Commit updates for v1.10.4

Author: rambaut

build.xml

@@ -321,10 +321,10 @@
     <!--
     <property name="version" value="1.9"/>
      -->
-    <property name="version" value="1.10.4pre"/>
+    <property name="version" value="1.10.4"/>
     <property name="jvm_version" value="1.7+"/>
 
-    <property name="version_number" value="1.10.3"/>
+    <property name="version_number" value="1.10.4"/>
     <property name="copyright" value="Copyright 2002-2018"/>
 
     <property name="release_dir" value="release"/>

release/common/README.txt

@@ -1,4 +1,4 @@
-                    BEAST v1.10.3 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 - 28th October 2018
+Last updated: a.rambaut@ed.ac.uk - 9th November 2018
 
 Contents:
 1) INTRODUCTION

release/common/VERSION HISTORY.txt

@@ -1,4 +1,4 @@
-                    BEAST v1.10.3 2002-2018
+                    BEAST v1.10.4 2002-2018
         Bayesian Evolutionary Analysis Sampling Trees
                               by
       Alexei J. Drummond, Andrew Rambaut & Marc A. Suchard
@@ -17,11 +17,22 @@
 
 
 Version History
-Last updated: a.rambaut@ed.ac.uk - 28th 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:

src/dr/inferencexml/MCMCParser.java

@@ -81,9 +81,9 @@ private MCMC parseMCMC(String id, XMLObject xo) throws XMLParseException {
         }
         long adaptationDelay = chainLength / 100;
         adaptationDelay =
-                xo.getAttribute(AUTO_OPTIMIZE_DELAY,
                 xo.getAttribute(ADAPTATION_DELAY,
-                xo.getAttribute(PRE_BURNIN, adaptationDelay)));
+                        xo.getAttribute(AUTO_OPTIMIZE_DELAY,
+                                xo.getAttribute(PRE_BURNIN, adaptationDelay)));
 
         double adaptationTarget = 0.234;
         if (System.getProperty("mcmc.adaptation_target") != null) {
@@ -162,9 +162,9 @@ private MCMC parseMCMC(String id, XMLObject xo) throws XMLParseException {
         loggers.toArray(loggerArray);
 
         java.util.logging.Logger.getLogger("dr.inference").info("\nCreating the MCMC chain:" +
-                "\n  chainLength=" + options.getChainLength() +
-                "\n  autoOptimize=" + options.useAdaptation() +
-                (options.useAdaptation() ? "\n  autoOptimize delayed for " + options.getAdaptationDelay() + " steps" : "") +
+                "\n  chain length = " + options.getChainLength() +
+                "\n  operator adaption = " + options.useAdaptation() +
+                (options.useAdaptation() ? "\n  adaptation delayed for " + options.getAdaptationDelay() + " steps" : "") +
                 (options.getFullEvaluationCount() == 0 ? "\n  full evaluation test off" : "")
         );