more v2.7 migration

BEAST2-Dev · Oct 9, 2022 · 94bc3da · 94bc3da
1 parent e39e497
commit 94bc3da
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Showing 12 changed files with 184 additions and 162 deletions.
diff --git a/build.xml b/build.xml
@@ -7,6 +7,7 @@
 
     <!-- Location to check for local copy of beast2 repository -->
     <property name="beastDir" location="../beast2"/>
+    <property name="BeastFXDir" location="../BeastFX"/>
 
     <!-- BEAST 2 currently uses Java 1.8 -->
     <property name="sourceVersion" value="1.8"/>
@@ -16,7 +17,7 @@
     <property name="doc" location="doc"/>
     <property name="examples" location="examples"/>
     <property name="scripts" location="scripts"/>
-    <property name="templates" location="templates"/>
+    <property name="fxtemplates" location="fxtemplates"/>
 
     <!-- BEAST branch and version to build against
          (only different for version tags because of
@@ -45,8 +46,8 @@
 
         <!-- 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}"/>
@@ -178,7 +179,7 @@
         <mkdir dir="${pack}"/>
         <mkdir dir="${pack}/examples"/>
         <mkdir dir="${pack}/scripts"/>
-        <mkdir dir="${pack}/templates"/>
+        <mkdir dir="${pack}/fxtemplates"/>
         <mkdir dir="${pack}/lib"/>
         <mkdir dir="${pack}/doc"/>
 
@@ -188,7 +189,11 @@
         <copy todir="${pack}/lib">
             <fileset dir="${lib}" includes="*.jar" />
         </copy>
-        <jar jarfile="${pack}/lib/${fullName}.jar" basedir="${build}" />
+        <jar jarfile="${pack}/lib/${fullName}.jar">
+            <fileset  dir="${build}">
+                <include name="bdsky/**/*.class"/>
+            </fileset>
+        </jar>
 
         <copy file="README.md" tofile="${pack}/README" />
         <copy file="COPYING" todir="${pack}" />
@@ -211,8 +216,8 @@
 
 
         <mkdir dir="${templates}" />
-        <copy todir="${pack}/templates">
-            <fileset dir="${templates}" includes="*.xml" />
+        <copy todir="${pack}/fxtemplates">
+            <fileset dir="${fxtemplates}" includes="*.xml" />
         </copy>
 
         <mkdir dir="${doc}" />
@@ -305,7 +310,7 @@
         <mkdir dir="${test}"/>
         <mkdir dir="${lib}"/>
         <mkdir dir="${examples}"/>
-        <mkdir dir="${templates}"/>
+        <mkdir dir="${fxtemplates}"/>
         <mkdir dir="${doc}"/>
 
         <echo/>
@@ -316,7 +321,7 @@
         <echo>${test} - your junit tests go here (You _are_ going to write, those, aren't you!)</echo>
         <echo>${doc} - your documentation goes here</echo>
         <echo>${examples} - your example XML scripts go here</echo>
-        <echo>${templates} - your BEAUti templates go here</echo>
+        <echo>${fxtemplates} - your BEAUti templates go here</echo>
         <echo/>
         <echo>To build your package, just type "ant" at the command line.</echo>
         <echo/>

diff --git a/examples/BDSKY_contemp.xml b/examples/BDSKY_contemp.xml
@@ -32,7 +32,7 @@
 
 	<tree spec="beast.base.evolution.tree.ClusterTree" clusterType="upgma" taxa="@alignment" id="tree"/>
 
-	<BirthDeathSkylineModel spec="BirthDeathSkylineModel" id="birthDeath" tree="@tree" contemp="true">
+	<BirthDeathSkylineModel spec="bdsky.evolution.speciation.BirthDeathSkylineModel" id="birthDeath" tree="@tree" contemp="true">
 		<parameter name="origin" id="origin" value ="100" lower="0."/>  	
 
 		<!-- dimension of reproductiveNumber, becomeUninfectiousRate and samplingProportion must be either equal to intervalNumber, or 1 (i.e. rate is constant over time) -->

diff --git a/examples/BDSKY_sequential.xml b/examples/BDSKY_sequential.xml
@@ -32,7 +32,7 @@
 
 	<tree id="tree" spec="beast.base.evolution.tree.ClusterTree" clusterType="upgma" taxa="@alignment"/>
 
-	<BirthDeathSkylineModel spec="BirthDeathSkylineModel" id="birthDeath" tree="@tree">
+	<BirthDeathSkylineModel spec="bdsky.evolution.speciation.BirthDeathSkylineModel" id="birthDeath" tree="@tree">
 		<parameter name="origin" id="origin" value ="100" lower="0."/>  	
 
 		<!-- dimension of reproductiveNumber, becomeUninfectiousRate and samplingProportion must be either equal to intervalNumber, or 1 (i.e. rate is constant over time) -->

diff --git a/examples/HCV_ad_e1_type4_rev.xml b/examples/HCV_ad_e1_type4_rev.xml
@@ -70,7 +70,7 @@
 
     <tree spec='beast.base.evolution.tree.ClusterTree' id='tree' clusterType='upgma' taxa='@alignment'/>
 
-	<BirthDeathSkylineModel spec="BirthDeathSkylineModel" id="birthDeath" tree="@tree" contemp="true" birthRateTimesRelative="true" deathRateTimesRelative="true">
+	<BirthDeathSkylineModel spec="bdsky.evolution.speciation.BirthDeathSkylineModel" id="birthDeath" tree="@tree" contemp="true" birthRateTimesRelative="true" deathRateTimesRelative="true">
 
 		<parameter name="intervalTimes" id="intervalTimes" value="0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9"/>
 		<parameter name="origin" id="orig_root" value ="1" lower="0." upper="1000."/>

diff --git a/fxtemplates/BDSKY_contemp_bdsparam.xml b/fxtemplates/BDSKY_contemp_bdsparam.xml
@@ -4,37 +4,37 @@
 <!-- tree priors -->
 <mergewith point='treePriorTemplates'> 
 
-        <subtemplate id='BirthDeathSkylineContemporaryBDSParam' class='beast.evolution.speciation.BirthDeathSkylineModel' mainid='BirthDeathSkyContemporaryBDSParam.t:$(n)'
-suppressInputs='beast.evolution.speciation.BirthDeathSkylineModel.intervalTimes,
-	beast.evolution.speciation.BirthDeathSkylineModel.reproductiveNumber,
-	beast.evolution.speciation.BirthDeathSkylineModel.becomeUninfectiousRate,
-	beast.evolution.speciation.BirthDeathSkylineModel.samplingProportion,
-	beast.evolution.speciation.BirthDeathSkylineModel.samplingRate,
-	beast.evolution.speciation.BirthDeathSkylineModel.S0,
-	beast.evolution.speciation.BirthDeathSkylineModel.tree,
-	beast.evolution.speciation.BirthDeathSkylineModel.treeIntervals,
-	beast.evolution.speciation.BirthDeathSkylineModel.forceRateChange, 
-	beast.evolution.speciation.BirthDeathSkylineModel.conditionOnSurvival, 
-	beast.evolution.speciation.BirthDeathSkylineModel.conditionOnRoot, 
+        <subtemplate id='BirthDeathSkylineContemporaryBDSParam' class='bdsky.evolution.speciation.BirthDeathSkylineModel' mainid='BirthDeathSkyContemporaryBDSParam.t:$(n)'
+suppressInputs='bdsky.evolution.speciation.BirthDeathSkylineModel.intervalTimes,
+	bdsky.evolution.speciation.BirthDeathSkylineModel.reproductiveNumber,
+	bdsky.evolution.speciation.BirthDeathSkylineModel.becomeUninfectiousRate,
+	bdsky.evolution.speciation.BirthDeathSkylineModel.samplingProportion,
+	bdsky.evolution.speciation.BirthDeathSkylineModel.samplingRate,
+	bdsky.evolution.speciation.BirthDeathSkylineModel.S0,
+	bdsky.evolution.speciation.BirthDeathSkylineModel.tree,
+	bdsky.evolution.speciation.BirthDeathSkylineModel.treeIntervals,
+	bdsky.evolution.speciation.BirthDeathSkylineModel.forceRateChange, 
+	bdsky.evolution.speciation.BirthDeathSkylineModel.conditionOnSurvival, 
+	bdsky.evolution.speciation.BirthDeathSkylineModel.conditionOnRoot, 
 	beast.base.inference.distribution.MarkovChainDistribution.parameter,
-	beast.evolution.speciation.BirthDeathSkylineModel.birthRateTimesRelative,
-	beast.evolution.speciation.BirthDeathSkylineModel.deathRateTimesRelative,
-	beast.evolution.speciation.BirthDeathSkylineModel.samplingRateTimesRelative,
-	beast.evolution.speciation.BirthDeathSkylineModel.reverseTimeArrays,
-	beast.evolution.speciation.BirthDeathSkylineModel.originIsRootEdge,
-	beast.evolution.speciation.BirthDeathSkylineModel.origin,
-	beast.evolution.speciation.BirthDeathSkylineModel.rhoSamplingTimes,
-	beast.evolution.speciation.BirthDeathSkylineModel.deathRateChangeTimes,
-	beast.evolution.speciation.BirthDeathSkylineModel.samplingRateChangeTimes,
-	beast.evolution.speciation.BirthDeathSkylineModel.birthRateChangeTimes,
-	beast.evolution.speciation.BirthDeathSkylineModel.removalProbabilityChangeTimes,
-	beast.evolution.speciation.BirthDeathSkylineModel.removalProbability,
-	beast.evolution.speciation.BirthDeathSkylineModel.turnOver,
-	beast.evolution.speciation.BirthDeathSkylineModel.netDiversification,
-	beast.evolution.speciation.BirthDeathSkylineModel.conditionOnRhoSampling'>
+	bdsky.evolution.speciation.BirthDeathSkylineModel.birthRateTimesRelative,
+	bdsky.evolution.speciation.BirthDeathSkylineModel.deathRateTimesRelative,
+	bdsky.evolution.speciation.BirthDeathSkylineModel.samplingRateTimesRelative,
+	bdsky.evolution.speciation.BirthDeathSkylineModel.reverseTimeArrays,
+	bdsky.evolution.speciation.BirthDeathSkylineModel.originIsRootEdge,
+	bdsky.evolution.speciation.BirthDeathSkylineModel.origin,
+	bdsky.evolution.speciation.BirthDeathSkylineModel.rhoSamplingTimes,
+	bdsky.evolution.speciation.BirthDeathSkylineModel.deathRateChangeTimes,
+	bdsky.evolution.speciation.BirthDeathSkylineModel.samplingRateChangeTimes,
+	bdsky.evolution.speciation.BirthDeathSkylineModel.birthRateChangeTimes,
+	bdsky.evolution.speciation.BirthDeathSkylineModel.removalProbabilityChangeTimes,
+	bdsky.evolution.speciation.BirthDeathSkylineModel.removalProbability,
+	bdsky.evolution.speciation.BirthDeathSkylineModel.turnOver,
+	bdsky.evolution.speciation.BirthDeathSkylineModel.netDiversification,
+	bdsky.evolution.speciation.BirthDeathSkylineModel.conditionOnRhoSampling'>
 <![CDATA[
 <!-- Sequential Birth Death Skyline model-->
-	<BirthDeathSkylineModel spec="beast.evolution.speciation.BirthDeathSkylineModel" id="BirthDeathSkyContemporaryBDSParam.t:$(n)" tree="@Tree.t:$(n)" conditionOnRoot="true" contemp="true">
+	<BirthDeathSkylineModel spec="bdsky.evolution.speciation.BirthDeathSkylineModel" id="BirthDeathSkyContemporaryBDSParam.t:$(n)" tree="@Tree.t:$(n)" conditionOnRoot="true" contemp="true">
 		<parameter name="birthRate" id="birthRateBDS.t:$(n)" value="2.0" lower="0." upper="Infinity" dimension="1"/>
 		<parameter name="deathRate" id="deathRateBDS.t:$(n)" value="0.5" lower="0." upper="Infinity" dimension="1"/>
 		<parameter name="samplingRate" id="samplingRateBDS.t:$(n)" value="0."/>