convert templates and tests, fix build.xml #8

BEAST2-Dev · Nov 11, 2022 · 999c974 · 999c974
1 parent b1dc41a
commit 999c974
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Showing 18 changed files with 132 additions and 112 deletions.
diff --git a/build.xml b/build.xml
@@ -7,10 +7,14 @@
 
     <!-- Location to check for local copy of beast2 repository -->
     <property name="beastDir" location="../beast2"/>
+    <property name="beastFX" location="../BeastFX" />
+    <property name="lib" location="lib" />
 
-    <!-- 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"/>
+
+    <property name="ZuluJDK" location="../../Downloads/zulu17.36.13-ca-fx-jdk17.0.4-macosx_x64/zulu-17.jdk/Contents/Home/bin/javac" />
 
     <!-- Directories necessary for all BEAST 2 packages -->
     <property name="doc" location="doc"/>
@@ -33,7 +37,7 @@
     <property name="pack" location="${dist}/package"/>
 
     <!-- Prepare for compilation -->
-    <target name="init">
+    <target name="init" depends="clean">
 
         <available file="version.xml" property="versionAvailable"/>
         <fail unless="versionAvailable">
@@ -45,16 +49,13 @@
 
         <!-- 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="${build-lib}">
-            <fileset dir="${lib}" includes="*.jar"/>
-        </copy-->
     </target>
 
     <!-- Get beast -->
@@ -83,6 +84,7 @@
         <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"/>
+            <fileset dir="${build-beast}/beast2-${beast-version}/lib/junit" includes="junit-*.jar"/>
         </copy>
 
         <delete dir="${build-beast}" />
@@ -91,43 +93,84 @@
     <target name="build-local-beast" depends="find-beast" if="localBeastAvailable">
         <echo>Compiling against beast2 source found at ${beastDir}.</echo>
 
+        <!-- Read package name and version from xml file -->
+        <xmlproperty file="${beastDir}/version.xml" prefix="BeastVersionFile" />
+        <property name="beastName" value="${BeastVersionFile.package(name)}" />
+        <property name="beastVersion" value="${BeastVersionFile.package(version)}" />
+
         <mkdir dir="${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>
-        <jar jarfile="${build-lib}/beast2.jar" basedir="${build-beast}" />
+        <jar jarfile="${build-lib}/beast.v${beastVersion}.jar" basedir="${build-beast}" />
         <copy todir="${build-lib}">
             <fileset dir="${beastDir}/lib" includes="*.jar"/>
+            <fileset dir="${beastDir}/lib/junit" includes="junit-*.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">
+    <target name="build-BeastFX" depends="build-beast">
+        <echo>Compiling BeastFX source found at ${beastFX}.</echo>
+
+        <!-- Read package name and version from xml file -->
+        <xmlproperty file="${beastFX}/version.xml" prefix="BeastFXVersionFile" />
+        <property name="beastFXName" value="${BeastFXVersionFile.package(name)}" />
+        <property name="beastFXVersion" value="${BeastFXVersionFile.package(version)}" />
+
+        <mkdir dir="${build-beast}"/>
+
+        <javac target="${targetVersion}" source="${sourceVersion}"
+               srcdir="${beastFX}/src" destdir="${build-beast}"
+               executable="${ZuluJDK}" fork="true" includeantruntime="false">
             <classpath>
                 <pathelement path="${classpath}"/>
                 <fileset dir="${build-lib}" includes="*.jar"/>
             </classpath>
+            <include name="beastfx/**/**" />
         </javac>
-    </target>
 
-    <target name="copy-resources" depends="compile">
-        <copy todir="${build}">
-            <fileset dir="${src}"
-                     includes="**/*.png" />
+        <jar jarfile="${build-lib}/beastFX.v${beastFXVersion}.jar" basedir="${build-beast}" />
+        <copy todir="${build-lib}">
+<!--            <fileset dir="${beastFX}/locallib" includes="*.jar"/>-->
+            <fileset dir="${beastFX}/src" includes="**/*.png" />
+            <fileset dir="${beastFX}/src" includes="**/*.fxml" />
+            <fileset dir="${beastFX}/resources" includes="**/*.css" />
         </copy>
+
+        <delete dir="${build-beast}" />
+
+        <echo message="Successfully compiled beastFX v${beastFXVersion}." />
     </target>
 
+    <!-- Compile -->
+    <target name="compile" depends="build-BeastFX">
+        <javac target="${targetVersion}" source="${sourceVersion}" srcdir="${src}" destdir="${build}"
+               executable="${ZuluJDK}" fork="true" includeantruntime="false">
+            <classpath>
+                <pathelement path="${classpath}"/>
+                <fileset dir="${build-lib}" includes="*.jar"/>
+            </classpath>
+            <include name="codonmodels/**/**" />
+        </javac>
+    </target>
+
+<!--    <target name="copy-resources" depends="compile">-->
+<!--        <copy todir="${build}">-->
+<!--            <fileset dir="${src}"-->
+<!--                     includes="**/*.png" />-->
+<!--        </copy>-->
+<!--    </target>-->
+
     <!-- Prepare for unit test compilation -->
     <target name="init-test" depends="init">
         <mkdir dir="${build-test}"/>
@@ -136,7 +179,7 @@
 
 
     <!-- Compile unit tests -->
-    <target name="compile-test" depends="init-test,compile,copy-resources">
+    <target name="compile-test" depends="init-test,compile">
         <javac target="${targetVersion}" source="${sourceVersion}" srcdir="${test}" destdir="${build-test}" includeantruntime="false">
             <classpath>
                 <pathelement path="${classpath}"/>
@@ -151,7 +194,6 @@
     <target name="test" depends="compile-test">
         <junit printsummary="yes" failureproperty="testFailed" showoutput="true">
             <classpath>
-                <pathelement path="${classpath}"/>
                 <pathelement path="${build}" />
                 <pathelement path="${build-test}" />
                 <fileset dir="${build-lib}" includes="*.jar"/>
@@ -170,7 +212,7 @@
 
 
     <!-- Create BEAST 2 package -->
-    <target name="build" depends="compile,copy-resources">
+    <target name="build" depends="compile">
         <property name="fullName" value="${projName}.v${projVersion}"/>
 
         <mkdir dir="${pack}"/>
@@ -181,30 +223,24 @@
 
         <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-->
+        <copy file="LICENSE" tofile="${pack}/LICENSE" />
 
-        <mkdir dir="${examples}" />
         <copy todir="${pack}/examples">
             <fileset dir="${examples}" includes="**/*.xml" />
             <fileset dir="${examples}" includes="**/*.nex" />
         </copy>
 
-        <mkdir dir="${templates}" />
         <copy todir="${pack}/fxtemplates">
             <fileset dir="${fxtemplates}" includes="*.xml" />
         </copy>
 
-        <mkdir dir="${doc}" />
         <copy todir="${pack}/doc">
             <fileset dir="${doc}" includes="*.tex,*.doc,*.lyx,*.txt"/>
         </copy>

diff --git a/fxtemplates/CMSubstModels.xml b/fxtemplates/CMSubstModels.xml
@@ -1,9 +1,12 @@
-<beast version='2.0'
-       namespace='beast.app.beauti:beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.branchratemodel
-       :beast.evolution.speciation:beast.evolution.tree.coalescent:beast.core.util
-       :beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel
-       :beast.evolution.substitutionmodel:beast.evolution.likelihood:beast.evolution:beast.math.distributions
-       :beast.evolution.alignment:beast.evolution.datatype:codonmodels'>
+<beast version='2.7'
+       namespace='beast.base.core:beast.base.inference:beast.base.inference.util:
+       beast.evolution.nuc:beast.base.evolution.alignment:beast.base.evolution.datatype:
+       beast.base.evolution.branchratemodel:beast.base.evolution.speciation:beast.base.evolution.tree.coalescent:
+       beast.base.evolution.operator:beast.base.inference.operator:beast.evolution:beast.base.math.distributions:
+       beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood:
+       codonmodels:codonmodels.evolution:codonmodels.evolution.alignment:codonmodels.evolution.datatype:
+       codonmodels.evolution.likelihood:codonmodels.evolution.operators:codonmodels.evolution.tree'
+       templateinfo='sub-template for codon substitution models'>
 
 
     <mergewith point='codonSubstModelTemplates'>

diff --git a/fxtemplates/CodonSubstModels.xml b/fxtemplates/CodonSubstModels.xml
@@ -1,9 +1,11 @@
-<beast version='2.0'
-       namespace='beast.app.beauti:beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.branchratemodel
-       :beast.evolution.speciation:beast.evolution.tree.coalescent:beast.base.util:beast.util
-       :beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel
-       :beast.evolution.substitutionmodel:beast.evolution.likelihood:beast.evolution:beast.math.distributions
-       :beast.evolution.alignment:beast.evolution.datatype:codonmodels'
+<beast version='2.7'
+       namespace='beast.base.core:beast.base.inference:beast.base.inference.util:
+       beast.evolution.nuc:beast.base.evolution.alignment:beast.base.evolution.datatype:
+       beast.base.evolution.branchratemodel:beast.base.evolution.speciation:beast.base.evolution.tree.coalescent:
+       beast.base.evolution.operator:beast.base.inference.operator:beast.evolution:beast.base.math.distributions:
+       beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood:
+       codonmodels:codonmodels.evolution:codonmodels.evolution.alignment:codonmodels.evolution.datatype:
+       codonmodels.evolution.likelihood:codonmodels.evolution.operators:codonmodels.evolution.tree'
 	templateinfo='template for codon substitution models'>
 
 <map name='connect' reserved='true'>beastfx.app.inputeditor.BeautiConnector</map>
@@ -19,7 +21,7 @@
 <map name='InverseGamma'>beast.base.inference.distribution.InverseGamma</map>
 <map name='prior'>beast.base.inference.distribution.Prior</map>
 
-    <beauticonfig spec='BeautiConfig'
+    <beauticonfig spec='beastfx.app.inputeditor.BeautiConfig'
         inputLabelMap='beast.base.inference.MCMC.operator=Operators,
 	        beast.base.inference.MCMC.logger=Loggers,
 			beast.base.evolution.sitemodel.SiteModel.mutationRate =Substitution Rate,
@@ -82,10 +84,7 @@
 	        beast.base.evolution.substitutionmodel.MTREV.frequencies,
 	        beast.base.evolution.substitutionmodel.GTR.rates,
 	        beast.base.evolution.substitutionmodel.JukesCantor.frequencies,
-	        codonmodels.M0Model.rates,
-	        codonmodels.M0Model.eigenSystem,
-	        codonmodels.M0Model.verbose,
-            beast.base.inference.distribution.Prior.x,
+	        beast.base.inference.distribution.Prior.x,
             beast.base.evolution.tree.MRCAPrior.tree,
             beast.base.evolution.tree.MRCAPrior.monophyletic,
             beast.base.evolution.tree.MRCAPrior.taxonset,
@@ -101,71 +100,73 @@
             beast.base.evolution.tree.coalescent.BayesianSkyline.treeIntervals,
             beast.base.evolution.tree.coalescent.BayesianSkyline.groupSizes,
             beast.base.evolution.tree.coalescent.BayesianSkyline.popSizes,
-            beast.base.evolution.speciation.YuleModel.originHeight
-            '
+            beast.base.evolution.speciation.YuleModel.originHeight,
+            codonmodels.M0Model.rates,
+	        codonmodels.M0Model.eigenSystem,
+	        codonmodels.M0Model.verbose'
         buttonLabelMap='beast.app.beauti.BeautiInitDlg.&gt;&gt; details=Edit parameters'
     >
         <!--disableMenus='Mode'-->
 
-        <panel spec='BeautiPanelConfig' panelname="Partitions" tiptext="Codon Data Partitions"
+        <panel spec='beastfx.app.inputeditor.BeautiPanelConfig' panelname="Partitions" tiptext="Codon Data Partitions"
             path='distribution/distribution[id="likelihood"]/distribution/data'
             hasPartitions="none" icon='2220.png.x' forceExpansion='FALSE'
             type='beast.base.evolution.alignment.Alignment'
         />
 		<mergepoint id='aux-partitions-panels'/>
 
-		<panel spec='BeautiPanelConfig' panelname="Tip Dates" tiptext="Allows to specify data that a taxon was sampled"
+		<panel spec='beastfx.app.inputeditor.BeautiPanelConfig' panelname="Tip Dates" tiptext="Allows to specify data that a taxon was sampled"
             path='tree'
             hasPartitions="Tree" icon='2.png.x' forceExpansion='TRUE'
             isVisible='true'
         />
 		<mergepoint id='aux-tipdates-panels'/>
 
-        <panel spec='BeautiPanelConfig' panelname="Site Model"
+        <panel spec='beastfx.app.inputeditor.BeautiPanelConfig' panelname="Site Model"
                tiptext="Site model and codon substitution model specifications"
                path='siteModel' hasPartitions="SiteModel" icon='3.png.x' forceExpansion='TRUE'
         />
 
 		<mergepoint id='aux-sitemodel-panels'/>
 
-		<panel spec='BeautiPanelConfig' panelname="Clock Model" tiptext="Clock model"
+		<panel spec='beastfx.app.inputeditor.BeautiPanelConfig' panelname="Clock Model" tiptext="Clock model"
             path='branchRateModel'
             hasPartitions="ClockModel" icon='4.png.x' forceExpansion='TRUE'
         />
 		<mergepoint id='aux-clockmodel-panels'/>
-		<panel spec='BeautiPanelConfig' panelname="Initialization" tiptext="Initial state"
+		<panel spec='beastfx.app.inputeditor.BeautiPanelConfig' panelname="Initialization" tiptext="Initial state"
             path='state/stateNode'
             hasPartitions="none" icon='6.png.x' forceExpansion='TRUE_START_COLLAPSED'
             isVisible='false'
         />
 		<mergepoint id='aux-initilisation-panels'/>
-		<panel spec='BeautiPanelConfig' panelname="Starting tree" tiptext="Starting tree"
+		<panel spec='beastfx.app.inputeditor.BeautiPanelConfig' panelname="Starting tree" tiptext="Starting tree"
             path='init'
             hasPartitions="none" icon='6.png.x' forceExpansion='TRUE'
             isVisible='false'
         />
 
-		<panel spec='BeautiPanelConfig' panelname="Priors" tiptext="Other priors"
+		<panel spec='beastfx.app.inputeditor.BeautiPanelConfig' panelname="Priors" tiptext="Other priors"
             path='distribution/distribution[id="prior"]/distribution'
             hasPartitions="none" icon='7.png.x' forceExpansion='TRUE_START_COLLAPSED'
             type='beast.base.inference.Distribution'
         />
 		<mergepoint id='aux-priors-panels'/>
 
-		<panel spec='BeautiPanelConfig' panelname="Operators" tiptext="MCMC Operator details"
+		<panel spec='beastfx.app.inputeditor.BeautiPanelConfig' panelname="Operators" tiptext="MCMC Operator details"
             path='operator'
             hasPartitions="none" icon='8.png.x' forceExpansion='TRUE_START_COLLAPSED'
             isVisible='false' buttonStatus='ADD_ONLY'
         />
 		<mergepoint id='aux-operators-panels'/>
 
-		<panel spec='BeautiPanelConfig' panelname="MCMC" tiptext="MCMC parameters"
+		<panel spec='beastfx.app.inputeditor.BeautiPanelConfig' panelname="MCMC" tiptext="MCMC parameters"
             path=''
             hasPartitions="none" icon='9.png.x' forceExpansion='TRUE'
         />
 		<mergepoint id='aux-panels'/>
 
-		<alignmentProvider id="Codon Alignment" spec='CodonAlignmentProvider' template='@CodonPartitionTemplate'/>
+		<alignmentProvider id="Codon Alignment" spec='codonmodels.app.beauti.CodonAlignmentProvider' template='@CodonPartitionTemplate'/>
 
 
         <partitiontemplate id='CodonPartitionTemplate' spec='BeautiSubTemplate' class='beast.base.evolution.likelihood.ThreadedTreeLikelihood' mainid='mcmc'>

diff --git a/src/test/beast/evolution/CodonData.java → test/codonmodels/evolution/CodonData.java b/src/test/beast/evolution/CodonData.java → test/codonmodels/evolution/CodonData.java
@@ -1,12 +1,12 @@
-package test.beast.evolution;
+package codonmodels.evolution;
 
-import beast.base.inference.parameter.RealParameter;
 import beast.base.evolution.alignment.Alignment;
 import beast.base.evolution.alignment.Sequence;
 import beast.base.evolution.likelihood.TreeLikelihood;
 import beast.base.evolution.sitemodel.SiteModel;
 import beast.base.evolution.tree.Tree;
 import beast.base.evolution.tree.TreeParser;
+import beast.base.inference.parameter.RealParameter;
 import codonmodels.CodonFrequencies;
 import codonmodels.M0Model;
 import codonmodels.evolution.datatype.Codon;

diff --git a/...olution/alignment/CodonAlignmentTest.java → ...olution/alignment/CodonAlignmentTest.java b/...olution/alignment/CodonAlignmentTest.java → ...olution/alignment/CodonAlignmentTest.java
@@ -1,12 +1,10 @@
-package test.beast.evolution.alignment;
+package codonmodels.evolution.alignment;
 
 import beast.base.evolution.alignment.Alignment;
 import beast.base.evolution.alignment.Sequence;
-import codonmodels.evolution.alignment.CodonAlignment;
+import codonmodels.evolution.CodonData;
 import codonmodels.evolution.datatype.Codon;
-
 import org.junit.Test;
-import test.beast.evolution.CodonData;
 
 import java.util.List;
 

diff --git a/...t/beast/evolution/datatype/CodonTest.java → ...nmodels/evolution/datatype/CodonTest.java b/...t/beast/evolution/datatype/CodonTest.java → ...nmodels/evolution/datatype/CodonTest.java
@@ -1,12 +1,10 @@
-package test.beast.evolution.datatype;
+package codonmodels.evolution.datatype;
 
 import beast.base.evolution.datatype.DataType;
 import beast.base.evolution.datatype.Nucleotide;
-import codonmodels.evolution.datatype.Codon;
-
+import codonmodels.evolution.CodonData;
 import org.junit.Before;
 import org.junit.Test;
-import test.beast.evolution.CodonData;
 
 import java.util.ArrayList;
 import java.util.Arrays;