laduplessis · walterxie · Nov 21, 2022 · Nov 21, 2022 · Dec 5, 2022 · Dec 5, 2022
diff --git a/Dockerfile b/Dockerfile
@@ -1,6 +1,6 @@
 # Dockerfile to build container for unit testing
 
-FROM openjdk:10
+FROM openjdk:17
 
 RUN apt-get update && apt-get install -y git ant
 

diff --git a/README.md b/README.md
@@ -13,7 +13,7 @@ KV Parag, L du Plessis, OG Pybus. _Jointly inferring the dynamics of population
 
 To install BESP:
 
-1. Download and install [BEAST2](www.beast2.org) (at least version 2.5.0).
+1. Download and install [BEAST2](www.beast2.org) (at least version 2.7.0).
 2. Launch the BEAUti application distributed with BEAST2.
 3. From the File menu select "Manage Packages".
 4. Click the "Package repositories" button at the bottom of the Package Manager dialog box.
@@ -26,7 +26,7 @@ To install BESP:
 
 To build this package from source, ensure that  you have the following installed:
 
-- Java JDK v1.8
+- Java JDK v17
 - Apache Ant v1.9 or later
 - An internet connection
 

diff --git a/ScreenShotIntelliJ.png b/ScreenShotIntelliJ.png
diff --git a/build.xml b/build.xml
@@ -7,15 +7,16 @@
 
     <!-- Location to check for local copy of beast2 repository -->
     <property name="beastDir" location="../beast2"/>
+    <property name="BeastFXpath" location="../BeastFX" />
 
-    <!-- BEAST 2 currently uses Java 1.8 -->
-    <property name="sourceVersion" value="1.8"/>
-    <property name="targetVersion" value="1.8"/>
+    <!-- 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="templates" location="templates"/>
+    <property name="templates" location="fxtemplates"/>
 
     <!-- BEAST branch and version to build against
          (only different for version tags because of
@@ -44,15 +45,18 @@
 
         <!-- 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)}" />
+        <property name="projName" value="${fromVersionFile.package(name)}" />
+        <property name="projVersion" value="${fromVersionFile.package(version)}" />
 
         <mkdir dir="${build}"/>
         <mkdir dir="${build-lib}"/>
         <mkdir dir="${dist}"/>
 
-        <copy todir="${build-lib}" failonerror="false" quiet="true">
-            <fileset dir="${lib}" includes="*.jar"/>
+        <copy todir="${build-lib}">
+<!--            <fileset dir="${lib}" includes="*.jar"/>-->
+            <fileset dir="${beastDir}/lib" includes="*.jar"/>
+            <fileset dir="${beastDir}/lib/junit" includes="junit-*.jar"/>
+            <fileset dir="${BeastFXpath}/locallib" includes="*.jar"/>
         </copy>
     </target>
 
@@ -65,7 +69,7 @@
     <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 ${beast-version} from GitHub.</echo>
-
+        <!--  TODO not tested    -->
         <property name="build-beast" location="build-beast"/>
         <mkdir dir="${build-beast}"/>
 
@@ -80,10 +84,41 @@
                 <fileset dir="${build-beast}/beast2-${beast-version}/lib" includes="*.jar"/>
             </classpath>
         </javac>
-        <jar jarfile="${build-lib}/beast2.jar" basedir="${build-beast}/beast2-${beast-version}/build" />
+
+        <mkdir dir="${build-beast}/beast2-${beast-version}/test"/>
+        <javac target="${targetVersion}" source="${sourceVersion}"
+               srcdir="${build-beast}/beast2-${beast-version}/test"
+               destdir="${build-beast}/beast2-${beast-version}/build"
+               includeantruntime="false">
+            <classpath>
+                <pathelement path="${classpath}"/>
+                <fileset dir="${build-beast}/beast2-${beast-version}/lib" includes="*.jar"/>
+                <fileset dir="${beastDir}/lib/junit" includes="junit-*.jar"/>
+            </classpath>
+        </javac>
+
         <copy todir="${build-lib}">
             <fileset dir="${build-beast}/beast2-${beast-version}/lib" includes="*.jar"/>
+            <fileset dir="${beastDir}/lib/junit" includes="junit-*.jar"/>
         </copy>
+        <jar jarfile="${build-lib}/beast2.jar" basedir="${build-beast}/beast2-${beast-version}/build" />
+
+        <get src="https://github.com/CompEvol/BeastFX/archive/${beast-branch}.zip" dest="${build-beast}/beastFX.zip"/>
+        <unzip src="${build-beast}/beastFX.zip" dest="${build-beast}"/>
+        <mkdir dir="${build-beast}/beastFX-${beast-version}/build"/>
+        <!-- Java FX  -->
+        <!-- if Zulu is not installed, it can specify javac, e.g. add  -->
+        <!-- executable="../../Downloads/zulu17.36.13-ca-fx-jdk17.0.4-macosx_x64/bin/javac"  -->
+        <javac target="${targetVersion}" source="${sourceVersion}"
+               srcdir="${build-beast}/beastFX-${beast-version}/src"
+               destdir="${build-beast}/beastFX-${beast-version}/build"
+               fork="true"  includeantruntime="false">
+            <classpath>
+                <pathelement path="${classpath}"/>
+                <fileset dir="${build-lib}" includes="*.jar"/>
+            </classpath>
+        </javac>
+        <jar jarfile="${build-lib}/beastFX.jar" basedir="${build-beast}/beastFX-${beast-version}/build" />
 
         <delete dir="${build-beast}" />
     </target>
@@ -95,21 +130,36 @@
         <mkdir dir="${build-beast}"/>
 
         <javac target="${targetVersion}" source="${sourceVersion}"
-            srcdir="${beastDir}/src"
-            destdir="${build-beast}" includeantruntime="false">
+               srcdir="${beastDir}/src" destdir="${build-beast}"
+               includeantruntime="false">
             <classpath>
                 <pathelement path="${classpath}"/>
                 <fileset dir="${beastDir}/lib" includes="*.jar"/>
             </classpath>
         </javac>
+        <!-- for testing -->
+        <javac target="${targetVersion}" source="${sourceVersion}"
+               srcdir="${beastDir}/test" destdir="${build-beast}"
+               includeantruntime="false">
+            <classpath>
+                <pathelement path="${classpath}"/>
+                <fileset dir="${build-lib}" includes="*.jar"/>
+            </classpath>
+        </javac>
+
+        <!-- Java FX  -->
+        <!-- if Zulu is not installed, it can specify javac, e.g. add  -->
+        <!-- executable="../../Downloads/zulu17.36.13-ca-fx-jdk17.0.4-macosx_x64/bin/javac"  -->
+        <javac target="${targetVersion}" source="${sourceVersion}"
+               srcdir="${BeastFXpath}/src" destdir="${build-beast}"
+               fork="true"  includeantruntime="false">
+            <classpath>
+                <pathelement path="${classpath}"/>
+                <fileset dir="${build-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>
-        <copy todir="${build}">
-            <fileset dir="${beastDir}/src"
-                     includes="**/*.png" />
-        </copy>
 
         <delete dir="${build-beast}" />
     </target>
@@ -123,7 +173,9 @@
 
     <!-- Compile -->
     <target name="compile" depends="build-beast, get-dependencies">
-        <javac target="${targetVersion}" source="${sourceVersion}" srcdir="${src}" destdir="${build}" includeantruntime="false">
+        <javac target="${targetVersion}" source="${sourceVersion}"
+               srcdir="${src}" destdir="${build}"
+               includeantruntime="false">
             <classpath>
                 <pathelement path="${classpath}"/>
                 <fileset dir="${build-lib}" includes="*.jar"/>
@@ -144,10 +196,11 @@
         <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">
+        <javac target="${targetVersion}" source="${sourceVersion}"
+               srcdir="${test}" destdir="${build-test}"
+               includeantruntime="false">
             <classpath>
                 <pathelement path="${classpath}"/>
                 <pathelement path="${build}" />
@@ -186,7 +239,7 @@
 
         <mkdir dir="${pack}"/>
         <mkdir dir="${pack}/examples"/>
-        <mkdir dir="${pack}/templates"/>
+        <mkdir dir="${pack}/fxtemplates"/>
         <mkdir dir="${pack}/lib"/>
         <mkdir dir="${pack}/doc"/>
 
@@ -211,8 +264,8 @@
             <fileset dir="${examples}" includes="**/*.fasta" />
         </copy>
 
-        <mkdir dir="${templates}" />
-        <copy todir="${pack}/templates">
+        <mkdir dir="fxtemplates" />
+        <copy todir="${pack}/fxtemplates">
             <fileset dir="${templates}" includes="*.xml" />
         </copy>
 

diff --git a/examples/BESP/bison_besp_mcpgamma_limits_densdefined.xml b/examples/BESP/bison_besp_mcpgamma_limits_densdefined.xml
@@ -1,21 +1,20 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <beast beautitemplate='Standard' 
        beautistatus='' 
-       namespace="beast.core
-                 :beast.evolution.alignment
-                 :beast.evolution.tree.coalescent
-                 :beast.util
-                 :beast.core.util
-                 :beast.core.parameter
-                 :beast.evolution.nuc
-                 :beast.evolution.operators
-                 :beast.evolution.sitemodel
-                 :beast.evolution.substitutionmodel
-                 :beast.evolution.likelihood
+       namespace="beast.base.core:beast.base.inference
+                 :beast.base.evolution.alignment
+                 :beast.base.evolution.tree.coalescent
+                 :beast.base.util
+                 :beast.base.inference.parameter
+                 :beast.base.evolution.nuc
+                 :beast.base.evolution.operator:beast.base.inference.operator
+                 :beast.base.evolution.sitemodel
+                 :beast.base.evolution.substitutionmodel
+                 :beast.base.evolution.likelihood
                  :bsp.distributions
                  :bsp.util" 
-       required="BEAST v2.5.0" 
-       version="2.5">
+       required="BEAST v2.7.2"
+       version="2.7">
 
 
     <data id="bison_2013" name="alignment">
@@ -181,23 +180,23 @@
 
 
 
-<map name="Uniform" >beast.math.distributions.Uniform</map>
-<map name="Exponential" >beast.math.distributions.Exponential</map>
-<map name="LogNormal" >beast.math.distributions.LogNormalDistributionModel</map>
-<map name="Normal" >beast.math.distributions.Normal</map>
-<map name="Beta" >beast.math.distributions.Beta</map>
-<map name="Gamma" >beast.math.distributions.Gamma</map>
-<map name="LaplaceDistribution" >beast.math.distributions.LaplaceDistribution</map>
-<map name="prior" >beast.math.distributions.Prior</map>
-<map name="InverseGamma" >beast.math.distributions.InverseGamma</map>
-<map name="OneOnX" >beast.math.distributions.OneOnX</map>
+<map name="Uniform" >beast.base.inference.distribution.Uniform</map>
+<map name="Exponential" >beast.base.inference.distribution.Exponential</map>
+<map name="LogNormal" >beast.base.inference.distribution.LogNormalDistributionModel</map>
+<map name="Normal" >beast.base.inference.distribution.Normal</map>
+<map name="Beta" >beast.base.inference.distribution.Beta</map>
+<map name="Gamma" >beast.base.inference.distribution.Gamma</map>
+<map name="LaplaceDistribution" >beast.base.inference.distribution.LaplaceDistribution</map>
+<map name="prior" >beast.base.inference.distribution.Prior</map>
+<map name="InverseGamma" >beast.base.inference.distribution.InverseGamma</map>
+<map name="OneOnX" >beast.base.inference.distribution.OneOnX</map>
 
 
 <run id="mcmc" spec="MCMC" chainLength="20000000">
     <state id="state" storeEvery="50000000">
 
         <tree id="Tree.t:bison_2013" name="stateNode">
-            <trait id="dateTrait.t:bison_2013" spec="beast.evolution.tree.TraitSet" traitname="date-backward">
+            <trait id="dateTrait.t:bison_2013" spec="beast.base.evolution.tree.TraitSet" traitname="date-backward">
                 U12959_0_0=0,
                 U12958_0_0=0,
                 U12957_0_0=0,
@@ -367,24 +366,24 @@
     </state>
 
     <!-- Initial tree -->
-    <init id="RandomTree.t:bison_2013" spec="beast.evolution.tree.RandomTree" estimate="false" initial="@Tree.t:bison_2013" taxa="@bison_2013">
+    <init id="RandomTree.t:bison_2013" spec="beast.base.evolution.tree.coalescent.RandomTree" estimate="false" initial="@Tree.t:bison_2013" taxa="@bison_2013">
         <populationModel id="ConstantPopulation0.t:bison_2013" spec="ConstantPopulation">
             <parameter id="randomPopSize.t:bison_2013" name="popSize">1.0</parameter>
         </populationModel>
     </init>
 
-    <distribution id="posterior" spec="util.CompoundDistribution">
+    <distribution id="posterior" spec="beast.base.inference.CompoundDistribution">
 
         <!-- Begin prior -->
-        <distribution id="prior" spec="util.CompoundDistribution">
+        <distribution id="prior" spec="beast.base.inference.CompoundDistribution">
 
             <!-- Treeprior (Bayesian Skyline Plot) -->
             <distribution id="BayesianSkyline.t:bison_2013" spec="BESP" popSizeGroupSizes="@bGroupSizes.t:bison_2013" popSizes="@bPopSizes.t:bison_2013" minWidth="100" samplingIntensity="@bSamplingIntensity.t:bison_2013">
-                <treeIntervals id="BESPTreeIntervals.t:bison_2013" spec="TreeIntervals" tree="@Tree.t:bison_2013"/>
+                <treeIntervals id="BESPTreeIntervals.t:bison_2013" spec="beast.base.evolution.tree.TreeIntervals" tree="@Tree.t:bison_2013"/>
             </distribution>
 
             <!-- Smoothing prior -->
-            <distribution id="MarkovChainedPopSizes.t:bison_2013" spec="beast.math.distributions.MarkovChainDistribution" jeffreys="true" parameter="@bPopSizes.t:bison_2013"/>
+            <distribution id="MarkovChainedPopSizes.t:bison_2013" spec="beast.base.inference.distribution.MarkovChainDistribution" jeffreys="true" parameter="@bPopSizes.t:bison_2013"/>
 
             <!-- Sampling Intensity Prior -->
             <prior id="SamplingIntensityPrior.t:bison_2013" name="distribution" x="@bSamplingIntensity.t:bison_2013">
@@ -404,7 +403,7 @@
         <!-- End prior -->
 
         <!-- Begin likelihood -->
-        <distribution id="likelihood" spec="util.CompoundDistribution" useThreads="true">
+        <distribution id="likelihood" spec="beast.base.inference.CompoundDistribution" useThreads="true">
 
             <!-- Alignment likelihood -->
             <distribution id="treeLikelihood.bison_2013" spec="ThreadedTreeLikelihood" data="@bison_2013" tree="@Tree.t:bison_2013">
@@ -420,7 +419,7 @@
                 </siteModel>
 
                 <!-- Clock model (strict clock) -->
-                <branchRateModel id="StrictClock.c:bison_2013" spec="beast.evolution.branchratemodel.StrictClockModel" clock.rate="@clockRate.c:bison_2013"/>
+                <branchRateModel id="StrictClock.c:bison_2013" spec="beast.base.evolution.branchratemodel.StrictClockModel" clock.rate="@clockRate.c:bison_2013"/>
 
             </distribution>            
         </distribution>
@@ -476,7 +475,7 @@
         <log idref="freqParameter.s:bison_2013"/>
         <log idref="clockRate.c:bison_2013"/>
 
-        <log id="TreeHeight.t:bison_2013" spec="beast.evolution.tree.TreeHeightLogger" tree="@Tree.t:bison_2013"/>
+        <log id="TreeHeight.t:bison_2013" spec="beast.base.evolution.tree.TreeHeightLogger" tree="@Tree.t:bison_2013"/>
         <log idref="bPopSizes.t:bison_2013"/>
         <log idref="bGroupSizes.t:bison_2013"/>
         <log id="bPopSizeChangeTimes.t:bison_2013" spec="popSizeChangeTimeLogger" skyline="@BayesianSkyline.t:bison_2013"/> 
@@ -493,7 +492,7 @@
     </logger>
 
     <logger id="treelog" fileName="output/$(filebase)_$(seed).trees" logEvery="10000" mode="tree">
-        <log id="TreeWithMetaDataLogger.t:bison_2013" spec="beast.evolution.tree.TreeWithMetaDataLogger" tree="@Tree.t:bison_2013"/>
+        <log id="TreeWithMetaDataLogger.t:bison_2013" spec="beast.base.evolution.TreeWithMetaDataLogger" tree="@Tree.t:bison_2013"/>
     </logger>
 
 </run>