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Commits on Sep 17, 2015
  1. @ngoto
  2. @ngoto
  3. @ngoto

    Delete Bio::PhyloXML tutorial

     * Tutorial for Bio::PhyloXML is deleted from BioRuby core.
       It is now moved to bio-phyloxml gem. New tutorial for
       Bio::PhyloXML is available at:
       https://github.com/bioruby/bioruby-phyloxml/blob/master/doc/Tutorial.rd
    ngoto committed Sep 17, 2015
  4. @ngoto
  5. @ngoto

    Remove PhyloXML (split out bio-phyloxml gem)

     * Bio::PhyloXML is removed from BioRuby core.
       It will soon be released as separate bio-phyloxml gem.
       The development repository of the new Bio::PhyloXML is
       https://github.com/bioruby/bioruby-phyloxml
    ngoto committed Sep 17, 2015
  6. @ngoto

    Delete autoload of Bio::PhyloXML

     * Delete autoload of Bio::PhyloXML, for preparation of spliting
       out Bio::PhyloXML.
    ngoto committed Sep 17, 2015
Commits on Sep 15, 2015
  1. @ngoto
  2. @ngoto

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

     * Bio::Taxonomy in lib/bio/db/phyloxml/phyloxml_elements.rb was
       written for PhyloXML, but it was intended to become general
       taxonomy data class in BioRuby. However, no efforts have been
       made to improve the Bio::Taxonomy class, and it still remains
       to be a PhyloXML specific class. As the first step to split out
       Bio::PhyloXML to a new Gem (Biogem) package, we now decide to
       remove Bio::Taxonomy and merge it to Bio::PhyloXML::Taxonomy.
    
     * Codes using Bio::Taxonomy should be modified. Changing
       Bio::Taxonomy to Bio::PhyloXML::Taxonomy, or adding the
       following monkey patch is needed.
    
          module Bio
             unless defined? Taxonomy
                Taxonomy = Bio::PhyloXML::Taxonomy
             end
          end
    ngoto committed Sep 15, 2015
Commits on Sep 14, 2015
  1. @ngoto
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Commits on Jul 2, 2015
  1. @ngoto

    ChangeLog since 1.5.0 release

    ngoto committed Jul 2, 2015
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Commits on Jul 1, 2015
  1. @ngoto

    BioRuby 1.5.0 is released

    ngoto committed Jul 1, 2015
Commits on Jun 30, 2015
  1. @ngoto
  2. @ngoto
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  11. @ngoto

    prepare to release BioRuby 1.5.0

    ngoto committed Jun 30, 2015
  12. @ngoto

    RELEASE_NOTES.rdoc: update many

    ngoto committed Jun 30, 2015
  13. @ngoto

    Bug fix: Bio::UniProtKB#gene_name should not raise NoMethodError

     * Bug fix: Bio::UniProtKB#gene_name raised NoMethodError when
       gene_names method returns nil. It should return nil.
       Thanks to Jose Irizarry who reports and sends suggested fix.
       (#83 )
    ngoto committed Jun 30, 2015
  14. @ngoto
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  16. @ngoto

    delete description about SOAP4R

    ngoto committed Jun 30, 2015
Commits on Jun 29, 2015
  1. @ngoto

    .travis.yml: test/unit no longer bundled with Ruby 2.2

     * For Ruby 2.2, use a new Gemfile named Gemfile.travis-ruby2.2
       that include 'gem "test-unit"' line because test/unit have been
       provided by bundled gem since Ruby 2.2.
    ngoto committed Jun 30, 2015
  2. @ngoto

    bump up version to 1.5.0-dev; simplify the versioning rules

     * Bump up version to 1.5.0-dev (1.5.0.20150630)
     * Simplify the versioning rules.
     * We will adopt the Semantic Versioning since BioRuby 1.5.1.
    ngoto committed Jun 30, 2015
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