Skip to content

Commit

Permalink
finalise v2.4.1 release #548
Browse files Browse the repository at this point in the history
  • Loading branch information
@rbouckaert
rbouckaert committed Apr 25, 2016
1 parent 4ab846b commit 0a39677
Show file tree
Hide file tree
Showing 4 changed files with 24 additions and 24 deletions.
2 changes: 1 addition & 1 deletion release/common/VERSION HISTORY.txt
View file
Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,7 @@ Version 2.4.1 April 2016
import of calibrations from NEXUS files
add App Launcher menu
make missing *BEAST template available again

save in old style XML, with less restricions on taxa names
Streamlined upgrades of BEAST

BEAST
Expand Down
2 changes: 1 addition & 1 deletion src/beast/app/BEASTVersion.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,7 @@ public class BEASTVersion extends Version {

private static final String DATE_STRING = "2002-2016";

private static final boolean IS_PRERELEASE = true;
private static final boolean IS_PRERELEASE = false;

private static final String BEAST2_WEBPAGE = "http://beast2.org/";

Expand Down
2 changes: 1 addition & 1 deletion src/beast/app/BEASTVersion2.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@ public class BEASTVersion2 extends BEASTVersion {

private static final String DATE_STRING = "2002-2016";

private static final boolean IS_PRERELEASE = true;
private static final boolean IS_PRERELEASE = false;
//
// private static final String BEAST2_WEBPAGE = "http://beast2.org/";
//
Expand Down
42 changes: 21 additions & 21 deletions src/beast/app/beastapp/BeastMain.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -156,16 +156,16 @@ public BeastMain(final BeastMCMC beastMCMC, final BeastConsoleApp consoleApp, fi
// This call never returns as another RuntimeException exception is raised by
// the error log handler???
infoLogger.warning("Error running file: " + fileName);
Log.err.println("Fatal exception: " + rex.getMessage());
System.err.println("Fatal exception: " + rex.getMessage());
rex.printStackTrace(System.err);
}
*/
} catch (XMLParserException e) {
Log.info.println(e.getMessage());
System.out.println(e.getMessage());
//e.printStackTrace();
} catch (Exception e) {
Log.info.println("Fatal exception: " + e.getMessage());
e.printStackTrace(Log.err);
System.out.println("Fatal exception: " + e.getMessage());
e.printStackTrace(System.err);
infoLogger.severe("Fatal exception: " + e.getMessage());
}
}
Expand Down Expand Up @@ -206,22 +206,22 @@ public static void centreLine(final String line, final int pageWidth) {
final int n = pageWidth - line.length();
final int n1 = n / 2;
for (int i = 0; i < n1; i++) {
Log.info.print(" ");
System.out.print(" ");
}
Log.info.println(line);
System.out.println(line);
}

public static void printTitle() {

int pageWidth = 72;

Log.info.println();
System.out.println();
centreLine("BEAST " + version.getVersionString() + ", " + version.getDateString(), pageWidth);
centreLine("Bayesian Evolutionary Analysis Sampling Trees", pageWidth);
for (final String creditLine : version.getCredits()) {
centreLine(creditLine, pageWidth);
}
Log.info.println();
System.out.println();
}

public static void printUsage(final Arguments arguments) {
Expand Down Expand Up @@ -279,15 +279,15 @@ public static void main(final String[] args) throws java.io.IOException {
try {
arguments.parseArguments(args);
} catch (Arguments.ArgumentException ae) {
Log.info.println();
Log.info.println(ae.getMessage());
Log.info.println();
System.out.println();
System.out.println(ae.getMessage());
System.out.println();
printUsage(arguments);
System.exit(1);
}

if (arguments.hasOption("version")) {
Log.info.println((new BEASTVersion2()).getVersionString());
System.out.println((new BEASTVersion2()).getVersionString());
System.exit(0);
}

Expand Down Expand Up @@ -389,14 +389,14 @@ public void write(int b) {
}
if (threadCount <= 0) {
threadCount = Runtime.getRuntime().availableProcessors();
Log.warning.println("Setting number of threads to " + threadCount);
System.err.println("Setting number of threads to " + threadCount);
}

if (arguments.hasOption("seed")) {
seed = arguments.getLongOption("seed");
if (seed <= 0) {
printTitle();
Log.err.println("The random number seed should be > 0");
System.err.println("The random number seed should be > 0");
System.exit(1);
}
}
Expand Down Expand Up @@ -486,7 +486,7 @@ public void write(int b) {

inputFile = dialog.getInputFile();
if (!beagleShowInfo && inputFile == null) {
Log.err.println("No input file specified");
System.err.println("No input file specified");
System.exit(1);
}

Expand All @@ -510,8 +510,8 @@ public void write(int b) {
final String[] args2 = arguments.getLeftoverArguments();

if (args2.length > 1) {
Log.err.println("Unknown option: " + args2[1]);
Log.err.println();
System.err.println("Unknown option: " + args2[1]);
System.err.println();
printUsage(arguments);
System.exit(1);
}
Expand Down Expand Up @@ -577,7 +577,7 @@ public void write(int b) {

if (stateFileName!= null && stateFileName.trim().length() > 0) {
System.setProperty("state.file.name", stateFileName.trim());
Log.info.println("Writing state to file " + stateFileName);
System.out.println("Writing state to file " + stateFileName);
}

// if (allowOverwrite) {
Expand All @@ -599,8 +599,8 @@ public void write(int b) {
MCMCargs.add(seed + "");
Randomizer.setSeed(seed);

Log.info.println("Random number seed: " + seed);
Log.info.println();
System.out.println("Random number seed: " + seed);
System.out.println();

// Construct the beast object
final BeastMCMC beastMCMC = new BeastMCMC();
Expand All @@ -613,7 +613,7 @@ public void write(int b) {
if (!doNotRun) {
new BeastMain(beastMCMC, consoleApp, maxErrorCount);
} else {
Log.info.println("Done!");
System.out.println("Done!");
}
} catch (RuntimeException rte) {
if (window) {
Expand Down

0 comments on commit 0a39677

Please sign in to comment.