Merge pull request #14 from jordandouglas/master

CoalRe for beast 2.7
nicfel · Dec 15, 2022 · 3cb6fdd · 3cb6fdd
2 parents 9369ea7 + 60e835a
commit 3cb6fdd
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Showing 73 changed files with 314 additions and 237 deletions.
diff --git a/Dockerfile b/Dockerfile
@@ -9,3 +9,21 @@ WORKDIR /root
 ADD . ./
 
 ENTRYPOINT ant test
+
+
+
+# Dockerfile to build container for unit testing
+
+FROM debian:stable
+
+RUN apt-get update
+RUN apt-get install -y openjdk-17-jdk openjfx
+RUN apt-get install -y ant
+RUN apt-get install -y jblas
+
+WORKDIR /root
+
+ADD . ./
+
+
+ENTRYPOINT JAVA_FX_HOME=/usr/share/java/ ant test
diff --git a/build.xml b/build.xml
@@ -15,7 +15,7 @@
     <!-- 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
@@ -44,8 +44,8 @@
 
         <!-- 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}"/>
@@ -100,11 +100,12 @@
             <classpath>
                 <pathelement path="${classpath}"/>
                 <fileset dir="${beastDir}/lib" includes="*.jar"/>
+                <pathelement path="../BeastFX/build"/>
             </classpath>
         </javac>
         <jar jarfile="${build-lib}/beast2.jar" basedir="${build-beast}" />
         <copy todir="${build-lib}">
-            <fileset dir="${beastDir}/lib" includes="*.jar"/>
+            <fileset dir="${beastDir}/lib" includes="colt.jar"/>
         </copy>
 
         <delete dir="${build-beast}" />
@@ -118,6 +119,7 @@
             <classpath>
                 <pathelement path="${classpath}"/>
                 <fileset dir="${build-lib}" includes="*.jar"/>
+                <pathelement path="../BeastFX/build"/>
             </classpath>
         </javac>
     </target>
@@ -143,6 +145,10 @@
                 <pathelement path="${classpath}"/>
                 <pathelement path="${build}" />
                 <fileset dir="${build-lib}" includes="*.jar"/>
+                <fileset dir="${beastDir}/lib" includes="*.jar"/>
+                <fileset dir="${beastDir}/lib/junit" includes="*.jar"/>
+                <pathelement path="../BeastFX/build"/>
+                <pathelement path="${beastDir}/build"/>
             </classpath>
         </javac>
     </target>
@@ -156,6 +162,7 @@
                 <pathelement path="${build}" />
                 <pathelement path="${build-test}" />
                 <fileset dir="${build-lib}" includes="*.jar"/>
+                <fileset dir="${beastDir}/lib/junit" includes="*.jar"/>
             </classpath>
             <batchtest fork="yes" todir="${test-reports}">
                 <fileset dir="${test}">
@@ -176,7 +183,7 @@
 
         <mkdir dir="${pack}"/>
         <mkdir dir="${pack}/examples"/>
-        <mkdir dir="${pack}/templates"/>
+        <mkdir dir="${pack}/fxtemplates"/>
         <mkdir dir="${pack}/lib"/>
         <mkdir dir="${pack}/doc"/>
 
@@ -202,7 +209,7 @@
         </copy>
 
         <mkdir dir="${templates}" />
-        <copy todir="${pack}/templates">
+        <copy todir="${pack}/fxtemplates">
             <fileset dir="${templates}" includes="*.xml" />
         </copy>
 

diff --git a/templates/CoalRe.xml → fxtemplates/CoalRe.xml b/templates/CoalRe.xml → fxtemplates/CoalRe.xml
@@ -23,22 +23,20 @@
                      inlineInputs="coalre.distribution.CoalescentWithReassortment.networkIntervals"
                      suppressInputs="coalre.distribution.NetworkIntervals.network">
             <![CDATA[
-            <stateNode id="reassortmentRateCwR.alltrees" spec="beast.core.parameter.RealParameter" value="0.1" estimate="true"/>
-            <stateNode id="popSizeCwR.alltrees" spec="beast.core.parameter.RealParameter" value="1.0" estimate="true"/>
-            <stateNode id="binomialProbCwR.alltrees" spec="beast.core.parameter.RealParameter" lower="0.0" upper="1.0" value="0.5" estimate="false"/>
+            <stateNode id="reassortmentRateCwR.alltrees" spec="beast.base.inference.parameter.RealParameter" value="0.1" estimate="true"/>
+            <stateNode id="popSizeCwR.alltrees" spec="beast.base.inference.parameter.RealParameter" value="1.0" estimate="true"/>
+            <stateNode id="binomialProbCwR.alltrees" spec="beast.base.inference.parameter.RealParameter" lower="0.0" upper="1.0" value="0.5" estimate="false"/>
 
             <stateNode id="networkCwR.alltrees" spec="coalre.simulator.SimulatedCoalescentNetwork" nSegments="1"
                         enableSegmentTreeUpdate="false" estimate="true">
-                <reassortmentRate spec="beast.core.parameter.RealParameter" value="0.0"/>
-                <populationModel spec="beast.evolution.tree.coalescent.ConstantPopulation">
-                    <popSize spec="beast.core.parameter.RealParameter" value="1.0"/>
+                <reassortmentRate spec="beast.base.inference.parameter.RealParameter" value="0.0"/>
+                <populationModel spec="beast.base.evolution.tree.coalescent.ConstantPopulation">
+                    <popSize spec="beast.base.inference.parameter.RealParameter" value="1.0"/>
                 </populationModel>
 
-                <taxonSet spec="beast.evolution.alignment.TaxonSet" alignment="@$(n)"/>
+                <taxonSet spec="beast.base.evolution.alignment.TaxonSet" alignment="@$(n)"/>
             </stateNode>
             
-            <init id="networkCwR.segmentInitializer" spec="SegmentTreeInitializer" network="@networkCwR.alltrees">
-            </init>
 
             <init id="segmentTreeInitializerCwR.t:$(n)" spec="coalre.network.SegmentTreeInitializer"
                   network="@networkCwR.alltrees">
@@ -49,7 +47,7 @@
 
             <prior spec="coalre.distribution.CoalescentWithReassortment" id="CoalescentWithReassortmentPrior.alltrees">
                 <reassortmentRate idref="reassortmentRateCwR.alltrees"/>
-                <populationModel id="constantPopSizeCwR.alltrees" spec="beast.evolution.tree.coalescent.ConstantPopulation">
+                <populationModel id="constantPopSizeCwR.alltrees" spec="beast.base.evolution.tree.coalescent.ConstantPopulation">
                     <popSize idref="popSizeCwR.alltrees"/>
                 </populationModel>
                 <networkIntervals id="networkIntervalsCwR.alltrees" spec="coalre.distribution.NetworkIntervals">
@@ -68,7 +66,7 @@
             </prior>
 
             <prior id="binomialProbCwRPrior.alltrees" x="@binomialProbCwR.alltrees">
-                <distr spec="beast.math.distributions.Uniform" lower="0" upper="1"/>
+                <distr spec="beast.base.inference.distribution.Uniform" lower="0" upper="1"/>
             </prior>
 
 

diff --git a/lib/antlr-runtime-4.7.jar b/lib/antlr-runtime-4.7.jar
diff --git a/src/coalre/distribution/CoalescentWithReassortment.java b/src/coalre/distribution/CoalescentWithReassortment.java
@@ -1,10 +1,10 @@
 package coalre.distribution;
 
-import beast.core.CalculationNode;
-import beast.core.Description;
-import beast.core.Function;
-import beast.core.Input;
-import beast.evolution.tree.coalescent.PopulationFunction;
+import beast.base.inference.CalculationNode;
+import beast.base.core.Description;
+import beast.base.core.Function;
+import beast.base.core.Input;
+import beast.base.evolution.tree.coalescent.PopulationFunction;
 
 import java.util.List;
 

diff --git a/src/coalre/distribution/NetworkDistribution.java b/src/coalre/distribution/NetworkDistribution.java
@@ -1,9 +1,9 @@
 package coalre.distribution;
 
-import beast.core.Distribution;
-import beast.core.Input;
-import beast.core.Input.Validate;
-import beast.core.State;
+import beast.base.inference.Distribution;
+import beast.base.core.Input;
+import beast.base.core.Input.Validate;
+import beast.base.inference.State;
 
 import java.util.List;
 import java.util.Random;

diff --git a/src/coalre/distribution/NetworkIntervals.java b/src/coalre/distribution/NetworkIntervals.java
@@ -2,11 +2,11 @@
 
 
 
-import beast.core.CalculationNode;
-import beast.core.Function;
-import beast.core.Input;
-import beast.core.Input.Validate;
-import beast.core.parameter.RealParameter;
+import beast.base.inference.CalculationNode;
+import beast.base.core.Function;
+import beast.base.core.Input;
+import beast.base.core.Input.Validate;
+import beast.base.inference.parameter.RealParameter;
 import coalre.network.Network;
 
 import java.util.ArrayList;

diff --git a/src/coalre/distribution/TipPrior.java b/src/coalre/distribution/TipPrior.java
@@ -8,16 +8,16 @@
 import java.util.Random;
 import java.util.Set;
 
-import beast.core.Description;
-import beast.core.Distribution;
-import beast.core.Input;
-import beast.core.Input.Validate;
-import beast.core.State;
-import beast.core.parameter.RealParameter;
-import beast.evolution.alignment.TaxonSet;
-import beast.evolution.tree.Node;
-import beast.evolution.tree.Tree;
-import beast.math.distributions.ParametricDistribution;
+import beast.base.core.Description;
+import beast.base.inference.Distribution;
+import beast.base.core.Input;
+import beast.base.core.Input.Validate;
+import beast.base.inference.State;
+import beast.base.inference.parameter.RealParameter;
+import beast.base.evolution.alignment.TaxonSet;
+import beast.base.evolution.tree.Node;
+import beast.base.evolution.tree.Tree;
+import beast.base.inference.distribution.ParametricDistribution;
 import coalre.network.Network;
 import coalre.network.NetworkNode;
 

diff --git a/src/coalre/distribution/emptyNetworkEdgesPrior.java b/src/coalre/distribution/emptyNetworkEdgesPrior.java
@@ -1,13 +1,13 @@
 package coalre.distribution;
 
-import beast.core.Description;
-import beast.core.Function;
-import beast.core.Input;
-import beast.core.Input.Validate;
-import beast.core.parameter.IntegerParameter;
-import beast.core.parameter.RealParameter;
-import beast.evolution.tree.coalescent.PopulationFunction;
-import beast.math.distributions.ParametricDistribution;
+import beast.base.core.Description;
+import beast.base.core.Function;
+import beast.base.core.Input;
+import beast.base.core.Input.Validate;
+import beast.base.inference.parameter.IntegerParameter;
+import beast.base.inference.parameter.RealParameter;
+import beast.base.evolution.tree.coalescent.PopulationFunction;
+import beast.base.inference.distribution.ParametricDistribution;
 import coalre.network.NetworkEdge;
 
 import java.util.BitSet;

diff --git a/src/coalre/network/Network.java b/src/coalre/network/Network.java
@@ -1,9 +1,9 @@
 package coalre.network;
 
-import beast.core.StateNode;
-import beast.evolution.alignment.TaxonSet;
-import beast.evolution.tree.Node;
-import beast.evolution.tree.Tree;
+import beast.base.inference.StateNode;
+import beast.base.evolution.alignment.TaxonSet;
+import beast.base.evolution.tree.Node;
+import beast.base.evolution.tree.Tree;
 import coalre.network.parser.NetworkBaseVisitor;
 import coalre.network.parser.NetworkLexer;
 import coalre.network.parser.NetworkParser;

diff --git a/src/coalre/network/NetworkNode.java b/src/coalre/network/NetworkNode.java
@@ -6,8 +6,8 @@
 import java.util.Map;
 import java.util.TreeMap;
 
-import beast.evolution.tree.TraitSet;
-import beast.evolution.tree.Tree;
+import beast.base.evolution.tree.TraitSet;
+import beast.base.evolution.tree.Tree;
 
 public class NetworkNode {
 

diff --git a/src/coalre/network/SegmentTreeInitializer.java b/src/coalre/network/SegmentTreeInitializer.java
@@ -1,10 +1,10 @@
 package coalre.network;
 
-import beast.core.BEASTObject;
-import beast.core.Input;
-import beast.core.StateNode;
-import beast.core.StateNodeInitialiser;
-import beast.evolution.tree.Tree;
+import beast.base.core.BEASTObject;
+import beast.base.core.Input;
+import beast.base.inference.StateNode;
+import beast.base.inference.StateNodeInitialiser;
+import beast.base.evolution.tree.Tree;
 import cern.colt.Arrays;
 
 import java.util.ArrayList;

diff --git a/src/coalre/networkannotator/ColoredTreeExtractor.java b/src/coalre/networkannotator/ColoredTreeExtractor.java
@@ -17,14 +17,14 @@
 
 package coalre.networkannotator;
 
-import beast.core.BEASTObject;
-import beast.core.Function;
-import beast.core.parameter.Parameter;
-import beast.core.parameter.RealParameter;
-import beast.core.util.Log;
-import beast.evolution.branchratemodel.BranchRateModel;
-import beast.evolution.tree.Node;
-import beast.evolution.tree.Tree;
+import beast.base.core.BEASTObject;
+import beast.base.core.Function;
+import beast.base.inference.parameter.Parameter;
+import beast.base.inference.parameter.RealParameter;
+import beast.base.core.Log;
+import beast.base.evolution.branchratemodel.BranchRateModel;
+import beast.base.evolution.tree.Node;
+import beast.base.evolution.tree.Tree;
 import coalre.network.Network;
 import coalre.network.NetworkEdge;
 import coalre.network.NetworkNode;

diff --git a/src/coalre/networkannotator/NetworkCladeSystem.java b/src/coalre/networkannotator/NetworkCladeSystem.java
@@ -11,7 +11,7 @@
 
 import javax.swing.plaf.synth.SynthSeparatorUI;
 
-import beast.math.statistic.DiscreteStatistics;
+import beast.base.util.DiscreteStatistics;
 import coalre.network.Network;
 import coalre.network.NetworkEdge;
 import coalre.network.NetworkNode;

diff --git a/src/coalre/networkannotator/ReassortmentAnnotator.java b/src/coalre/networkannotator/ReassortmentAnnotator.java
@@ -17,7 +17,7 @@
 
 package coalre.networkannotator;
 
-import beast.util.Randomizer;
+import beast.base.util.Randomizer;
 import coalre.network.Network;
 import coalre.network.NetworkEdge;
 import coalre.network.NetworkNode;

diff --git a/src/coalre/networkannotator/ReassortmentDistance.java b/src/coalre/networkannotator/ReassortmentDistance.java
@@ -17,7 +17,7 @@
 
 package coalre.networkannotator;
 
-import beast.core.util.Log;
+import beast.base.core.Log;
 import coalre.network.Network;
 import coalre.network.NetworkEdge;
 import coalre.network.NetworkNode;

diff --git a/src/coalre/networkannotator/ReassortmentEventCladeSystem.java b/src/coalre/networkannotator/ReassortmentEventCladeSystem.java
@@ -10,7 +10,7 @@
 import java.util.List;
 import java.util.Set;
 
-import beast.math.statistic.DiscreteStatistics;
+import beast.base.util.DiscreteStatistics;
 import coalre.network.Network;
 import coalre.network.NetworkEdge;
 import coalre.network.NetworkNode;

diff --git a/src/coalre/networkannotator/ReassortmentEventProbabilities.java b/src/coalre/networkannotator/ReassortmentEventProbabilities.java
@@ -17,7 +17,7 @@
 
 package coalre.networkannotator;
 
-import beast.core.util.Log;
+import beast.base.core.Log;
 import coalre.network.Network;
 import coalre.network.NetworkNode;
 

diff --git a/src/coalre/networkannotator/ReassortmentNetworkSummarizer.java b/src/coalre/networkannotator/ReassortmentNetworkSummarizer.java
@@ -17,7 +17,7 @@
 
 package coalre.networkannotator;
 
-import beast.core.util.Log;
+import beast.base.core.Log;
 import coalre.network.Network;
 import coalre.network.NetworkNode;
 

diff --git a/src/coalre/networkannotator/TrunkReassortment.java b/src/coalre/networkannotator/TrunkReassortment.java
@@ -17,7 +17,7 @@
 
 package coalre.networkannotator;
 
-import beast.core.util.Log;
+import beast.base.core.Log;
 import coalre.network.Network;
 import coalre.network.NetworkEdge;
 import coalre.network.NetworkNode;

diff --git a/src/coalre/operators/AddRemoveReassortment.java b/src/coalre/operators/AddRemoveReassortment.java
@@ -1,8 +1,8 @@
 package coalre.operators;
 
-import beast.core.Input;
-import beast.util.Package;
-import beast.util.Randomizer;
+import beast.base.core.Input;
+import beast.pkgmgmt.Package;
+import beast.base.util.Randomizer;
 import coalre.network.Network;
 import coalre.network.NetworkEdge;
 import coalre.network.NetworkNode;

diff --git a/src/coalre/operators/AddRemoveReassortmentCoalescent.java b/src/coalre/operators/AddRemoveReassortmentCoalescent.java
@@ -1,7 +1,7 @@
 package coalre.operators;
 
-import beast.core.Input;
-import beast.util.Randomizer;
+import beast.base.core.Input;
+import beast.base.util.Randomizer;
 import coalre.distribution.CoalescentWithReassortment;
 import coalre.distribution.NetworkEvent;
 import coalre.network.NetworkEdge;