BEAUti template bug fix

This is a patch release which fixes a critical error in the bacter beauti interface, which made it impossible to use anything besides a Jukes-Cantor substitution model. (This error was due to the original 3.0.0 release failing to adapt to the new class of operators used in beast 2.7.)

First release for BEAST 2 version 7.0.

This release provides compatibility with version 7.0 of BEAST 2.

Many thanks to @jordandouglas for his amazing help with this port!

Fixed bug introduced by previous release.

This release fixes a serialization bug introduced by the previous release. A unit test for this bug has been added to avoid future regression.

Fixed bug in initialising from extended Newick

This release patches a bug relating to the extendedNewick input provided by the ConversionGraph class, which was causing array index out-of-bounds errors when networks were initialised this way.

Fixed BEAST 2.6 compatibility bug.

The previous release claimed to be compatible with BEAST 2.6.0. It was not. This release fixes this problem.

Brought up-to-date with BEAST 2.6.0

This release is explicitly compatible with the latest version of BEAST.

Bug-fix release: State resume bug.

This release fixes a state resumption bug introduced upstream.

Direct priors on number of conversions.

This release allows priors to be placed directly on the number of conversions in an ARG. This allows analyses to be set up where an arbitrary tree prior is placed on the clonal frame and the conversions are described separately to the tree model.

Bug-fix release: ACGAnnotator LaF bug

The default swing LaF was preventing output file names from being set under MacOS. This update causes ACGAnnotator to use the cross-platform Metal LaF for which this problem does not occur.

Conversion-free loci

This release adds the ability to specify conversion-free loci: loci on which recombination is not allowed.

Currently, disabling conversions on a locus requires editing the BEAST XML file. Happily the modification is trivial. Simply locate the opening tag for the locus you wish to disable conversions on, for instance

 <locus id="locus.partition_name" spec="bacter.Locus">

where partition_name is the name of the alignment corresponding to the locus. Then just add the attribute conversionsAllowed="false":

 <locus id="locus.partition_name" spec="bacter.Locus" conversionsAllowed="false">

The analysis should now avoid proposing conversions on this locus.