Prerelease v2.7.7 #1152

CompEvol · Jun 10, 2024 · d638eec · d638eec
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diff --git a/release/common/README.txt b/release/common/README.txt
@@ -1,7 +1,7 @@
-                    BEAST v2.7.6 2023
-                 Beast 2 development team 2011-2023
+                    BEAST v2.7.7 2024
+                 Beast 2 development team 2011-2024
 
-Last updated: October 2023
+Last updated: June 2024
 
 Contents:
 1) INTRODUCTION
@@ -42,16 +42,11 @@ adjustment and a number of runs to get a valid answer. Sorry.
 ___________________________________________________________________________
 2) INSTALLING BEAST
 
-BEAST requires a Java Virtual Machine to run. Many systems will already
-have this installed. It requires at least version 1.8 of Java to run. The
-latest versions of Java can be downloaded from:
-
-<http://java.com/>
-
-If in doubt type "java -version" to see what version of java is installed
-(or if it is installed at all).
-
-Mac OS X will already have a suitable version of Java installed.
+BEAST requires a Java Virtual Machine version 17 and JavaFX to run. The
+BEAST installation packages come with a suitable Java + JavaFX and it is
+recommended to use these versions of Java + JavaFX. It is possible to use
+different versions, but it will require considerable time configuring them,
+so that is not recommended.
 
 Within the BEAST package will be the following directories:
 Directory       Contents
@@ -60,7 +55,7 @@ examples/       Some NEXUS and XML files
 lib/            Java & native libraries used by BEAST 
 bin/            Scripts of the corresponding OS
 fxtemplates/    Templates to initiate BEAUti
-
+jre/            Suitable java runtime
 ___________________________________________________________________________
 3) CONVERTING SEQUENCES
 

diff --git a/release/common/VERSION HISTORY.txt b/release/common/VERSION HISTORY.txt
@@ -1,10 +1,26 @@
-                    BEAST v2.7.5 2023
-                 Beast 2 development team 2011-2023
+                    BEAST v2.7.7 2024
+                 Beast 2 development team 2011-2024
 Version History
-Last updated: November 2023
+Last updated: June 2024
 
 All issues can be viewed at https://github.com/CompEvol/beast2/issues
 ================================================================================
+Version 2.7.7 June 2024
+	o Add CCD to the list of recommended packages for TreeAnnotator CompEvol/beast2#1138
+	TreeAnnotator GUI to pick up correct topology setting method CompEvol/beast2#1143
+	BEAST
+	o allow launch through `java -jar launcher.jar` CompEvol/beast2#1151
+	o make alignment a StateNode CompEvol/beast2#1150
+	o make Randomizer thread aware for better replicability of threaded runs CompEvol/beast2#1141	
+	o make the AdaptableOperatorSampler ignore zero weight operators CompEvol/beast2#1136
+	BEAUti
+	o robustify for drag/dropping alignments CompeVol/BeastFX/#72
+	o enable importing of alignments in files with .txt extension CompeVol/BeastFX/#78
+	o remove HTML error messages CompeVol/BeastFX/#65
+	LogAnalyser 
+	o check added to prevent out of bound exception CompeVol/BeastFX/#81
+	o add threading option to loganalyser when running with the oneline option CompeVol/BeastFX/#80
+
 Version 2.7.6 November 2023
 	TreeAnnotator allows packages to define new methods for creating summary trees CompEvol/BeastFX#71
 	BEAST

diff --git a/src/beast/base/core/BEASTVersion2.java b/src/beast/base/core/BEASTVersion2.java
@@ -11,9 +11,9 @@ public class BEASTVersion2 extends BEASTVersion {
     /**
      * Version string: assumed to be in format x.x.x
      */
-    private static final String VERSION = "2.7.6";
+    private static final String VERSION = "2.7.7";
 
-    private static final String DATE_STRING = "2002-2023";
+    private static final String DATE_STRING = "2002-2024";
 
     private static final boolean IS_PRERELEASE = true;
 //

diff --git a/src/beast/base/evolution/operator/EpochFlexOperator.java b/src/beast/base/evolution/operator/EpochFlexOperator.java
@@ -87,8 +87,13 @@ public double proposal() {
 			intervalLow = treeIntervals.getIntervalTime(j);
 			intervalHi = treeIntervals.getIntervalTime(j + groupSizes.getValue(k));
 		} else {
-			intervalLow = lower0 + Randomizer.nextDouble() * (upper - lower0);
-			intervalHi  = lower0 + Randomizer.nextDouble() * (upper - lower0);
+			int x = Randomizer.nextInt(tree.getInternalNodeCount());
+			intervalLow = tree.getNode(tree.getLeafNodeCount() + x).getHeight();
+			int y = x;
+			while (x == y) {
+				y = Randomizer.nextInt(tree.getInternalNodeCount());
+				intervalHi  = tree.getNode(tree.getLeafNodeCount() + y).getHeight();
+			}
 		}
 
 		if (intervalHi < intervalLow) {
@@ -106,7 +111,7 @@ public double proposal() {
 			if (!node.isFake()) {
 				// only change "real" internal nodes, not ancestral ones
 				double h = node.getHeight();
-				if (h > intervalLow && h < intervalHi) {
+				if (h > intervalLow && h <= intervalHi) {
 					h = intervalLow + scale * (h-intervalLow);
 					node.setHeight(h);
 					scaled++;
@@ -154,12 +159,7 @@ public double proposal() {
 			}
 		}
 
-		double newHeight = tree.getRoot().getHeight();
-
 		double logHR = scaled * Math.log(scale);
-		if (groupSizes == null) {
-			logHR += 2 * Math.log(newHeight/oldHeight);
-		}
 		return logHR;
     }
 

diff --git a/src/beast/pkgmgmt/BEASTVersion.java b/src/beast/pkgmgmt/BEASTVersion.java
@@ -17,9 +17,9 @@ public class BEASTVersion extends Version {
     /**
      * Version string: assumed to be in format x.x.x
      */
-    private static final String VERSION = "2.7.6";
+    private static final String VERSION = "2.7.7";
 
-    private static final String DATE_STRING = "2002-2023";
+    private static final String DATE_STRING = "2002-2024";
 
     private static final boolean IS_PRERELEASE = true;
 

diff --git a/src/beast/pkgmgmt/PackageManager.java b/src/beast/pkgmgmt/PackageManager.java
@@ -91,7 +91,7 @@ public enum UpdateStatus {AUTO_CHECK_AND_ASK, AUTO_UPDATE, DO_NOT_CHECK};
     		BEASTVersion.INSTANCE.getMajorVersion() +".xml";
     public final static String PACKAGES_XML_BACKUP = "https://bitbucket.org/rrb/cbanclone/raw/master/packages2.7.xml";
 
-    private final static Set<String> RECOMMENDED_PACKAGES = new HashSet<>(Arrays.asList("ORC", "starbeast3"));
+    private final static Set<String> RECOMMENDED_PACKAGES = new HashSet<>(Arrays.asList("ORC", "starbeast3", "CCD"));
 
     public final static String ARCHIVE_DIR = "archive";
 

diff --git a/version.xml b/version.xml
@@ -1,4 +1,4 @@
-<package name="BEAST.base" version="2.7.6">
+<package name="BEAST.base" version="2.7.7">
 <!-- note version="2.7.x" must be double quotes for Mac release script release/Mac/createdmg.sh -->
 
             <!-- data types -->