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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)

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Other new features

  • (tbd)

  • (tbd)

Bug fixes

(tbd)

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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)

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Known issues

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

  • (tbd)

Other important news

(tbd)

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