Final updates to packaging for release

beast-dev · Jun 10, 2018 · 9b742df · 9b742df
1 parent abe23d6
commit 9b742df
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Showing 10 changed files with 43 additions and 33 deletions.
diff --git a/build.xml b/build.xml
@@ -536,8 +536,9 @@
                     jvmversion="${jvm_version}"
                     vmoptions="-d64 -Xmx2048M"
                     arguments="-window -working -options"
+                    highresolutioncapable="true"
                     version="${version}"
-                    copyright="${BEAST_name} v${version}, ${copyright}, Alexei Drummond, Andrew Rambaut and Marc Suchard"
+                    copyright="${BEAST_name} v${version}, ${copyright}, Alexei J. Drummond, Andrew Rambaut and Marc A. Suchard"
                     bundleid="dr.app.beast">
             <javaproperty name="apple.laf.useScreenMenuBar" value="true"/>
             <!--<javaproperty name="java.library.path" value="$JAVAROOT:/usr/local/lib"/>-->
@@ -562,14 +563,15 @@
         <jarbundler dir="${Mac_package_dir}"
                     name="${BEAUti_name} v${version}"
                     mainclass="dr.app.beauti.BeautiApp"
-                    stubfile="${packaging_tools}/mac/universalJavaApplicationStub_quaqua"
+                    stubfile="${packaging_tools}/mac/universalJavaApplicationStub   "
 					useJavaXKey="true"
                     icon="${common_dir}/icons/beauti.icns"
                     jvmversion="${jvm_version}"
                     vmoptions="-d64 -Xmx2048M"
                     arguments=""
                     version="${version}"
-                    copyright="${BEAUti_name} v${version}, ${copyright}, Alexei Drummond, Andrew Rambaut, Marc Suchard and Walter Xie"
+                    highresolutioncapable="true"
+                    copyright="${BEAUti_name} v${version}, ${copyright}, Alexei J. Drummond, Andrew Rambaut and Marc A. Suchard"
                     bundleid="dr.app.beauti">
             <documenttype name="BEAUti document"
                           extensions="beauti bti"
@@ -605,9 +607,10 @@
                     icon="${common_dir}/icons/utility.icns"
                     jvmversion="${jvm_version}"
                     vmoptions="-d64 -Xmx2048M"
+                    highresolutioncapable="true"
                     arguments=""
                     version="${version}"
-                    copyright="${LogCombiner_name} v${version}, ${copyright}, Alexei Drummond, Andrew Rambaut, Marc Suchard and Walter Xie"
+                    copyright="${LogCombiner_name} v${version}, ${copyright}, Alexei J. Drummond, Andrew Rambaut and Marc A. Suchard"
                     bundleid="dr.app.tools.logcombiner">
             <jarfileset dir="${Mac_package_dir}/lib">
                 <include name="**/beast.jar"/>
@@ -633,9 +636,10 @@
                     icon="${common_dir}/icons/utility.icns"
                     jvmversion="${jvm_version}"
                     vmoptions="-d64 -Xmx4096M"
+                    highresolutioncapable="true"
                     arguments=""
                     version="${version}"
-                    copyright="${TreeAnnotator_name} v${version}, ${copyright}, Alexei Drummond, Andrew Rambaut, Marc Suchard and Walter Xie"
+                    copyright="${TreeAnnotator_name} v${version}, ${copyright}, Alexei J. Drummond, Andrew Rambaut and Marc A. Suchard"
                     bundleid="dr.app.tools.treeannotator">
             <jarfileset dir="${Mac_package_dir}/lib">
                 <include name="**/beast.jar"/>
@@ -661,9 +665,10 @@
                     icon="${common_dir}/icons/TreeStat.icns"
                     jvmversion="${jvm_version}"
                     vmoptions="-d64 -Xmx1024M"
+                    highresolutioncapable="true"
                     arguments=""
                     version="${version}"
-                    copyright="${TreeStat_name} v${version}, ${copyright}, Alexei Drummond and Andrew Rambaut"
+                    copyright="${TreeStat_name} v${version}, ${copyright}, Alexei J. Drummond and Andrew Rambaut"
                     bundleid="dr.app.treestat">
             <jarfileset dir="${Mac_package_dir}/lib">
                 <include name="**/beast.jar"/>

diff --git a/packaging_tools/mac/universalJavaApplicationStub b/packaging_tools/mac/universalJavaApplicationStub
@@ -11,8 +11,8 @@
 #                                                                                #
 # @author    Tobias Fischer                                                      #
 # @url       https://github.com/tofi86/universalJavaApplicationStub              #
-# @date      2018-03-10                                                          #
-# @version   3.0.1                                                               #
+# @date      2018-04-12                                                          #
+# @version   3.0.2                                                               #
 #                                                                                #
 ##################################################################################
 #                                                                                #
@@ -741,7 +741,7 @@ fi
 export CFProcessPath="$0"
 
 # remove Apples ProcessSerialNumber from passthru arguments (#39)
-if [[ $@ == -psn* ]] ; then
+if [[ "$*" == -psn* ]] ; then
 	ArgsPassthru=()
 else
 	ArgsPassthru=("$@")
@@ -756,18 +756,18 @@ stub_logger "[WorkingDirectory] ${WorkingDirectory}"
 # - splash image
 # - dock icon
 # - app name
-# - JVM options
-# - JVM default options
+# - JVM options / properties (-D)
+# - JVM default options (-X)
 # - main class
-# - main arguments
-# - passthru arguments
+# - main class arguments
+# - passthrough arguments from Terminal or Drag'n'Drop to Finder icon
 stub_logger "[Exec] \"$JAVACMD\" -cp \"${JVMClassPath}\" -splash:\"${ResourcesFolder}/${JVMSplashFile}\" -Xdock:icon=\"${ResourcesFolder}/${CFBundleIconFile}\" -Xdock:name=\"${CFBundleName}\" ${JVMOptionsArr:+$(printf "'%s' " "${JVMOptionsArr[@]}") }${JVMDefaultOptions:+$JVMDefaultOptions }${JVMMainClass}${MainArgsArr:+ $(printf "'%s' " "${MainArgsArr[@]}")}${ArgsPassthru:+ $(printf "'%s' " "${ArgsPassthru[@]}")}"
 exec "${JAVACMD}" \
 		-cp "${JVMClassPath}" \
 		-splash:"${ResourcesFolder}/${JVMSplashFile}" \
 		-Xdock:icon="${ResourcesFolder}/${CFBundleIconFile}" \
 		-Xdock:name="${CFBundleName}" \
-		${JVMOptions:+"$JVMOptions[@]}" }\
+		${JVMOptions:+"${JVMOptions[@]}" }\
 		${JVMDefaultOptions:+$JVMDefaultOptions }\
 		"${JVMMainClass}"\
 		${MainArgsArr:+ "${MainArgsArr[@]}"}\

diff --git a/release/Windows/BEAST_launch4j.xml b/release/Windows/BEAST_launch4j.xml
@@ -9,7 +9,7 @@
   </jre>    
   <versionInfo>
     <fileDescription>BEAST</fileDescription>    
-        <copyright>2002-2017</copyright>
+        <copyright>2002-2018</copyright>
     <productName>BEAST</productName>
     <internalName>BEAST</internalName>
     <originalFilename>BEAST.exe</originalFilename>    

diff --git a/release/Windows/BEAUti_launch4j.xml b/release/Windows/BEAUti_launch4j.xml
@@ -8,7 +8,7 @@
   </jre>    
   <versionInfo>
     <fileDescription>BEAUti</fileDescription>
-        <copyright>2002-2017</copyright>
+        <copyright>2002-2018</copyright>
     <productName>BEAUti</productName>
     <internalName>BEAUti</internalName>
     <originalFilename>BEAUti.exe</originalFilename>    

diff --git a/release/Windows/LogAnalyser_launch4j.xml b/release/Windows/LogAnalyser_launch4j.xml
@@ -12,7 +12,7 @@
   </jre>    
   <versionInfo>
     <fileDescription>LogAnalyser</fileDescription>    
-        <copyright>2002-2017</copyright>
+        <copyright>2002-2018</copyright>
     <productName>LogAnalyser</productName>
     <internalName>LogAnalyser</internalName>
     <originalFilename>LogAnalyser.exe</originalFilename>    

diff --git a/release/Windows/LogCombiner_launch4j.xml b/release/Windows/LogCombiner_launch4j.xml
@@ -12,7 +12,7 @@
   </jre>    
   <versionInfo>
     <fileDescription>LogCombiner</fileDescription>    
-        <copyright>2002-2017</copyright>
+        <copyright>2002-2018</copyright>
     <productName>LogCombiner</productName>
     <internalName>LogCombiner</internalName>
     <originalFilename>LogCombiner.exe</originalFilename>    

diff --git a/release/Windows/TreeAnnotator_launch4j.xml b/release/Windows/TreeAnnotator_launch4j.xml
@@ -12,7 +12,7 @@
   </jre>    
   <versionInfo>
     <fileDescription>TreeAnnotator</fileDescription>    
-        <copyright>2002-2017</copyright>
+        <copyright>2002-2018</copyright>
     <productName>TreeAnnotator</productName>
     <internalName>TreeAnnotator</internalName>
     <originalFilename>TreeAnnotator.exe</originalFilename>    

diff --git a/release/Windows/TreeStat_launch4j.xml b/release/Windows/TreeStat_launch4j.xml
@@ -12,7 +12,7 @@
   </jre>    
   <versionInfo>
     <fileDescription>TreeStat</fileDescription>
-        <copyright>2002-2017</copyright>
+        <copyright>2002-2018</copyright>
     <productName>TreeStat</productName>
     <internalName>TreeStat</internalName>
     <originalFilename>TreeStat.exe</originalFilename>

diff --git a/release/common/README.txt b/release/common/README.txt
@@ -1,4 +1,4 @@
-            	BEAST v1.10 VEME2017 2002-2017
+            	BEAST v1.10 VEME2017 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 - 24 Aug 2017
+Last updated: a.rambaut@ed.ac.uk - 10 June 2018
 
 Contents:
 1) INTRODUCTION
@@ -189,13 +189,15 @@ viewed in a new program called 'FigTree' which is available from:
 ___________________________________________________________________________
 6) NATIVE LIBRARIES
 
-Some of the core of the BEAST program has been converted into 'C' and can
-be compiled into native code. This involves compiling the source code in
-'/native' into a shared library that Java can find and use. We have
-compiled this library for Mac OS X, Windows and Linux on x86 machines. BEAST
-should automatically find these libraries and use them. If a suitable version
-of this library is not found then BEAST will use a Java version of the core
-which will be slower.
+BEAST uses the BEAGLE library to provide fast, native, likelihood 
+calculations. This library is distributed independently and should
+be installed prior to using BEAST.
+
+BEAGLE can be downloaded from here:
+<https://github.com/beagle-dev/beagle-lib>
+
+Further information about using BEAGLE with BEAST can be found here:
+<http://beast.community/beagle>
 
 ___________________________________________________________________________
 7) SUPPORT & LINKS

diff --git a/release/common/VERSION HISTORY.txt b/release/common/VERSION HISTORY.txt
@@ -1,4 +1,4 @@
-                    BEAST v1.10.0 2002-2017
+                    BEAST v1.10.0 2002-2018
         Bayesian Evolutionary Analysis Sampling Trees
                               by
       Alexei J. Drummond, Andrew Rambaut & Marc A. Suchard
@@ -17,13 +17,16 @@
 
 
 Version History
-Last updated: a.rambaut@ed.ac.uk - 24th August 2017
+Last updated: a.rambaut@ed.ac.uk - 10th June 2018
 All issues can be viewed at https://github.com/beast-dev/beast-mcmc/issues
 
 ================================================================================
 
-Version 1.10.0 VEME2017 pre-release 24th August 2017
-
+Version 1.10.0  released 10th June 2018
+
+	This is a major new release with too many features to enumerate here.
+	See http://beast.community/ for more details.
+
 ================================================================================
 
 Version 1.8.4 released 17th June 2016