Compatibility with 2.7

build.xml

@@ -117,7 +117,7 @@
       <echo>Downloading dependencies...</echo>
 
       <echo>BDSKY:</echo>
-      <get src="https://github.com/BEAST2-Dev/bdsky/releases/download/1.4.0/BDSKY.addon.1.4.0.zip"
+      <get src="https://github.com/BEAST2-Dev/bdsky/releases/download/v1.5.0/BDSKY.v1.5.0.zip"
            dest="${build-lib}/BDSKY.zip"/>
       <mkdir dir="${build-lib}/BDSKY"/>
       <unzip src="${build-lib}/BDSKY.zip" dest="${build-lib}/BDSKY"/>
@@ -191,7 +191,7 @@
 
         <mkdir dir="${pack}"/>
         <mkdir dir="${pack}/examples"/>
-        <mkdir dir="${pack}/templates"/>
+        <mkdir dir="${pack}/fxtemplates"/>
         <mkdir dir="${pack}/lib"/>
         <mkdir dir="${pack}/doc"/>
 
@@ -217,7 +217,7 @@
         </copy>
 
         <mkdir dir="${templates}" />
-        <copy todir="${pack}/templates">
+        <copy todir="${pack}/fxtemplates">
             <fileset dir="${templates}" includes="*.xml" />
         </copy>
 

examples/smoothingpriors/comparison/hcv_bdsky.xml

@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<beast beautitemplate='Standard' beautistatus='' namespace="beast.core
+<beast beautitemplate='Standard' beautistatus='' namespace="beast.pkgmgmt:beast.base.core:beast.base.inference
                                                            :beast.evolution.alignment
                                                            :beast.evolution.tree.coalescent
                                                            :beast.core.util
@@ -12,16 +12,16 @@
 
 
 
-<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>
 
 
 <data id="hcv" name="alignment">
@@ -119,21 +119,21 @@
     </state>
 
     <!-- Initial tree -->
-    <init id="RandomTree.t:hcv" spec="beast.evolution.tree.RandomTree" estimate="false" initial="@Tree.t:hcv" taxa="@hcv">
+    <init id="RandomTree.t:hcv" spec="beast.base.evolution.tree.coalescent.RandomTree" estimate="false" initial="@Tree.t:hcv" taxa="@hcv">
         <populationModel id="ConstantPopulation0.t:hcv" spec="ConstantPopulation">
             <parameter id="randomPopSize.t:hcv" 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 (BDSKY contemporary) -->
                <distribution id="BirthDeathSkyContemporary.t:hcv" 
-                             spec="beast.evolution.speciation.BirthDeathSkylineModel" 
+                             spec="bdsky.evolution.speciation.BirthDeathSkylineModel" 
                              tree="@Tree.t:hcv"
                              reproductiveNumber="@reproductiveNumber.t:hcv" 
                              becomeUninfectiousRate="@becomeUninfectiousRate.t:hcv"                                                           
@@ -186,7 +186,7 @@
 
 
           <!-- 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.hcv" spec="ThreadedTreeLikelihood" data="@hcv" tree="@Tree.t:hcv">
@@ -202,7 +202,7 @@
                     </siteModel>
 
                     <!-- Clock model (fixed clock-rate) -->
-                    <branchRateModel id="StrictClock.c:hcv" spec="beast.evolution.branchratemodel.StrictClockModel">
+                    <branchRateModel id="StrictClock.c:hcv" spec="beast.base.evolution.branchratemodel.StrictClockModel">
                          <parameter id="clockRate.c:hcv" estimate="false" name="clock.rate">7.9E-4</parameter>
                     </branchRateModel>
 
@@ -267,21 +267,21 @@
         <log idref="rateGT.s:hcv"/>
         <log idref="freqParameter.s:hcv"/>
 
-        <log id="TreeHeight.t:hcv" spec="beast.evolution.tree.TreeHeightLogger" tree="@Tree.t:hcv"/>        
+        <log id="TreeHeight.t:hcv" spec="beast.base.evolution.tree.TreeHeightLogger" tree="@Tree.t:hcv"/>        
         <log idref="origin.t:hcv"/>
         <log idref="reproductiveNumber.t:hcv"/>        
         <log idref="becomeUninfectiousRate.t:hcv"/>
         <log idref="rho.t:hcv"/>
 
-        <log id="birth.t:hcv" spec="beast.math.statistic.RPNcalculator" expression="reproductiveNumber.t:hcv becomeUninfectiousRate.t:hcv *">
+        <log id="birth.t:hcv" spec="beast.base.inference.util.RPNcalculator" expression="reproductiveNumber.t:hcv becomeUninfectiousRate.t:hcv *">
             <parameter idref="becomeUninfectiousRate.t:hcv"/>
             <parameter idref="reproductiveNumber.t:hcv"/>
         </log>
-        <log id="death.t:hcv" spec="beast.math.statistic.RPNcalculator" expression="becomeUninfectiousRate.t:hcv 1 samplingProportion.t:hcv - *">
+        <log id="death.t:hcv" spec="beast.base.inference.util.RPNcalculator" expression="becomeUninfectiousRate.t:hcv 1 samplingProportion.t:hcv - *">
             <parameter idref="becomeUninfectiousRate.t:hcv"/>
             <parameter idref="samplingProportion.t:hcv"/>
         </log>
-        <log id="sampling.t:hcv" spec="beast.math.statistic.RPNcalculator" expression="becomeUninfectiousRate.t:hcv samplingProportion.t:hcv *">
+        <log id="sampling.t:hcv" spec="beast.base.inference.util.RPNcalculator" expression="becomeUninfectiousRate.t:hcv samplingProportion.t:hcv *">
             <parameter idref="becomeUninfectiousRate.t:hcv"/>
             <parameter idref="samplingProportion.t:hcv"/>
         </log>
@@ -295,7 +295,7 @@
     </logger>
 
     <!--logger id="treelog.t:hcv" fileName="hcv_bdsky_$(tree).trees" logEvery="4000" mode="tree">
-        <log id="TreeWithMetaDataLogger.t:hcv" spec="beast.evolution.tree.TreeWithMetaDataLogger" tree="@Tree.t:hcv"/>
+        <log id="TreeWithMetaDataLogger.t:hcv" spec="beast.base.evolution.TreeWithMetaDataLogger" tree="@Tree.t:hcv"/>
     </logger-->
 
 </run>

examples/smoothingpriors/ouprior_test1.xml

@@ -1,5 +1,5 @@
 <beast version='2.0'
-       namespace='beast.core:beast.evolution.speciation:beast.core.util:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.math.distributions:beast.evolution.branchratemodel:beast.evolution.likelihood:beast.core.parameter:skylinetools.distributions'>
+       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.speciation:beast.base.util:beast.base.math:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.math.distributions:beast.base.evolution.branchratemodel:beast.base.evolution.likelihood:beast.base.inference.parameter:skylinetools.distributions'>
 
     <!-- Test XML for the Ornstein-Uhlenbeck prior -->
 

examples/smoothingpriors/ouprior_test2.xml

@@ -1,5 +1,5 @@
 <beast version='2.0'
-       namespace='beast.core:beast.evolution.speciation:beast.core.util:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.math.distributions:beast.evolution.branchratemodel:beast.evolution.likelihood:beast.core.parameter:skylinetools.distributions'>
+       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.speciation:beast.base.util:beast.base.math:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.math.distributions:beast.base.evolution.branchratemodel:beast.base.evolution.likelihood:beast.base.inference.parameter:skylinetools.distributions'>
 
     <!-- Test XML for the Ornstein-Uhlenbeck prior -->
 

examples/smoothingpriors/ouprior_test3.xml

@@ -1,18 +1,18 @@
 <beast version='2.0'
-       namespace='beast.core:beast.evolution.speciation:beast.core.util:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.math.distributions:beast.evolution.branchratemodel:beast.evolution.likelihood:beast.core.parameter:skylinetools.distributions'>
+       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.speciation:beast.base.util:beast.base.math:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.math.distributions:beast.base.evolution.branchratemodel:beast.base.evolution.likelihood:beast.base.inference.parameter:skylinetools.distributions'>
 
     <!-- Test XML for the Ornstein-Uhlenbeck prior -->
 
-    <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 spec="MCMC" id="mcmc" chainLength="10000000"> <!--autoOptimize="true"-->
         <state>
@@ -29,7 +29,7 @@
                 <parameter spec='RealParameter' name='mean' id='mu' dimension="1" value="1"/>
                 <parameter spec='RealParameter' name='sigma' id='sigma' dimension="1" value="0.5"/>
                 <parameter spec='RealParameter' name='nu' id='nu' dimension="1" value="0.1"/>
-                <distribution spec='beast.math.distributions.Uniform' name="x0Prior" lower="1.5" upper="2.5"/>
+                <distribution spec='beast.base.inference.distribution.Uniform' name="x0Prior" lower="1.5" upper="2.5"/>
             </distribution>
 
             <prior id="muPrior" name="distribution" x="@mu">                      

examples/smoothingpriors/ouprior_test4.xml

@@ -1,18 +1,18 @@
 <beast version='2.0'
-       namespace='beast.core:beast.evolution.speciation:beast.core.util:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.math.distributions:beast.evolution.branchratemodel:beast.evolution.likelihood:beast.core.parameter:skylinetools.distributions:skylinetools.parameter'>
+       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.speciation:beast.base.util:beast.base.math:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.math.distributions:beast.base.evolution.branchratemodel:beast.base.evolution.likelihood:beast.base.inference.parameter:skylinetools.distributions:skylinetools.parameter'>
 
     <!-- Test XML for the Ornstein-Uhlenbeck prior -->
 
-    <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 spec="MCMC" id="mcmc" chainLength="200000000"> <!--autoOptimize="true"-->
         <state>

examples/smoothingpriors/ouprior_test5.xml

@@ -1,5 +1,5 @@
 <beast version='2.0'
-       namespace='beast.core:beast.evolution.speciation:beast.core.util:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.math.distributions:beast.evolution.branchratemodel:beast.evolution.likelihood:beast.core.parameter:skylinetools.distributions:skylinetools.parameter'>
+       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.speciation:beast.base.util:beast.base.math:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.math.distributions:beast.base.evolution.branchratemodel:beast.base.evolution.likelihood:beast.base.inference.parameter:skylinetools.distributions:skylinetools.parameter'>
 
     <!-- Test XML for the Ornstein-Uhlenbeck prior -->
 

src/beast/evolution/speciation/BirthDeathSkylineModelTestHelper.java

@@ -1,5 +1,6 @@
 package beast.evolution.speciation;
 
+import bdsky.evolution.speciation.BirthDeathSkylineModel;
 import java.util.List;
 
 /**
@@ -17,4 +18,4 @@ public class BirthDeathSkylineModelTestHelper extends BirthDeathSkylineModel {
 
     public List<Double> rChangeTimes() { return rChangeTimes; }
 
-}
+}

src/skylinetools/distributions/BMPrior.java

@@ -1,11 +1,11 @@
 package skylinetools.distributions;
 
-import beast.core.Distribution;
-import beast.core.Function;
-import beast.core.Input;
-import beast.core.State;
-import beast.core.parameter.RealParameter;
-import beast.math.distributions.ParametricDistribution;
+import beast.base.inference.Distribution;
+import beast.base.core.Function;
+import beast.base.core.Input;
+import beast.base.inference.State;
+import beast.base.inference.parameter.RealParameter;
+import beast.base.inference.distribution.ParametricDistribution;
 
 import java.util.List;
 import java.util.Random;

src/skylinetools/distributions/OUPrior.java

@@ -1,11 +1,11 @@
 package skylinetools.distributions;
 
-import beast.core.Distribution;
-import beast.core.Function;
-import beast.core.Input;
-import beast.core.State;
-import beast.core.parameter.RealParameter;
-import beast.math.distributions.ParametricDistribution;
+import beast.base.inference.Distribution;
+import beast.base.core.Function;
+import beast.base.core.Input;
+import beast.base.inference.State;
+import beast.base.inference.parameter.RealParameter;
+import beast.base.inference.distribution.ParametricDistribution;
 
 import java.util.Arrays;
 import java.util.List;

src/skylinetools/parameter/DateParser.java

@@ -1,8 +1,8 @@
 package skylinetools.parameter;
 
-import beast.core.Input;
-import beast.core.parameter.RealParameter;
-import beast.core.util.Log;
+import beast.base.core.Input;
+import beast.base.inference.parameter.RealParameter;
+import beast.base.core.Log;
 
 import java.time.LocalDate;
 import java.time.format.DateTimeFormatter;

src/skylinetools/parameter/RealParameterSequence.java

@@ -1,8 +1,8 @@
 package skylinetools.parameter;
 
-import beast.core.Description;
-import beast.core.Input;
-import beast.core.parameter.RealParameter;
+import beast.base.core.Description;
+import beast.base.core.Input;
+import beast.base.inference.parameter.RealParameter;
 
 import java.util.Arrays;
 

src/skylinetools/util/TreeDateLogger.java

@@ -1,12 +1,12 @@
 package skylinetools.util;
 
-import beast.core.CalculationNode;
-import beast.core.Function;
-import beast.core.Input;
-import beast.core.Loggable;
-import beast.core.parameter.RealParameter;
-import beast.core.util.Log;
-import beast.evolution.tree.Tree;
+import beast.base.inference.CalculationNode;
+import beast.base.core.Function;
+import beast.base.core.Input;
+import beast.base.core.Loggable;
+import beast.base.inference.parameter.RealParameter;
+import beast.base.core.Log;
+import beast.base.evolution.tree.Tree;
 
 import java.io.PrintStream;
 

src/skylinetools/util/TreeDateSlicer.java

@@ -1,9 +1,9 @@
 package skylinetools.util;
 
-import beast.core.Function;
-import beast.core.Input;
-import beast.evolution.tree.Tree;
-import beast.util.HeapSort;
+import beast.base.core.Function;
+import beast.base.core.Input;
+import beast.base.evolution.tree.Tree;
+import beast.base.util.HeapSort;
 
 import java.util.Arrays;
 

src/skylinetools/util/TreeSliceDateLogger.java

@@ -1,9 +1,9 @@
 package skylinetools.util;
 
-import beast.core.CalculationNode;
-import beast.core.Function;
-import beast.core.Input;
-import beast.core.Loggable;
+import beast.base.inference.CalculationNode;
+import beast.base.core.Function;
+import beast.base.core.Input;
+import beast.base.core.Loggable;
 
 import java.io.PrintStream;
 

src/skylinetools/util/TreeSlicer.java

@@ -1,11 +1,11 @@
 package skylinetools.util;
 
-import beast.core.*;
-import beast.core.parameter.Parameter;
-import beast.core.parameter.RealParameter;
-import beast.evolution.tree.Node;
-import beast.evolution.tree.Tree;
-import beast.util.HeapSort;
+import beast.base.core.*;
+import beast.base.inference.parameter.Parameter;
+import beast.base.inference.parameter.RealParameter;
+import beast.base.evolution.tree.Node;
+import beast.base.evolution.tree.Tree;
+import beast.base.util.HeapSort;
 
 import java.util.ArrayList;
 import java.util.Arrays;

test/beast/evolution/speciation/SkylineTimesTest.java

@@ -1,17 +1,17 @@
 package beast.evolution.speciation;
 
-import beast.core.parameter.BooleanParameter;
-import beast.core.parameter.RealParameter;
-import beast.evolution.speciation.BirthDeathSkylineModelTestHelper;
-import beast.evolution.tree.Tree;
-import beast.util.TreeParser;
+import beast.base.inference.parameter.BooleanParameter;
+import beast.base.inference.parameter.RealParameter;
+import bdsky.evolution.speciation.BirthDeathSkylineModelTestHelper;
+import beast.base.evolution.tree.Tree;
+import beast.base.evolution.tree.TreeParser;
 import org.junit.Test;
 import junit.framework.TestCase;
 
 import java.util.List;
 
 /**
- * This test is to check how bdsky (beast.evolution.speciation.BirthDeathSkylineModel) sets change-point times, depending
+ * This test is to check how bdsky (bdsky.evolution.speciation.BirthDeathSkylineModel) sets change-point times, depending
  * on the input.
  *
  * There are 5 different ways to set the change-point times: