HOME/bin/java
 fi
-$JAVA -Xms256m -Xmx4g -Djava.library.path="$BEAST_LIB" -cp "$BEAST_LIB/launcher.jar" beast.app.beauti.BeautiLauncher -capture $*
+$JAVA -Xms256m -Xmx4g -Djava.library.path="$BEAST_LIB" -Duser.language=en -cp "$BEAST_LIB/launcher.jar" beast.app.beauti.BeautiLauncher -capture $*
 

release/Linux/bin/densitree

@@ -29,5 +29,5 @@ if [ -z "$JAVA_HOME" ]; then
 else
   JAVA=$JAVA_HOME/bin/java
 fi
-$JAVA -Xms256m -Xmx4g -Djava.library.path="$BEAST_LIB" -cp "$BEAST_LIB/DensiTree.jar" viz.DensiTree $*
+$JAVA -Xms256m -Xmx4g -Djava.library.path="$BEAST_LIB" -cp "$BEAST_LIB/DensiTree.jar:$BEAST/DensiTree.app/Contents/Java/DensiTree.jar" viz.DensiTree $*
 

release/Linux/bin/loganalyser

@@ -29,5 +29,5 @@ if [ -z "$JAVA_HOME" ]; then
 else
   JAVA=$JAVA_HOME/bin/java
 fi
-$JAVA -Xms256m -Xmx4g -Djava.library.path="$BEAST_LIB" -cp "$BEAST_LIB/beast.jar" beast.util.LogAnalyser $*
+$JAVA -Xms256m -Xmx4g -Djava.library.path="$BEAST_LIB" -Duser.language=en -cp "$BEAST_LIB/beast.jar" beast.util.LogAnalyser $*
 

release/Linux/bin/logcombiner

@@ -29,5 +29,5 @@ if [ -z "$JAVA_HOME" ]; then
 else
   JAVA=$JAVA_HOME/bin/java
 fi
-$JAVA -Xms256m -Xmx4g -Djava.library.path="$BEAST_LIB" -cp "$BEAST_LIB/launcher.jar" beast.app.tools.LogCombinerLauncher $*
+$JAVA -Xms256m -Xmx4g -Djava.library.path="$BEAST_LIB" -Duser.language=en -cp "$BEAST_LIB/launcher.jar" beast.app.tools.LogCombinerLauncher $*