diff --git a/release/common/README.txt b/release/common/README.txt
index f78d0575..b41d8a0a 100644
--- 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:
-
-
-
-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
index 043dfd9e..c1c1361d 100644
--- 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
index 9811b84d..44239fc5 100644
--- 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
index fc251e1b..d6e78cee 100644
--- 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
index f8c452ec..9dba0a94 100644
--- 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
index 42710bf6..6f98bea0 100644
--- 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 RECOMMENDED_PACKAGES = new HashSet<>(Arrays.asList("ORC", "starbeast3"));
+ private final static Set RECOMMENDED_PACKAGES = new HashSet<>(Arrays.asList("ORC", "starbeast3", "CCD"));
public final static String ARCHIVE_DIR = "archive";
diff --git a/version.xml b/version.xml
index 46dcc113..caa4c2f4 100644
--- a/version.xml
+++ b/version.xml
@@ -1,4 +1,4 @@
-
+