3 February 2016 by Remco Bouckaert

Most significant upcoming changes are

• Annotated constructor support, so instead of using Input and initAndValidate you can use constructors and use most of the info that now goes into and Input in a @Param annotation. See, for example AnnotatedRunnableTestClass and JSONTest.
• Better JSON support for BEAST specifications, using a non-evil JSON library.
• Removal of Exceptions in favour of classes that derive from Exception. This means that many methods that previously were throwing Exceptions, are throwing more specialised Exceptions, or nothing at all (if only RuntimeExceptions are thrown).
• Cleaned up code, better conforming to Java 8 constructions and naming conventions. Also, attempt to remove the term ‘Plugin’ and replace with BEAST object where appropriate, since the term plugin is not used any more.

Code changes

This is a (still evolving) list of changes for package developers containing possible changes required to make packages compatible with BEAST v2.4.0. Mostly, there are minor method signature changes, and some member variables name changes, with the exception of Exceptions.

Exceptions

However, the biggest change is that throws Exception on initAndValidate will be removed. initAndValidate is supposed to check validity of values of inputs, and initialise. If for some reason this fails, the most appropriate exception to throw is IllegalArgumentException or RuntimeException.

Note you can always throw fewer exceptions than the method derived from, so you can change your code to work with both v2.3 and v2.4 by just removing or specialising the exception that is thrown.

Signature changes

The signature of BeautiDoc.deepCopyPlugin changes: requires an extra argument to tell which partition to copy from.

Access changes

A number of package private member and methods now are protected to allow access from difference packages.
BeautiAlignmentProvider.getAlignments(),

Most inputs are now final, so cannot be re-assigned.

Name changes

SubtreeSlide.fSize is now SubtreeSlide.size
InputEditor.m_plugin is now InputEditor.beastObject
BeautiConfig.inlinePlugin, collapsedPlugins, suppressPlugins are now inlineBEASTObject, collapsedBEASTObjects, suppressBEASTObjects

Deprecated

BEASTObject.outputs is now private. Use BEASTObject.getOutputs() to access the set of outputs.