more v2.7 migration

CompEvol · Oct 10, 2022 · ee765d2 · ee765d2
1 parent 1f60926
commit ee765d2
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Showing 59 changed files with 240 additions and 166 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"/>
 
     <!-- Location to check for local copy of BEASTLabs repository -->
     <property name="beastLabsDir" location="../BEASTLabs"/>
@@ -18,7 +19,7 @@
     <!-- Directories necessary for all BEAST 2 packages -->
     <property name="doc" location="doc"/>
     <property name="examples" location="examples"/>
-    <property name="templates" location="templates"/>
+    <property name="fxtemplates" location="fxtemplates"/>
 
     <!-- BEAST branch and version to build against
          (only different for version tags because of
@@ -106,6 +107,25 @@
                 <fileset dir="${beastDir}/lib" includes="*.jar"/>
             </classpath>
         </javac>
+        <javac target="${targetVersion}" source="${sourceVersion}"
+            srcdir="${beastDir}/test"
+            destdir="${build-beast}" includeantruntime="false">
+            <classpath>
+                <pathelement path="${classpath}"/>
+                <fileset dir="${beastDir}/lib" includes="*.jar"/>
+                <fileset dir="${beastDir}/lib/junit" includes="*.jar"/>
+            </classpath>
+        </javac>
+        <javac target="${targetVersion}" source="${sourceVersion}"
+            srcdir="${BeastFXDir}/src"
+            destdir="${build-beast}" includeantruntime="false">
+            <classpath>
+                <pathelement path="${classpath}"/>
+                <fileset dir="${beastDir}/lib" includes="*.jar"/>
+                <fileset dir="${beastDir}/lib/junit" includes="*.jar"/>
+                <fileset dir="${BeastFXDir}/locallib" includes="*.jar"/>
+            </classpath>
+        </javac>
         <jar jarfile="${build-lib}/beast2.jar" basedir="${build-beast}" />
         <copy todir="${build-lib}">
             <fileset dir="${beastDir}/lib" includes="*.jar"/>
@@ -158,6 +178,7 @@
         <javac target="${targetVersion}" source="${sourceVersion}"
             srcdir="${beastLabsDir}/src"
             destdir="${build-beastlabs}" includeantruntime="false">
+            <include name="beastlabs/**/**" />
             <classpath>
                 <pathelement path="${classpath}"/>
                 <fileset dir="${beastLabsDir}/lib" includes="*.jar"/>
@@ -238,7 +259,7 @@
 
         <mkdir dir="${pack}"/>
         <mkdir dir="${pack}/examples"/>
-        <mkdir dir="${pack}/templates"/>
+        <mkdir dir="${pack}/fxtemplates"/>
         <mkdir dir="${pack}/lib"/>
         <mkdir dir="${pack}/doc"/>
 
@@ -261,9 +282,9 @@
             <fileset dir="${examples}" includes="**/*" />
         </copy>
 
-        <mkdir dir="${templates}" />
-        <copy todir="${pack}/templates">
-            <fileset dir="${templates}" includes="*.xml" />
+        <mkdir dir="${fxtemplates}" />
+        <copy todir="${pack}/fxtemplates">
+            <fileset dir="${fxtemplates}" includes="*.xml" />
         </copy>
 
         <mkdir dir="${doc}" />
@@ -356,7 +377,7 @@
         <mkdir dir="${test}"/>
         <mkdir dir="${lib}"/>
         <mkdir dir="${examples}"/>
-        <mkdir dir="${templates}"/>
+        <mkdir dir="${fxtemplates}"/>
         <mkdir dir="${doc}"/>
 
         <echo/>
@@ -367,7 +388,7 @@
         <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 fxtemplates go here</echo>
         <echo/>
         <echo>To build your package, just type "ant" at the command line.</echo>
         <echo/>

diff --git a/examples/bears.xml b/examples/bears.xml
@@ -120,7 +120,7 @@ Ursus_spelaeus_0.054=0.054                <taxa id="TaxonSet.bears" spec="TaxonS
 
     <distribution id="posterior" spec="beast.base.inference.CompoundDistribution">
         <distribution id="prior" spec="beast.base.inference.CompoundDistribution">
-            <distribution id="FBD.t:bears" spec="beast.evolution.speciation.SABirthDeathModel" conditionOnRhoSampling="true" diversificationRate="@diversificationRateFBD.t:bears" origin="@originFBD.t:bears" samplingProportion="@samplingProportionFBD.t:bears" tree="@Tree.t:bears" turnover="@turnoverFBD.t:bears">
+            <distribution id="FBD.t:bears" spec="sa.evolution.speciation.SABirthDeathModel" conditionOnRhoSampling="true" diversificationRate="@diversificationRateFBD.t:bears" origin="@originFBD.t:bears" samplingProportion="@samplingProportionFBD.t:bears" tree="@Tree.t:bears" turnover="@turnoverFBD.t:bears">
                 <parameter id="rFBD.t:bears" lower="0.0" name="removalProbability" upper="1.0">0.0</parameter>
                 <parameter id="rhoFBD.t:bears" estimate="false" lower="0.0" name="rho" upper="1.0">1.0</parameter>
             </distribution>
@@ -196,19 +196,19 @@ Ursus_spelaeus_0.054=0.054                <taxa id="TaxonSet.bears" spec="TaxonS
 
     <operator id="samplingPScalerFBD.t:bears" spec="ScaleOperator" parameter="@samplingProportionFBD.t:bears" scaleFactor="0.75" weight="10.0"/>
 
-    <operator id="LeafToSAFBD.t:bears" spec="LeafToSampledAncestorJump" tree="@Tree.t:bears" weight="10.0"/>
+    <operator id="LeafToSAFBD.t:bears" spec="sa.evolution.operators.LeafToSampledAncestorJump" tree="@Tree.t:bears" weight="10.0"/>
 
-    <operator id="SAWilsonBaldingFBD.t:bears" spec="SAWilsonBalding" tree="@Tree.t:bears" weight="10.0"/>
+    <operator id="SAWilsonBaldingFBD.t:bears" spec="sa.evolution.operators.SAWilsonBalding" tree="@Tree.t:bears" weight="10.0"/>
 
-    <operator id="SAWideFBD.t:bears" spec="SAExchange" isNarrow="false" tree="@Tree.t:bears" weight="10.0"/>
+    <operator id="SAWideFBD.t:bears" spec="sa.evolution.operators.SAExchange" isNarrow="false" tree="@Tree.t:bears" weight="10.0"/>
 
-    <operator id="SANarrowFBD.t:bears" spec="SAExchange" tree="@Tree.t:bears" weight="10.0"/>
+    <operator id="SANarrowFBD.t:bears" spec="sa.evolution.operators.SAExchange" tree="@Tree.t:bears" weight="10.0"/>
 
-    <operator id="SAUniformOperatorFBD.t:bears" spec="SAUniform" tree="@Tree.t:bears" weight="20.0"/>
+    <operator id="SAUniformOperatorFBD.t:bears" spec="sa.evolution.operators.SAUniform" tree="@Tree.t:bears" weight="20.0"/>
 
-    <operator id="SATreeRootScalerFBD.t:bears" spec="SAScaleOperator" rootOnly="true" scaleFactor="0.95" tree="@Tree.t:bears" weight="1.0"/>
+    <operator id="SATreeRootScalerFBD.t:bears" spec="sa.evolution.operators.SAScaleOperator" rootOnly="true" scaleFactor="0.95" tree="@Tree.t:bears" weight="1.0"/>
 
-    <operator id="SATreeScalerFBD.t:bears" spec="SAScaleOperator" scaleFactor="0.95" tree="@Tree.t:bears" weight="3.0"/>
+    <operator id="SATreeScalerFBD.t:bears" spec="sa.evolution.operators.SAScaleOperator" scaleFactor="0.95" tree="@Tree.t:bears" weight="3.0"/>
 
     <logger id="tracelog" fileName="bears.log" logEvery="1000" model="@posterior" sanitiseHeaders="true" sort="smart">
         <log idref="posterior"/>
@@ -224,7 +224,7 @@ Ursus_spelaeus_0.054=0.054                <taxa id="TaxonSet.bears" spec="TaxonS
         <log idref="diversificationRateFBD.t:bears"/>
         <log idref="turnoverFBD.t:bears"/>
         <log idref="samplingProportionFBD.t:bears"/>
-        <log id="SACountFBD.t:bears" spec="beast.evolution.tree.SampledAncestorLogger" tree="@Tree.t:bears"/>
+        <log id="SACountFBD.t:bears" spec="sa.evolution.tree.SampledAncestorLogger" tree="@Tree.t:bears"/>
         <log idref="Canidae.prior"/>
     </logger>
 

diff --git a/examples/bears_ranges.xml b/examples/bears_ranges.xml
@@ -120,7 +120,7 @@ Ursus_spelaeus_0.054=0.054                <taxa id="TaxonSet.bears" spec="TaxonS
 
     <distribution id="posterior" spec="beast.base.inference.CompoundDistribution">
         <distribution id="prior" spec="beast.base.inference.CompoundDistribution">
-            <distribution id="FBD.t:bears" spec="beast.evolution.speciation.SABirthDeathModel" conditionOnRhoSampling="true" diversificationRate="@diversificationRateFBD.t:bears" origin="@originFBD.t:bears" samplingProportion="@samplingProportionFBD.t:bears" tree="@Tree.t:bears" turnover="@turnoverFBD.t:bears">
+            <distribution id="FBD.t:bears" spec="sa.evolution.speciation.SABirthDeathModel" conditionOnRhoSampling="true" diversificationRate="@diversificationRateFBD.t:bears" origin="@originFBD.t:bears" samplingProportion="@samplingProportionFBD.t:bears" tree="@Tree.t:bears" turnover="@turnoverFBD.t:bears">
                 <parameter id="rFBD.t:bears" lower="0.0" name="removalProbability" upper="1.0">0.0</parameter>
                 <parameter id="rhoFBD.t:bears" estimate="false" lower="0.0" name="rho" upper="1.0">1.0</parameter>
             </distribution>
@@ -196,25 +196,25 @@ Ursus_spelaeus_0.054=0.054                <taxa id="TaxonSet.bears" spec="TaxonS
 
     <operator id="samplingPScalerFBD.t:bears" spec="ScaleOperator" parameter="@samplingProportionFBD.t:bears" scaleFactor="0.75" weight="10.0"/>
 
-    <operator id="LeafToSAFBD.t:bears" spec="LeafToSampledAncestorJump" tree="@Tree.t:bears" weight="10.0"/>
+    <operator id="LeafToSAFBD.t:bears" spec="sa.evolution.operators.LeafToSampledAncestorJump" tree="@Tree.t:bears" weight="10.0"/>
 
-    <operator id="SAWilsonBaldingFBD.t:bears" spec="SAWilsonBalding" tree="@Tree.t:bears" weight="10.0"/>
+    <operator id="SAWilsonBaldingFBD.t:bears" spec="sa.evolution.operators.SAWilsonBalding" tree="@Tree.t:bears" weight="10.0"/>
 
-    <operator id="SAWideFBD.t:bears" spec="SAExchange" isNarrow="false" tree="@Tree.t:bears" weight="10.0"/>
+    <operator id="SAWideFBD.t:bears" spec="sa.evolution.operators.SAExchange" isNarrow="false" tree="@Tree.t:bears" weight="10.0"/>
 
-    <operator id="SANarrowFBD.t:bears" spec="SAExchange" tree="@Tree.t:bears" weight="10.0"/>
+    <operator id="SANarrowFBD.t:bears" spec="sa.evolution.operators.SAExchange" tree="@Tree.t:bears" weight="10.0"/>
 
-    <operator id="SAUniformOperatorFBD.t:bears" spec="SAUniform" tree="@Tree.t:bears" weight="20.0"/>
+    <operator id="SAUniformOperatorFBD.t:bears" spec="sa.evolution.operators.SAUniform" tree="@Tree.t:bears" weight="20.0"/>
 
-    <operator id="SATreeRootScalerFBD.t:bears" spec="SAScaleOperator" rootOnly="true" scaleFactor="0.95" tree="@Tree.t:bears" weight="1.0"/>
+    <operator id="SATreeRootScalerFBD.t:bears" spec="sa.evolution.operators.SAScaleOperator" rootOnly="true" scaleFactor="0.95" tree="@Tree.t:bears" weight="1.0"/>
 
-    <operator id="SATreeScalerFBD.t:bears" spec="SAScaleOperator" scaleFactor="0.95" tree="@Tree.t:bears" weight="3.0"/>
+    <operator id="SATreeScalerFBD.t:bears" spec="sa.evolution.operators.SAScaleOperator" scaleFactor="0.95" tree="@Tree.t:bears" weight="3.0"/>
 
     <!-- ADD FOSSIL OCCURRENCE DATE RANGES HERE AS FOLLOWS -->
 
     <!-- this operator allows to sample dates of fossil samples. The dates will be variable for all the
      taxa listed in the taxonset input and in the samplingDates inputs -->
-    <operator spec='SampledNodeDateRandomWalker' windowSize="1"  tree="@Tree.t:bears" weight="10">
+    <operator spec='sa.evolution.operators.SampledNodeDateRandomWalker' windowSize="1"  tree="@Tree.t:bears" weight="10">
         <!-- this input specify the taxa with variable dates. In this example only one taxon has a variable sampling date. Add more if you need.
          If this input is not specified then all the leaves except the most recent are assumed to have
          variable sampling dates. -->
@@ -225,7 +225,7 @@ Ursus_spelaeus_0.054=0.054                <taxa id="TaxonSet.bears" spec="TaxonS
          with a sampling date range. In this example, the only taxon with a varaible sampling date
          has also sampling date range with bounds 1 and 15. Note that if a samplingDates is specified for
          a taxon then the bounds will be used even if this taxon is not in the taxonset. -->
-        <samplingDates id="samplingDate1" spec="beast.evolution.tree.SamplingDate" taxon="Ursavus_primaevus_14.41" upper="15." lower="1."/>
+        <samplingDates id="samplingDate1" spec="sa.evolution.tree.SamplingDate" taxon="Ursavus_primaevus_14.41" upper="15." lower="1."/>
     </operator>
 
     <logger id="tracelog" fileName="bears.log" logEvery="1000" model="@posterior" sanitiseHeaders="true" sort="smart">
@@ -242,7 +242,7 @@ Ursus_spelaeus_0.054=0.054                <taxa id="TaxonSet.bears" spec="TaxonS
         <log idref="diversificationRateFBD.t:bears"/>
         <log idref="turnoverFBD.t:bears"/>
         <log idref="samplingProportionFBD.t:bears"/>
-        <log id="SACountFBD.t:bears" spec="beast.evolution.tree.SampledAncestorLogger" tree="@Tree.t:bears"/>
+        <log id="SACountFBD.t:bears" spec="sa.evolution.tree.SampledAncestorLogger" tree="@Tree.t:bears"/>
         <log idref="Canidae.prior"/>
     </logger>