Commit 68747615 authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 1.10.4+dfsg

parent d0aeeeb4

build.xml

+4 −10
Original line number Diff line number Diff line
@@ -83,6 +83,7 @@ 
            <include name="dr/app/beagle/**"/>

            <include name="dr/app/seqgen/**"/>

            <include name="dr/app/plugin/**"/>

            <include name="dr/app/realtime/**"/>

            <include name="dr/app/tools/**"/>

            <include name="dr/app/util/**"/>

            <include name="dr/app/treestat/**"/>
@@ -129,6 +130,7 @@ 
                <include name="dr/app/gui/**/*.class"/>

                <include name="dr/app/seqgen/**"/>

                <include name="dr/app/plugin/**"/>

                <include name="dr/app/realtime/**"/>

                <include name="dr/app/util/**/*.class"/>

                <include name="dr/app/tools/**/*.class"/>

                <include name="dr/app/treestat/**/*.class"/>
@@ -319,10 +321,10 @@ 
    <!--

    <property name="version" value="1.9"/>

     -->

    <property name="version" value="1.10.2"/>

    <property name="version" value="1.10.4"/>

    <property name="jvm_version" value="1.7+"/>



    <property name="version_number" value="1.10.2"/>

    <property name="version_number" value="1.10.4"/>

    <property name="copyright" value="Copyright 2002-2018"/>



    <property name="release_dir" value="release"/>
@@ -401,14 +403,6 @@ 
                  productVersion="${version_number}.0"

                  txtProductVersion="${version}"/>



        <!-- BEAST v?.?.?.exe -->

        <launch4j configFile="${Windows_dir}/BEAST_launch4j.xml"

                  outfile="${Windows_package_dir}/${BEAST_name} v${version}.exe"

                  fileVersion="${version_number}.0"

                  txtFileVersion="${version}"

                  productVersion="${version_number}.0"

                  txtProductVersion="${version}"/>



        <!-- TreeAnnotator v?.?.?.exe -->

        <launch4j configFile="${Windows_dir}/TreeAnnotator_launch4j.xml"

                  jar="${dist}/beast.jar"

build_bss.xml

+6 −3
Original line number Diff line number Diff line
@@ -43,6 +43,7 @@ 
            <include name="dr/inference/loggers/**/*.class" />

            <include name="dr/inference/distribution/**/*.class" />

            <include name="dr/evomodel/branchratemodel/**/*.class" />

            <include name="dr/evomodel/branchmodel/**/*.class" />

            <include name="dr/evomodel/substmodel/**/*.class" />

            <include name="dr/app/beagle/evomodel/substmodel/**/*.class" />

            <include name="dr/app/beagle/evomodel/branchmodel/**/*.class" />
@@ -107,6 +108,7 @@ 
         <include name="dr/inference/loggers/**" />

         <include name="dr/inference/distribution/**" />

         <include name="dr/evomodel/branchratemodel/**" />

         <include name="dr/evomodel/branchmodel/**" />

         <include name="dr/evomodel/substmodel/**" />

         <include name="dr/app/beagle/evomodel/substmodel/**" />

         <include name="dr/app/beagle/evomodel/branchmodel/**" />
@@ -149,7 +151,7 @@ 
      <echo message="Successfully compiled." />

   </target>



    <property name="version" value="1.0" />

    <property name="version" value="1.4" />

    <property name="release_dir" value="release_pibuss" />

    <property name="name" value="piBUSS" />
@@ -200,6 +202,7 @@ 
        <delete dir="${Linux_package_dir}" />

        <!-- Create the release directory -->

        <mkdir dir="${Linux_package_dir}" />

        <mkdir dir="${Linux_dir}/lib" />



        <copy todir="${Linux_package_dir}/bin">

            <fileset dir="${Linux_dir}/scripts"/>

build_tempest.xml

+7 −2
Original line number Diff line number Diff line
@@ -6,6 +6,10 @@ 
    <description>

        Build file for TempEst release versions.

    </description>



    <property name="JDK_SOURCE_VERSION" value="1.6"/>

    <property name="JDK_TARGET_VERSION" value="1.6"/>



    <!-- set global properties for this build -->

    <property name="src" location="src"/>

    <property name="build" location="build"/>
@@ -33,7 +37,7 @@ 


    <target name="compile" depends="init">

        <!-- Compile the java code from ${src} into ${build} -->

        <javac source="1.6" target="1.6" srcdir="${src}" destdir="${build}" classpathref="classpath">

        <javac source="${JDK_SOURCE_VERSION}" target="${JDK_TARGET_VERSION}" srcdir="${src}" destdir="${build}" classpathref="classpath">

            <include name="dr/app/tempest/**"/>

            <include name="dr/app/beauti/**"/>

            <include name="dr/app/tools/**"/>
@@ -95,7 +99,7 @@ 
        </jar>

    </target>



    <property name="version" value="1.5.2" />

    <property name="version" value="1.5.3" />

    <property name="packaging_tools" value="packaging_tools" />

    <property name="release_dir" value="release_tempest" />

    <property name="name" value="TempEst" />
@@ -193,6 +197,7 @@ 
                        name="${name} v${version}"

                        mainclass="dr.app.tempest.TempEstApp"

                        stubfile="${packaging_tools}/mac/universalJavaApplicationStub"

                        useJavaXKey="true"

                        icon="${Mac_dir}/icons/TempEst.icns"

                        jvmversion="1.6+"

                        arguments=""

release/common/README.txt

+2 −2
Original line number Diff line number Diff line 
                    BEAST v1.10.2 2002-2018

                    BEAST v1.10.4 2002-2018

        Bayesian Evolutionary Analysis Sampling Trees

                              by

      Alexei J. Drummond, Andrew Rambaut & Marc Suchard
@@ -16,7 +16,7 @@ 
                      msuchard@ucla.edu





Last updated: a.rambaut@ed.ac.uk - 6th October 2018

Last updated: a.rambaut@ed.ac.uk - 9th November 2018



Contents:

1) INTRODUCTION

release/common/VERSION HISTORY.txt

+21 −2
Original line number Diff line number Diff line 
                    BEAST v1.10.2 2002-2018

                    BEAST v1.10.4 2002-2018

        Bayesian Evolutionary Analysis Sampling Trees

                              by

      Alexei J. Drummond, Andrew Rambaut & Marc A. Suchard
@@ -17,11 +17,30 @@ 




Version History

Last updated: a.rambaut@ed.ac.uk - 6th October 2018

Last updated: a.rambaut@ed.ac.uk - 9th November 2018

All issues can be viewed at https://github.com/beast-dev/beast-mcmc/issues



================================================================================



Version 1.10.4  released 9th November 2018



    New Features:

        Command-line option to turn off operator adaptation.

        Command-line option to limit BEAGLE 3 thread usage.



	Bug Fixes:

		Issue 1038: Issue specifying burnin in the command-line LogCombiner.



================================================================================



Version 1.10.3  released 28th October 2018



	Bug Fixes:

		Issue 1037: Likelihood computation performance reduced with BEAGLE 3 on CPU.

	    Issue 1036: Truncated normals not working as priors.



================================================================================



Version 1.10.2  released 6th October 2018



	Bug Fixes: