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Commits on May 24, 2012

• Cleaned up comments.

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Commits on May 22, 2012

• Deleted stray bracket.

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Commits on May 18, 2012

• Style fixes: phyloXML not PhyloXML

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• Fixed up require declarations in sample code. Discussed migration.

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• Added require 'bio'.

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• Added proper credits.

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• Formatting fixes.

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• Attempted to write a proper README.

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• Set version to 0.9.0 for now to be on the safe side.

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• Set up more or less standard biogem skeleton.

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• require 'bio-phyloxml' -> require 'bio/phyloxml' -> requires the rest.

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• Repackaged unit tests.

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• Removed internal require and autoload definitions, all hierarchical now.

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• Repackaged files to lib/bio/phyloxml/*.rb to match class names.

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Commits on Nov 22, 2011

• Test bug fix: Opened files should be closed.

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• New method Bio::PhyloXML::Parser#closed?, and Bio::PhyloXML::Parser.open with block.

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Commits on Oct 21, 2010

• Merge branch 'test-defline-by-jtprince'

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Commits on Nov 18, 2009

• New version of PhyloXML schema, version 1.10.

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• Newly added sample script to test big PhyloXML data

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Commits on Nov 12, 2009

• The "libpath magic" in tests are replaced by the load of helper routine.

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Commits on Oct 23, 2009

• New class method Bio::PhyloXML::Parser.open(filename) and API change of new(), etc.

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• Rearrangement of require and autoload so as to correctly load PhyloXML classes

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Commits on Oct 22, 2009

• Fixed argument order of assert_equal(expected, actual), etc.

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Commits on Sep 20, 2009

• Removed "require 'rubygems'".

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• Changed to use temporary directory when writing a file, etc.

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Commits on Sep 19, 2009

• Added new test to check existence of libxml-ruby, instead of raising error.

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• Renamed output files generated by phyloxml_writer unit tests.

  

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• Added ncbi_taxonomy_mollusca_short.xml test file

  

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• Made the code compactible with libxml-ruby 1.1.3 (previous was 0.9.4) version.

  

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Commits on Sep 10, 2009

• Newly added PhyloXML support written by Diana Jaunzeikare.

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• Newly added Chromatogram classes contributed by Anthony Underwood.

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• Bio::BIORUBY_EXTRA_VERSION is changed to ".5000".

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Commits on Sep 2, 2009

• BioRuby 1.3.1 is released.

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• Preparation for bioruby-1.3.1 release.

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Commits on Sep 1, 2009

• bioruby.gemspec is regenerated

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