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Commits on May 24, 2012
  1. Cleaned up comments.

    committed May 24, 2012
Commits on May 22, 2012
  1. Deleted stray bracket.

    committed May 22, 2012
Commits on May 18, 2012
  1. Style fixes: phyloXML not PhyloXML

    committed May 18, 2012
  2. Added require 'bio'.

    committed May 18, 2012
  3. Added proper credits.

    committed May 18, 2012
  4. Formatting fixes.

    committed May 18, 2012
  5. Attempted to write a proper README.

    committed May 18, 2012
  6. Repackaged unit tests.

    committed May 18, 2012
Commits on Nov 22, 2011
  1. Test bug fix: Opened files should be closed.

     * Test bug fix: Opened files should be closed.  When finalizing writer
       tests, temporary files are not properly closed after verify reading,
       and removing the temporary files raise erro on Windows.
    ngoto committed Nov 22, 2011
  2. New method Bio::PhyloXML::Parser#closed?, and Bio::PhyloXML::Parser.o…

    …pen with block.
    
     * New method Bio::PhyloXML::Parser#closed? to check if it is closed
       or not.
     * Bio::PhyloXML::Parser.open and open_uri now can get a block.
       When a block is given, a Bio::PhyloXML::Parser object is passed
       to the block as an argument. When the block terminates, the object
       is closed.
     * Added tests about the above changes.
    ngoto committed Nov 22, 2011
Commits on Oct 21, 2010
Commits on Nov 18, 2009
  1. New version of PhyloXML schema, version 1.10.

     * Upgraded to New version of PhyloXML schema, version 1.10,
       developed by Christian M Zmasek.
    ngoto committed Nov 18, 2009
  2. Newly added sample script to test big PhyloXML data

     * Newly added a sample script to test big PhyloXML data based on
       Diana Jaunzeikare's work.
       (http://github.com/latvianlinuxgirl/bioruby/blob/
       20627fc5a443d6c2e3dc73ed50e9c578ffcbc330/
       test/unit/bio/db/test_phyloxml_big.rb).
    ngoto committed Nov 17, 2009
Commits on Nov 12, 2009
  1. The "libpath magic" in tests are replaced by the load of helper routine.

     * In all unit tests, the "libpath magic" are replaced by the load
       of helper routine.
     * Changed to use a constant BioRubyTestDataPath for generating test
       data file path.
     * Some "require" lines are modified.
     * "File.open(...).read" in some tests are replaced by "File.read(...)".
     * Header comment lines of some tests with wrong filename and/or
       class/module name information are fixed.
    ngoto committed Nov 12, 2009
Commits on Oct 23, 2009
  1. New class method Bio::PhyloXML::Parser.open(filename) and API change …

    …of new(), etc.
    
     * New class methods to create parser object from various data
       source are added: Bio::PhyloXML::Parser.open(filename),
       for_io(io), open_uri(uri).
     * API change of Bio::PhyloXML::Parser.new(). Now, new(filename)
       is deprecated and it can only take a XML-formatted string.
     * Tests are added and modified to reflect the above changes.
     * test/unit/bio/db/test_phyloxml_writer.rb: avoid using WeakRef
       for temporary directory maintenance.
    ngoto committed Oct 23, 2009
Commits on Oct 22, 2009
  1. Fixed argument order of assert_equal(expected, actual), etc.

     * Test bug fix: Argument order of assert_equal must be
       assert_equal(expected, actual).
     * assert_instance_of() instead of assert_equal() in
       TestPhyloXML1#test_init.
     * Removed some commented-out tests which may not be needed.
    ngoto committed Oct 22, 2009
Commits on Sep 20, 2009
  1. Removed "require 'rubygems'".

    ngoto committed Sep 20, 2009
  2. Changed to use temporary directory when writing a file, etc.

      * To avoid unexpected file corruption and possibly security risk,
        changed to use temporary directory when writing files. The
        temporary directory is normally removed when all tests end.
        To prevent removing the directory, set environment variable
        BIORUBY_TEST_DEBUG.
      * To avoid test class name conflict, TestPhyloXMLData is renamed
        to TestPhyloXMLWriterData.
      * Added a new test to check existence of libxml-ruby, and removed
        code to raise error when it is not found. The code of the new
        test is completely the same as of in test_phyloxml.rb, but it
        is added for the purpose when test_phyloxml_writer.rb is called
        independently.
    ngoto committed Sep 18, 2009
Commits on Sep 19, 2009
Commits on Sep 10, 2009
  1. Newly added PhyloXML support written by Diana Jaunzeikare.

     * Newly added PhyloXML support written by Diana Jaunzeikare.
       It have been written during the Google Summer of Code 2009
       "Implementing phyloXML support in BioRuby", mentored by
       Christian Zmasek et al. with NESCent. For details of development,
       see git://github.com/latvianlinuxgirl/bioruby.git and BioRuby
       mailing list archives.
     * This is a combination of 119 commits. The last commit date was
       Mon Aug 17 10:30:10 2009 -0400.
    latvianlinuxgirl committed with ngoto May 26, 2009
  2. Newly added Chromatogram classes contributed by Anthony Underwood.

     * Newly added Chromatogram classes contributed by Anthony Underwood.
       See git://github.com/aunderwo/bioruby.git for details of development
       before this merge.
    ngoto committed Sep 9, 2009
Commits on Sep 2, 2009
  1. BioRuby 1.3.1 is released.

    ChangeLog is modified, and bioruby.gemspec is regenerated.
    ngoto committed Sep 2, 2009
Commits on Sep 1, 2009
  1. bioruby.gemspec is regenerated

    ngoto committed Sep 1, 2009