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Commits on Mar 29, 2012
  1. bump version: 1.1.0

    * 1.9.2 support
    
    Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
    yeban committed Mar 28, 2012
  2. README: move API discussion from the wiki to README

    * Having the API discussion in README gives it an official status and is
      subject to the same development cycle as the rest of the code.
    * Yard generates a nice home page, on the lines of sinatrarb.com, for the
      documentation-website (http://nexml.github.com/bio-nexml/) out of README.
    * README is shipped with both gem and source which makes for offline
      documentation.
    
    Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
    yeban committed Mar 29, 2012
  3. do not autoload any files; load all of them at the start

    `autoload` is going to [go away][1] from Ruby.
    
    [1]: http://www.ruby-forum.com/topic/3036681
    
    Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
    yeban committed Mar 29, 2012
Commits on Mar 22, 2012
  1. travis: disable testing for jruby

    JRuby doesn't allow building native C extensions which is required for
    libxml-ruby.  So we can't really support JRuby yet.
    
    Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
    yeban committed Mar 22, 2012
  2. travis: notify Rutger and myself of the build status

    Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
    yeban committed Mar 22, 2012
  3. test/trees: fix assert on 1.9.2

    `assert` on 1.9.2 takes a String or Proc only.
    
    Tests now pass on both 1.8.7 and 1.9.2 (closes #4).  And given than bio-nexml's
    test coverage is pretty good, this also guarantees 1.9.2 support (closes #2).
    
    Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
    yeban committed Mar 22, 2012
  4. mapper: use define_method to define each_* methods for a has_n relation

    Should have used `define_method` from the start, but at that time I was under
    the impression that `define_method` could not be used to define methods that
    take a block, so I went with `class_eval`.  `class_eval`, however, was causing
    tests to fail on 1.9.2 (#4) for some weird reason, so we switch to
    `define_method`.
    
    Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
    yeban committed Mar 22, 2012
Commits on Mar 18, 2012
  1. README: use markdown instead of rdoc for markup

    I like markdown.
    
    Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
    yeban committed Mar 18, 2012
  2. README: request people to cite NeXML manuscript if they use bio-nexml

    Use blockquote instead of pre so links to the paper are recognized.
    
    Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
    yeban committed Mar 18, 2012
  3. README: use Rutger's full name and add my name in the copyright notice

    Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
    yeban committed Mar 18, 2012
  4. README: point to Github wiki for a discussion of the API

    Looks like the old 'NeXML Ruby API' page on the NESCent wiki has been removed.
    In any case, further changes to the document should be made on Github.
    
    Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
    yeban committed Mar 18, 2012
Commits on Mar 17, 2012
  1. travis: disable email notifications

    Don't need at the moment.
    
    Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
    yeban committed Mar 17, 2012
  2. README: show build status from nexml/bio-nexml instead of pjotr/bio-n…

    …exml
    
    Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
    yeban committed Mar 17, 2012
  3. gemspec: cap at libxml-ruby 1.1.4

    Latest version changes the API a bit, and segfaults like crazy!  Let's avoid it
    for the time being.
    
    Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
    yeban committed Mar 17, 2012
Commits on Mar 16, 2012
  1. Merge pull request #3 from pjotrp/master

    Fixes for bundler and Gemspec
    rvosa committed Mar 16, 2012
  2. Unit tests: fix assert on 1.9.2

    pjotrp committed Mar 16, 2012
  3. Unit tests: fix assert on 1.9.2

    pjotrp committed Mar 16, 2012
  4. - Updated repo path (for http://biogems.info/)

    - Fixed bundler
    pjotrp committed Mar 16, 2012
Commits on Dec 12, 2011
Commits on Sep 21, 2011
  1. Updated version number in gemspec

    rvosa committed with rvosa Sep 21, 2011
  2. Merge branch 'master' of github.com:rvosa/bio-nexml

    Conflicts:
    	bio-nexml.gemspec
    rvosa committed with rvosa Sep 21, 2011
Commits on Aug 8, 2011
  1. Regenerate gemspec for version 0.0.1

    rvosa committed with rvosa Aug 8, 2011
Commits on Aug 7, 2011
  1. version bump

    yeban committed Aug 7, 2011
  2. add Getting Started section to README

    When developing bio-nexml I had documented most of the API on NESCENT's
    wiki. It's not complete, but definitely enough to get started.
    yeban committed Aug 7, 2011
  3. load bio-nexml on require 'bio-nexml'

    Previously, require 'bio-nexml' would do nothing. To load bio-nexml
    _correctly_, the user would have to require 'bio', and then require
    'bio/db/nexml'.
    yeban committed Aug 7, 2011
  4. remove lib/bio.rb to avoid conflicts with BioRuby

    BioRuby sets up autolod definitions in lib/bio.rb for various core
    modules. bio-nexml carried over lib/bio.rb from the early development
    days when it was supposed to be a core part of BioRuby. Now, whichever
    appears first in the load path, bioruby or bio-nexml, gets loaded on
    require 'bio'. This can cause weird problems.
    yeban committed Aug 7, 2011
Commits on Aug 6, 2011
  1. update Gemfile to read dependencies from gemspec

    Avoid duplication.
    yeban committed Aug 6, 2011
  2. replace the old, Jeweler generated gemspec with a new, handcrafted one

    * clear the cruft generated by Jeweler
    * include Anurag Priyam (myself) as an author
    * include the new project homepage (Yard documentation hosted on Github)
    yeban committed May 3, 2011
  3. remove development dependency on Jeweler

    Jeweler is plainly retarded. It just duplicates the effort with no added
    advantage.
    yeban committed Aug 6, 2011
  4. remove Gemfile.lock from version control

    For gem development, Gemfile.lock should not be checked into version
    control, see [1].
    
    [1]: http://yehudakatz.com/2010/12/16/clarifying-the-roles-of-the-gemspec-and-gemfile/
    yeban committed Aug 6, 2011
Commits on May 3, 2011
Commits on Apr 27, 2011