LPhy 1.5.*, LPhyBEAST 1.1.*, LPhyBeastExt 0.3.* #7

beast2.7/bin/lphybeast-mod

@@ -1,4 +1,5 @@
-#!/bin/sh
+#!/bin/bash
+# It is preferable to place lphybeast inside the BEAST2 bin folder
 
 if [ -z "$BEAST" ]; then
 	## resolve links - $0 may be a link to application
@@ -22,10 +23,28 @@ if [ -z "$BEAST" ]; then
 	cd "$saveddir"
 fi
 
-BEAST_LIB="$BEAST/lib"
-JAVA="java"
+if [ -n "$BEAST" ]; then
+  # if not empty
+  BEAST_LIB="$BEAST/lib"
+else
+  echo "Error: cannot locate the BEAST 2 folder ! $BEAST"
+  exit 1
+fi
+
+if [ -d "$BEAST"/jre ]; then
+  # use Zulu JRE in the BEAST directory if it exists
+  JAVA="$BEAST"/jre/bin/java
+elif [ -n "$JAVA_HOME" ]; then
+  # else use $JAVA_HOME
+  JAVA="$JAVA_HOME"/bin/java
+else
+  # else
+  JAVA=java
+fi
+# print Java version
+echo $("$JAVA" -version)
 
-# use BEAGLE_LIB if the BEAGLE library is not in a standard location
+# use BEAGLE_LIB if it is not empty
 if [ -n "$BEAGLE_LIB" ]; then
 	if [ -n "$BEAST_EXTRA_LIBS" ]; then
 		BEAST_EXTRA_LIBS="$BEAST_EXTRA_LIBS:$BEAGLE_LIB"
@@ -43,19 +62,74 @@ else
     export LD_LIBRARY_PATH="$LD_LIBRARY_PATH":/usr/local/lib
 fi
 
+### $LPHY_LIB must be provided
+
+if [ -z "$LPHY_LIB" ]; then
+  # if $LPHY_LIB does not exist, detect the OS
+  if [[ "$OSTYPE" == "linux-gnu"* ]]; then
+      echo "Guessing LPHY_LIB on Linux ..."
+      # set working dir to ~
+      OS_PREFIX="$HOME"
+
+  elif [[ "$OSTYPE" == "darwin"* ]]; then
+      echo "Guessing LPHY_LIB on macOS ..."
+      OS_PREFIX="/Applications"
+
+#  elif [[ "$OSTYPE" == "cygwin" ]]; then
+#      echo "Running on Cygwin (Windows)"
+#  elif [[ "$OSTYPE" == "msys" ]]; then
+#      echo "Running on MSYS (Windows)"
+#  elif [[ "$OSTYPE" == "win32" ]]; then
+#      echo "Running on Windows"
+
+  else
+      echo "Cannot guess the LPhy library path LPHY_LIB in unknown OS: $OSTYPE !"
+      echo "Please set it as your environment variable."
+      echo "Get help from https://linguaphylo.github.io/setup"
+      exit 1
+  fi
+
+  # if multiple LPhy installed, sort the search result to get the latest version, usually last line
+  LPHY_DIR=$(find "$OS_PREFIX" -maxdepth 1 -type d -name 'lphy*studio-1*' | sort | tail -1)
+  # Guess LPHY_LIB
+  LPHY_LIB="$LPHY_DIR/lib"
+fi
+# set to specific path in script
+#LPHY_LIB="/Applications/BEAST 2.7.5/lphystudio-1.4.3/lib"
+
+if [ ! -d "$LPHY_LIB" ]; then
+  echo "Error: Invalid LPhy library path : $LPHY_LIB !"
+  echo "Please set an existing LPhy library path to LPHY_LIB as your environment variable."
+  echo "Get help from https://linguaphylo.github.io/setup"
+  exit 1
+fi
+echo "BEAST_LIB = $BEAST_LIB"
+echo "BEAST_EXTRA_LIBS = $BEAST_EXTRA_LIBS"
+echo "LPHY_LIB = $LPHY_LIB"
+echo ""
+
+# test if there is any lphy*.jar
+JAR_FILES=$(ls "$LPHY_LIB"/lphy*.jar)
+if [ -z "$JAR_FILES" ]; then
+  echo "Error: No core jar files found in $LPHY_LIB !"
+  echo "Please install LPhy properly. Get help from https://linguaphylo.github.io/setup"
+  exit 1
+fi
+
 ### lphy lib must be loaded to classpath
 "$JAVA" -version
 echo $(ls "$BEAST_LIB")
 
-LPHY_LIB="$BEAST/lphy-studio-1.4/lib"
+LPHY_LIB="$BEAST/lphy-studio-1.5/lib"
 echo "Set LPHY_LIB = $LPHY_LIB"
 echo $(ls "$LPHY_LIB")
+
+
 # must set -Dpicocli.disable.closures=true using picocli:4.7.0
-# it will throw otherwise java.lang.NoClassDefFoundError: groovy.lang.Closure
-ARG="-Dpicocli.disable.closures=true -Dlauncher.wait.for.exit=true -Xms256m -Xmx60g -Duser.language=en"
-LPHY_BEAST="beast.pkgmgmt.launcher.AppLauncherLauncher lphybeast"
+# otherwise it will throw otherwise java.lang.NoClassDefFoundError: groovy.lang.Closure
+ARG="-Xms256m -Xmx60g -Dpicocli.disable.closures=true -Dlauncher.wait.for.exit=true -Duser.language=en"
 if [ -n "$BEAST_EXTRA_LIBS" ]; then
-  "$JAVA" $ARG -Djava.library.path="$BEAST_EXTRA_LIBS" -cp "$BEAST_LIB/launcher.jar:$LPHY_LIB/*" $LPHY_BEAST $*
+  "$JAVA" $ARG -Djava.library.path="$BEAST_EXTRA_LIBS" -cp "$BEAST_LIB/launcher.jar:$LPHY_LIB/*" beast.pkgmgmt.launcher.AppLauncherLauncher lphybeast $*
 else
-  "$JAVA" $ARG -cp "$BEAST_LIB/launcher.jar:$LPHY_LIB/*" $LPHY_BEAST $*
+  "$JAVA" $ARG -cp "$BEAST_LIB/launcher.jar:$LPHY_LIB/*" beast.pkgmgmt.launcher.AppLauncherLauncher lphybeast $*
 fi

beast2.7/lib/packages/BEAST.app.version.xml

@@ -1,5 +1,5 @@
-<package name='BEAST.app' version='2.7.4'>
-	<depends on='BEAST.base' atleast='2.7.4' atmost="2.7.9"/>
+<package name='BEAST.app' version='2.7.6'>
+	<depends on='BEAST.base' atleast='2.7.6' atmost="2.7.9"/>
 
 			<service type="beastfx.app.beauti.ThemeProvider">
 				<provider classname="beastfx.app.beauti.theme.Default"/>
@@ -14,6 +14,7 @@
 				<provider classname="beastfx.app.inputeditor.BEASTObjectInputEditor"/>
 				<provider classname="beastfx.app.inputeditor.TypeTraitSetInputEditor"/>
 				<provider classname="beastfx.app.inputeditor.BooleanInputEditor"/>
+				<provider classname="beastfx.app.inputeditor.ConstantInputEditor"/>
 				<provider classname="beastfx.app.inputeditor.DoubleInputEditor"/>
 				<provider classname="beastfx.app.inputeditor.DoubleListInputEditor"/>
 				<provider classname="beastfx.app.inputeditor.EnumInputEditor"/>
@@ -46,6 +47,8 @@
 				<provider classname="beastfx.app.inputeditor.TipDatesInputEditor"/>
 				<provider classname="beastfx.app.beauti.ClockModelListInputEditor"/>
 				<provider classname="beastfx.app.beauti.ConstantPopulationInputEditor"/>
+				<provider classname="beastfx.app.beauti.ExponentialPopulationInputEditor"/>
+				<provider classname="beastfx.app.beauti.ScaledPopulationInputEditor"/>
 				<provider classname="beastfx.app.beauti.GeneTreeForSpeciesTreeDistributionInputEditor"/>
 				<provider classname="beastfx.app.beauti.OperatorListInputEditor"/>
 				<provider classname="beastfx.app.beauti.SpeciesTreePriorInputEditor"/>
@@ -88,6 +91,19 @@
 				<provider classname="beastfx.app.methodsection.XML2HTMLPaneFX"/>
 			</service>
 
+			<service type="beastfx.app.treeannotator.services.TopologySettingService">
+				<provider classname="beastfx.app.treeannotator.services.MCCTopologyService"/>
+				<provider classname="beastfx.app.treeannotator.services.MaxSumCladeCrediblityTopologyService"/>
+				<provider classname="beastfx.app.treeannotator.services.UserTargetTreeTopologyService"/>
+			</service>
+
+			<service type="beastfx.app.treeannotator.services.NodeHeightSettingService">
+				<provider classname="beastfx.app.treeannotator.services.CommonAncestorNodeHeigtService"/>
+				<provider classname="beastfx.app.treeannotator.services.KeepHeightsNodeHeightsService"/>
+				<provider classname="beastfx.app.treeannotator.services.MeanNodeHeightService"/>
+				<provider classname="beastfx.app.treeannotator.services.MedianNodeHeightService"/>
+			</service>
+
 	    <packageapp description="Interactive Methods Section Generator"
               class="beastfx.app.methodsection.XML2HTMLPaneFX"
             />

beast2.7/lib/packages/BEAST.base.version.xml

@@ -1,4 +1,4 @@
-<package name="BEAST.base" version="2.7.4">
+<package name="BEAST.base" version="2.7.6">
 <!-- note version="2.7.x" must be double quotes for Mac release script release/Mac/createdmg.sh -->
 
             <!-- data types -->

beast2.7/lib/prerelease.xml

@@ -2,17 +2,17 @@
 
 <!-- url="https://s01.oss.sonatype.org/content/repositories/releases/io/github/linguaphylo/lphybeast/0.3.1/lphybeast-0.3.1.zip"  -->    
 <!-- url="https://s01.oss.sonatype.org/content/repositories/snapshots/io/github/linguaphylo/lphybeast/0.4.1-SNAPSHOT/lphybeast-0.4.1-20220722.033341-1.zip"  -->
-    <package name="lphybeast" version="1.0.1"
-	     url="https://s01.oss.sonatype.org/content/repositories/snapshots/io/github/linguaphylo/lphybeast/1.0.1-SNAPSHOT/lphybeast-1.0.1-20230525.214335-1.zip"
+    <package name="lphybeast" version="1.1.0"
+	     url="https://s01.oss.sonatype.org/content/repositories/snapshots/io/github/linguaphylo/lphybeast/1.1.0-SNAPSHOT/lphybeast-1.1.0-20240124.023923-4.zip"
 	     projectURL="https://github.com/LinguaPhylo/LPhyBeast" 
 	     description="A command-line program that takes an LPhy model specification including a data block, 
 	                  and produces a BEAST 2 XML input file.">
-		<depends on='BEAST.base' atleast='2.7.4'/>
-		<depends on='BEAST.app' atleast='2.7.4'/>
+		<depends on='BEAST.base' atleast='2.7.6'/>
+		<depends on='BEAST.app' atleast='2.7.6'/>
 
-		<depends on='BEASTLabs' atleast='2.0.0'/>
-		<depends on='BEAST_CLASSIC' atleast='1.6.0'/>
-		<depends on='feast' atleast='9.2.0'
+		<depends on='BEASTLabs' atleast='2.0.2'/>
+		<depends on='BEAST_CLASSIC' atleast='1.6.3'/>
+		<depends on='feast' atleast='9.8.5'
 				 projectURL="https://github.com/tgvaughan/feast"
 				 description="Expands the flexibility of BEAST 2 XML."/>
 		<depends on='SSM' atleast='1.2.0'
@@ -22,11 +22,11 @@
 		<depends on='bdtree' atleast='0.0.1'/>
 	</package>
 
-    <package name="LPhyBeastExt" version="0.2.1"
-	     url="https://s01.oss.sonatype.org/content/repositories/snapshots/io/github/linguaphylo/LPhyBeastExt/0.2.1-SNAPSHOT/LPhyBeastExt-0.2.1-20230525.222434-1.zip"
+    <package name="LPhyBeastExt" version="0.3.0"
+	     url="https://s01.oss.sonatype.org/content/repositories/snapshots/io/github/linguaphylo/LPhyBeastExt/0.3.0-SNAPSHOT/LPhyBeastExt-0.3.0-20240124.221018-1.zip"
 	     projectURL="https://github.com/LinguaPhylo/LPhyBeastExt" 
 	     description="An extension of LPhyBEAST.">
-		<depends on='lphybeast' atleast='1.0.1'/>
+		<depends on='lphybeast' atleast='1.1.0'/>
 
 		<depends on='Mascot' atleast='3.0.0'
 				 description="Marginal approximation of the structured coalescent"

beast2.7/lphy-studio-1.4/bin/lphystudio → beast2.7/lphy-studio-1.5/bin/lphystudio

@@ -25,4 +25,4 @@ if [ -z "$LPHY" ]; then
 fi
 
 LPHY_LIB=$LPHY/lib
-java -Xms64m -Xmx5g -p $LPHY_LIB -m lphystudio $*
+java -Xms64m -Xmx5g -Duser.dir="$LPHY" -p $LPHY_LIB -m lphystudio $*

beast2.7/lphy-studio-1.4/bin/slphy → beast2.7/lphy-studio-1.5/bin/slphy

@@ -27,4 +27,4 @@ fi
 echo "LPHY path = $LPHY"
 
 LPHY_LIB="$LPHY/lib"
-java -Xms64m -Xmx5g -p "$LPHY_LIB" -m lphystudio/lphystudio.app.simulator.SLPhy $*
+java -Xms64m -Xmx5g -p "$LPHY_LIB" -m lphy.core/lphy.core.simulator.SLPhy $*

beast2.7/lphy-studio-1.4/bin/slphy.bat → beast2.7/lphy-studio-1.5/bin/slphy.bat

@@ -52,7 +52,7 @@ goto fail
 
 :findJavaFromJavaHome
 set JAVA_HOME=%JAVA_HOME:"=%
-set JAVA_EXE=%JAVA_HOME%/bin/java.exe
+set JAVA_EXE=%JAVA_HOME%\bin\java.exe
 
 if exist "%JAVA_EXE%" goto setLPHYLIB
 
@@ -65,24 +65,26 @@ echo location of your Java installation.
 goto fail
 
 :setLPHYLIB
-set LPHY_LIB=%APP_HOME%/../lib/
+set LPHY_LIB=%APP_HOME%..\lib
 echo set the LPHY_LIB to "%LPHY_LIB%"
 
 :execute
 @rem Setup the command line
 @rem Execute 
-"%JAVA_EXE%" %DEFAULT_JVM_OPTS% -p %LPHY_LIB% -m lphystudio/lphystudio.app.simulator.SLPhy %*
+set CMD="%JAVA_EXE%" %DEFAULT_JVM_OPTS% -p "%LPHY_LIB%" -m lphy.core/lphy.core.simulator.SLPhy %*
+%CMD%
 
 :end
 @rem End local scope for the variables with windows NT shell
 if "%ERRORLEVEL%"=="0" goto mainEnd
 
 :fail
-echo ERROR: fail to run 
-echo "%JAVA_EXE%" %DEFAULT_JVM_OPTS% -p %LPHY_LIB% -m lphystudio/lphystudio.app.simulator.SLPhy %*
-
+echo.
+echo ERROR: fail to run the command
+echo %CMD%
+echo.
+echo Get help from https://linguaphylo.github.io/setup
 
 :mainEnd
 if "%OS%"=="Windows_NT" endlocal
 
-:omega

beast2.7/lphy-studio-1.4/examples/birth-death/simpleBirthDeathSerial.lphy → beast2.7/lphy-studio-1.5/examples/birth-death/simpleBirthDeathSerial.lphy

@@ -1,8 +1,11 @@
-model {
+data {
   λ = 1;
   deathRate = 0.5;
   tmrca = 10;
-  ψ ~ BirthDeathSerialSampling(lambda=λ, mu=deathRate, rho=0.1, psi=1.0, rootAge=tmrca, ages=[0.0,1.0,2.0,3.0,4.0,5.0,6.0,7.0,8.0,9.0]);
+  ages = [0.0,1.0,2.0,3.0,4.0,5.0,6.0,7.0,8.0,9.0];
+}
+model {
+  ψ ~ BirthDeathSerialSampling(lambda=λ, mu=deathRate, rho=0.1, psi=1.0, rootAge=tmrca, ages=ages);
   TL = ψ.treeLength();
   rootAge = ψ.rootAge();
 }

beast2.7/lphy-studio-1.5/examples/birth-death/test.lphy

@@ -0,0 +1,3 @@
+data {
+  table = readDelim(file="data/bears_taxa.tsv", sep="\t");
+}

beast2.7/lphy-studio-1.4/examples/clock-model/hyperPrior3Layer.lphy → beast2.7/lphy-studio-1.5/examples/clock-model/hyperPrior3Layer.lphy

@@ -12,7 +12,7 @@ model {
 
   // multiplier in log space : 1.124022  2.300000  3.475978
   // real space :              3.077205  9.974182 32.329444
-  multiplierLg ~ LogNormal(meanlog=2.3, sdlog=0.6);
+  multiplierLg ~ Normal(mean=2.3, sd=0.6);
   // hyperMean * multiplier
   hyperLgMean2 = hyperLgMean + multiplierLg;
 

beast2.7/lphy-studio-1.4/examples/coalescent/jcCoalescent.lphy → beast2.7/lphy-studio-1.5/examples/coalescent/jcCoalescent.lphy

@@ -6,4 +6,5 @@ model {
   Θ ~ LogNormal(meanlog=3.0, sdlog=1.0);
   ψ ~ Coalescent(theta=Θ, taxa=taxa);
   D ~ PhyloCTMC(tree=ψ, L=L, Q=jukesCantor());
+  E = rmTaxa(names=1:3, alignment=D);
 }

beast2.7/lphy-studio-1.4/examples/coalescent/simpleMultispeciesCoalescentTaxa.lphy → beast2.7/lphy-studio-1.5/examples/coalescent/simpleMultispeciesCoalescentTaxa.lphy

@@ -1,8 +1,12 @@
-model {
-  taxa = taxa(names=["A1", "A2", "B1", "B2", "C1", "C2", "D1", "D2"], species=["A", "A", "B", "B", "C", "C", "D", "D"]);
+data {
+  // cannot wrap the line
+  taxa = taxa(names=["A1","A2","B1","B2","C1","C2","D1","D2"],species=["A","A","B","B","C","C","D","D"],ages=[0.0,1.0,2.0,3.0,4.0,5.0,6.0,7.0]);
+  // create new taxa from species
   species = species(taxa);
   speciesPopCount = species.nodeCount();
-  Θ ~ LogNormal(meanlog=-3.0, sdlog=0.5, replicates=speciesPopCount);
+}
+model {
+  Θ ~ LogNormal(meanlog=-3.0,sdlog=0.5, replicates=speciesPopCount);
   λ ~ LogNormal(meanlog=0.0, sdlog=1.0);
   sp ~ Yule(lambda=λ, taxa=species);
   g ~ MultispeciesCoalescent(theta=Θ, S=sp, taxa=taxa, replicates=2);

beast2.7/lphy-studio-1.5/examples/data-clamping/covidDPG.lphy

@@ -0,0 +1,46 @@
+data {
+  // extract dates
+  options={ageDirection="forward", ageRegex=".*\|(\d+\.\d+)$"};
+  D = readFasta(file="data/bluff-wedding-cluster.fasta", options=options);
+
+  // Bayesian Skyline
+  numGroups = 20;
+  taxa = D.taxa();
+  w = taxa.length()-1;
+  // i starts from 0
+  D_trait = extractTrait(taxa=taxa, sep="|", i=1);
+  K = D_trait.stateCount();
+  dim = K*(K-1)/2;
+  dataType = D_trait.dataType();
+}
+model {
+  κ ~ LogNormal(meanlog=1.0, sdlog=1.25);
+  π ~ Dirichlet(conc=[1.0,1.0,1.0,1.0]);
+
+  firstValue ~ LogNormal(meanlog=0.0, sdlog=2.0);
+  Θ ~ ExpMarkovChain(firstValue=firstValue, n=numGroups);
+  groupSizes ~ RandomComposition(n=w, k=numGroups);
+  ψ ~ SkylineCoalescent(theta=Θ, taxa=taxa, groupSizes=groupSizes);
+
+  // "7.87e-05" "9.12e-04" "1.06e-02"
+  clockRate ~ LogNormal(meanlog=-7.0, sdlog=1.25);
+
+  D ~ PhyloCTMC(L=D.nchar(), Q=hky(kappa=κ, freq=π), mu=clockRate, tree=ψ);
+
+  π_trait ~ Dirichlet(conc=rep(element=3.0, times=K));
+  // symmetric, rates dimension = n * (n-1) / 2
+  R_trait ~ Dirichlet(conc=rep(element=1.0, times=dim));
+
+  // trait indicators
+  I ~ Bernoulli(p=0.5, replicates=dim, minSuccesses=dim-2);
+//  S ~ Poisson(lambda=2, min=K, max=dim);
+//  I ~ RandomBooleanArray(length=dim, hammingWeight=S);
+
+  //μ_trait ~ Gamma(shape=0.001, scale=1000.0);
+  μ_trait ~ LogNormal(meanlog=2.0, sdlog=2.0);
+
+  // construct the GTR instantaneous rate matrix
+  Q_trait = generalTimeReversible(freq=π_trait, rates=select(x=R_trait, indicator=I));
+  // use the data type of trait alignment extracted from taxa names
+  D_trait ~ PhyloCTMC(L=1, Q=Q_trait, mu=μ_trait, tree=ψ, dataType=dataType);
+}

beast2.7/lphy-studio-1.5/examples/data-clamping/readDelim.lphy

@@ -0,0 +1,11 @@
+data {
+  table = readDelim(file="data/bears_taxa.tsv", sep="\t");
+  colNames = table.getColumnNames();
+  taxonNames = table.getColumn(0);
+  // cast doubles
+  minAges = toDouble(table.getColumn(1));
+  // otherwise it will be string
+  maxAges = table.getColumn(2);
+  // ages must be a double array
+  taxa = taxa(names = taxonNames, ages = minAges);
+}

beast2.7/lphy-studio-1.5/examples/data-clamping/simpleDataClamping.lphy

@@ -0,0 +1,7 @@
+data {
+  L = [22,11,33];
+  n = length(L);
+}
+model {
+  L ~ Poisson(lambda=1.0, replicates=n);
+}