= BioRuby 1.5.1 RELEASE NOTES

A lot of changes have been made to the BioRuby 1.5.1 after the version 1.5.0
is released. This document describes important and/or incompatible changes
since the BioRuby 1.5.0 release.

For known problems, see KNOWN_ISSUES.rdoc.

== New features

=== (tbd)

(paragraph)

=== Other new features

* (tbd)
* (tbd)

== Bug fixes

=== (tbd)

(paragraph)

=== Other bug fixes

* Fixed: (...)
* Fixed: (...)

== Incompatible changes

=== Bio::Taxonomy is removed and merged to Bio::PhyloXML::Taxonomy

Bio::Taxonomy in lib/bio/db/phyloxml/phyloxml_elements.rb was written for
PhyloXML in 2009. It was intended to become general taxonomy data class in
BioRuby in these days. However, no efforts have been made to improve the
Bio::Taxonomy class, and it still remains to be a PhyloXML specific class.
Because Bio::PhyloXML is split as a different Gem (Biogem) package, we now
decide to remove Bio::Taxonomy and merge it to Bio::PhyloXML::Taxonomy.

In the codes using Bio::Taxonomy directly, changing Bio::Taxonomy to
Bio::PhyloXML::Taxonomy or adding the following monkey patch may be needed.

   module Bio
      unless defined? Taxonomy
         Taxonomy = Bio::PhyloXML::Taxonomy
      end
   end

In the future, Bio::Taxonomy might be added as general taxonomy data class.
The new Bio::Taxonomy might be incompatible with the current Bio::Taxonmy.

=== (tbd)

(paragraph)

== Known issues

The following issues are added or updated. See KNOWN_ISSUES.rdoc for other
already known issues.

* (tbd)

== Other important news

(tbd)