version v1.0.0

Author: rbouckaert

build.xml

@@ -18,7 +18,7 @@
 	<property name="srcBeast2" location="${beast2path}/src" />
 	<property name="beast2classpath" location="${beast2path}/build" />
 	<property name="Add_on_dir" value="${release_dir}/add-on" />
-	<property name="version" value="0.1.0" />
+	<property name="version" value="1.0.0" />
 
 	<property name="buildMODEL_SELECTION" location="../model-selection/build"/>
 	<property name="buildBEAST_LABS" location="../BEASTLabs/build"/>
@@ -31,6 +31,7 @@
 
 	<path id="classpath">
         <pathelement path="${buildNS}"/>
+		<fileset dir="${libBeast2}" includes="antlr-runtime-4.7.jar"/>
 		<fileset dir="${libBeast2}" includes="junit-4.8.2.jar"/>
 		<fileset dir="${libBeast2}" includes="beagle.jar"/>
         <fileset dir="${libBeast2}" includes="jam.jar"/>

src/beast/core/NSLogger.java

@@ -10,6 +10,7 @@
 import beast.core.Logger;
 import beast.util.XMLProducer;
 
+@Description("Trace logger that logs NSLikelihood as second column (used by NSLogAnalyser to prodoce posterior sample)")
 public class NSLogger extends Logger {
 
 	@Override

src/beast/gss/NS.java

@@ -47,7 +47,7 @@
 */
 
 @Description("Nested sampling for phylogenetics")
-@Citation("Patricio Maturana, Brendon J. Brewer, Steffen Klaere, Remco Bouckaert. Model selection and parameter inference in phylogenetics using Nested Sampling. arXiv:1703.05471v3")
+@Citation("Patricio Maturana, Brendon J. Brewer, Steffen Klaere, Remco Bouckaert. Model selection and parameter inference in phylogenetics using Nested Sampling. Systematic Biology, In Press 2018")
 public class NS extends MCMC {
 	final static int SAMPLE_COUNT = 100;
 

src/beast/gss/NSThread.java

@@ -1,14 +1,16 @@
 
 package beast.gss;
 
+
 import java.io.IOException;
 import java.util.Map;
 import java.util.concurrent.CountDownLatch;
 
+import beast.core.Description;
 import beast.core.Distribution;
 import beast.util.Randomizer;
 
-/** class for performing a one-threaded NS as part of MultiThreadedNS */
+@Description("class for performing a one-threaded NS as part of MultiThreadedNS")
 public class NSThread extends NS {
 	CountDownLatch countDown;
 	Map<String, Double> particlePool;

version.xml

@@ -1,5 +1,7 @@
-<package name='NS' version='0.1.0'>
+<package name='NS' version='1.0.0'>
 	<depends on='beast2' atleast='2.5.0'/>
+	<depends on='BEASTLabs' atleast='1.8.0'/>
+	<depends on='MODEL_SELECTION' atleast='1.4.1'/>
 
     <packageapp description="Nested Sampling Log Analyser"
               class="beast.util.NSLogAnalyser"