bio-nexml 0.0.1 → 0.1.0

data/LICENSE.txt

@@ -1,4 +1,4 @@
-Copyright (c) 2011 rvosa
+Copyright (c) 2011 Rutger Vos and Anurag Priyam
 
 Permission is hereby granted, free of charge, to any person obtaining
 a copy of this software and associated documentation files (the

data/README.rdoc

@@ -25,6 +25,12 @@ semantics) that is both easy to work with, yet ready for the Semantic Web.
 
 To learn more, visit http://www.nexml.org
 
+== Getting Started
+
+https://www.nescent.org/wg_phyloinformatics/NeXML_and_RDF_API_for_BioRuby
+
+It is not complete, but definitely enough to get started.
+
 == Contributing to bio-nexml
  
 * Check out the latest master to make sure the feature hasn't been implemented

data/lib/bio-nexml.rb

@@ -0,0 +1,2 @@
+require 'bio'
+require 'bio/db/nexml'

metadata

@@ -1,87 +1,27 @@
 --- !ruby/object:Gem::Specification 
 name: bio-nexml
 version: !ruby/object:Gem::Version 
-  hash: 29
+  hash: 27
   prerelease: 
   segments: 
   - 0
-  - 0
   - 1
-  version: 0.0.1
+  - 0
+  version: 0.1.0
 platform: ruby
 authors: 
-- rvosa
+- Rutger Vos
+- Anurag Priyam
 autorequire: 
 bindir: bin
 cert_chain: []
 
-date: 2011-03-01 00:00:00 +01:00
-default_executable: 
+date: 2011-08-15 00:00:00 Z
 dependencies: 
-- !ruby/object:Gem::Dependency 
-  name: shoulda
-  prerelease: false
-  requirement: &id001 !ruby/object:Gem::Requirement 
-    none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 3
-        segments: 
-        - 0
-        version: "0"
-  type: :development
-  version_requirements: *id001
-- !ruby/object:Gem::Dependency 
-  name: bundler
-  prerelease: false
-  requirement: &id002 !ruby/object:Gem::Requirement 
-    none: false
-    requirements: 
-    - - ~>
-      - !ruby/object:Gem::Version 
-        hash: 23
-        segments: 
-        - 1
-        - 0
-        - 0
-        version: 1.0.0
-  type: :development
-  version_requirements: *id002
-- !ruby/object:Gem::Dependency 
-  name: jeweler
-  prerelease: false
-  requirement: &id003 !ruby/object:Gem::Requirement 
-    none: false
-    requirements: 
-    - - ~>
-      - !ruby/object:Gem::Version 
-        hash: 7
-        segments: 
-        - 1
-        - 5
-        - 2
-        version: 1.5.2
-  type: :development
-  version_requirements: *id003
-- !ruby/object:Gem::Dependency 
-  name: rcov
-  prerelease: false
-  requirement: &id004 !ruby/object:Gem::Requirement 
-    none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 3
-        segments: 
-        - 0
-        version: "0"
-  type: :development
-  version_requirements: *id004
 - !ruby/object:Gem::Dependency 
   name: bio
   prerelease: false
-  requirement: &id005 !ruby/object:Gem::Requirement 
+  requirement: &id001 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
     - - ">="
@@ -92,12 +32,12 @@ dependencies:
         - 4
         - 1
         version: 1.4.1
-  type: :development
-  version_requirements: *id005
+  type: :runtime
+  version_requirements: *id001
 - !ruby/object:Gem::Dependency 
   name: libxml-ruby
   prerelease: false
-  requirement: &id006 !ruby/object:Gem::Requirement 
+  requirement: &id002 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
     - - ">="
@@ -108,76 +48,32 @@ dependencies:
         - 1
         - 4
         version: 1.1.4
-  type: :development
-  version_requirements: *id006
-- !ruby/object:Gem::Dependency 
-  name: libxml-ruby
-  prerelease: false
-  requirement: &id007 !ruby/object:Gem::Requirement 
-    none: false
-    requirements: 
-    - - "="
-      - !ruby/object:Gem::Version 
-        hash: 27
-        segments: 
-        - 1
-        - 1
-        - 4
-        version: 1.1.4
   type: :runtime
-  version_requirements: *id007
-- !ruby/object:Gem::Dependency 
-  name: libxml-ruby
-  prerelease: false
-  requirement: &id008 !ruby/object:Gem::Requirement 
-    none: false
-    requirements: 
-    - - "="
-      - !ruby/object:Gem::Version 
-        hash: 27
-        segments: 
-        - 1
-        - 1
-        - 4
-        version: 1.1.4
-  type: :development
-  version_requirements: *id008
+  version_requirements: *id002
 description: This plugin reads, writes and generates NeXML
-email: rutgeraldo@gmail.com
+email: 
+- rutgeraldo@gmail.com
+- anurag08priyam@gmail.com
 executables: []
 
 extensions: []
 
-extra_rdoc_files: 
-- LICENSE.txt
-- README.rdoc
+extra_rdoc_files: []
+
 files: 
-- Gemfile
-- Gemfile.lock
-- LICENSE.txt
-- README.rdoc
-- Rakefile
-- TODO.txt
-- VERSION
-- bio-nexml.gemspec
-- extconf.rb
-- lib/bio-nexml.rb
-- lib/bio.rb
-- lib/bio/db/nexml.rb
-- lib/bio/db/nexml/mapper.rb
 - lib/bio/db/nexml/mapper/framework.rb
 - lib/bio/db/nexml/mapper/inflection.rb
 - lib/bio/db/nexml/mapper/repository.rb
+- lib/bio/db/nexml/mapper.rb
 - lib/bio/db/nexml/matrix.rb
 - lib/bio/db/nexml/parser.rb
-- lib/bio/db/nexml/schema/README.txt
 - lib/bio/db/nexml/schema/abstract.xsd
-- lib/bio/db/nexml/schema/characters/README.txt
 - lib/bio/db/nexml/schema/characters/abstractcharacters.xsd
 - lib/bio/db/nexml/schema/characters/characters.xsd
 - lib/bio/db/nexml/schema/characters/continuous.xsd
 - lib/bio/db/nexml/schema/characters/dna.xsd
 - lib/bio/db/nexml/schema/characters/protein.xsd
+- lib/bio/db/nexml/schema/characters/README.txt
 - lib/bio/db/nexml/schema/characters/restriction.xsd
 - lib/bio/db/nexml/schema/characters/rna.xsd
 - lib/bio/db/nexml/schema/characters/standard.xsd
@@ -185,31 +81,27 @@ files:
 - lib/bio/db/nexml/schema/external/xhtml-datatypes-1.xsd
 - lib/bio/db/nexml/schema/external/xlink.xsd
 - lib/bio/db/nexml/schema/external/xml.xsd
-- lib/bio/db/nexml/schema/meta/README.txt
 - lib/bio/db/nexml/schema/meta/annotations.xsd
 - lib/bio/db/nexml/schema/meta/meta.xsd
+- lib/bio/db/nexml/schema/meta/README.txt
 - lib/bio/db/nexml/schema/nexml.xsd
+- lib/bio/db/nexml/schema/README.txt
 - lib/bio/db/nexml/schema/taxa/README.txt
 - lib/bio/db/nexml/schema/taxa/taxa.xsd
-- lib/bio/db/nexml/schema/trees/README.txt
 - lib/bio/db/nexml/schema/trees/abstracttrees.xsd
 - lib/bio/db/nexml/schema/trees/network.xsd
+- lib/bio/db/nexml/schema/trees/README.txt
 - lib/bio/db/nexml/schema/trees/tree.xsd
 - lib/bio/db/nexml/schema/trees/trees.xsd
 - lib/bio/db/nexml/taxa.rb
 - lib/bio/db/nexml/trees.rb
 - lib/bio/db/nexml/writer.rb
-- test/data/nexml/test.xml
+- lib/bio/db/nexml.rb
+- lib/bio-nexml.rb
+- LICENSE.txt
+- README.rdoc
 - test/test_bio-nexml.rb
-- test/unit/bio/db/nexml/tc_factory.rb
-- test/unit/bio/db/nexml/tc_mapper.rb
-- test/unit/bio/db/nexml/tc_matrix.rb
-- test/unit/bio/db/nexml/tc_parser.rb
-- test/unit/bio/db/nexml/tc_taxa.rb
-- test/unit/bio/db/nexml/tc_trees.rb
-- test/unit/bio/db/nexml/tc_writer.rb
-has_rdoc: true
-homepage: http://github.com/rvosa/bioruby-nexml
+homepage: http://rvosa.github.com/bio-nexml/
 licenses: 
 - MIT
 post_install_message: 
@@ -238,16 +130,9 @@ required_rubygems_version: !ruby/object:Gem::Requirement
 requirements: []
 
 rubyforge_project: 
-rubygems_version: 1.4.2
+rubygems_version: 1.8.7
 signing_key: 
 specification_version: 3
 summary: BioRuby plugin for reading and writing NeXML (http://nexml.org)
 test_files: 
 - test/test_bio-nexml.rb
-- test/unit/bio/db/nexml/tc_factory.rb
-- test/unit/bio/db/nexml/tc_mapper.rb
-- test/unit/bio/db/nexml/tc_matrix.rb
-- test/unit/bio/db/nexml/tc_parser.rb
-- test/unit/bio/db/nexml/tc_taxa.rb
-- test/unit/bio/db/nexml/tc_trees.rb
-- test/unit/bio/db/nexml/tc_writer.rb

data/Gemfile

@@ -1,15 +0,0 @@
-source "http://rubygems.org"
-# Add dependencies required to use your gem here.
-# Example:
-#   gem "activesupport", ">= 2.3.5"
-
-# Add dependencies to develop your gem here.
-# Include everything needed to run rake, tests, features, etc.
-group :development do
-  gem "shoulda", ">= 0"
-  gem "bundler", "~> 1.0.0"
-  gem "jeweler", "~> 1.5.2"
-  gem "rcov", ">= 0"
-  gem "bio", ">= 1.4.1"
-  gem "libxml-ruby", ">= 1.1.4"
-end

data/Gemfile.lock

@@ -1,24 +0,0 @@
-GEM
-  remote: http://rubygems.org/
-  specs:
-    bio (1.4.1)
-    git (1.2.5)
-    jeweler (1.5.2)
-      bundler (~> 1.0.0)
-      git (>= 1.2.5)
-      rake
-    libxml-ruby (1.1.4)
-    rake (0.8.7)
-    rcov (0.9.9)
-    shoulda (2.11.3)
-
-PLATFORMS
-  ruby
-
-DEPENDENCIES
-  bio (>= 1.4.1)
-  bundler (~> 1.0.0)
-  jeweler (~> 1.5.2)
-  libxml-ruby (>= 1.1.4)
-  rcov
-  shoulda

data/Rakefile

@@ -1,55 +0,0 @@
-require 'rubygems'
-require 'bundler'
-begin
-  Bundler.setup(:default, :development)
-rescue Bundler::BundlerError => e
-  $stderr.puts e.message
-  $stderr.puts "Run `bundle install` to install missing gems"
-  exit e.status_code
-end
-require 'rake'
-
-require 'jeweler'
-Jeweler::Tasks.new do |gem|
-  # gem is a Gem::Specification... see http://docs.rubygems.org/read/chapter/20 for more options
-  gem.name = "bio-nexml"
-  gem.homepage = "http://github.com/rvosa/bioruby-nexml"
-  gem.license = "MIT"
-  gem.summary = %Q{BioRuby plugin for reading and writing NeXML (http://nexml.org)}
-  gem.description = %Q{This plugin reads, writes and generates NeXML}
-  gem.email = "rutgeraldo@gmail.com"
-  gem.authors = ["rvosa"]
-  gem.add_runtime_dependency 'libxml-ruby', '1.1.4'
-  gem.add_development_dependency 'libxml-ruby', '1.1.4'
-  # Include your dependencies below. Runtime dependencies are required when using your gem,
-  # and development dependencies are only needed for development (ie running rake tasks, tests, etc)
-  #  gem.add_runtime_dependency 'jabber4r', '> 0.1'
-  #  gem.add_development_dependency 'rspec', '> 1.2.3'
-end
-Jeweler::RubygemsDotOrgTasks.new
-
-require 'rake/testtask'
-Rake::TestTask.new(:test) do |test|
-  test.libs << 'lib' << 'test'
-  test.pattern = 'test/**/test_*.rb'
-  test.verbose = true
-end
-
-require 'rcov/rcovtask'
-Rcov::RcovTask.new do |test|
-  test.libs << 'test'
-  test.pattern = 'test/**/test_*.rb'
-  test.verbose = true
-end
-
-task :default => :test
-
-require 'rake/rdoctask'
-Rake::RDocTask.new do |rdoc|
-  version = File.exist?('VERSION') ? File.read('VERSION') : ""
-
-  rdoc.rdoc_dir = 'rdoc'
-  rdoc.title = "bio-nexml #{version}"
-  rdoc.rdoc_files.include('README*')
-  rdoc.rdoc_files.include('lib/**/*.rb')
-end

data/TODO.txt

@@ -1,6 +0,0 @@
-* it would be good if objects could only be instantiated in the right nesting
-  order, e.g. you wouldn't do cell = Cell.new, but you'd do
-  cell = Row.create_cell and the nesting is automatically handled for you.
-  I think the way to do this is to require the containing object to be passed
-  (recursively) to the constructors, while create_foo internally does this,
-  passing self to the constructor.

data/VERSION

@@ -1 +0,0 @@
-0.0.1

data/bio-nexml.gemspec

@@ -1,126 +0,0 @@
-# Generated by jeweler
-# DO NOT EDIT THIS FILE DIRECTLY
-# Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
-# -*- encoding: utf-8 -*-
-
-Gem::Specification.new do |s|
-  s.name = %q{bio-nexml}
-  s.version = "0.0.1"
-
-  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
-  s.authors = ["rvosa"]
-  s.date = %q{2011-03-01}
-  s.description = %q{This plugin reads, writes and generates NeXML}
-  s.email = %q{rutgeraldo@gmail.com}
-  s.extra_rdoc_files = [
-    "LICENSE.txt",
-    "README.rdoc"
-  ]
-  s.files = [
-    "Gemfile",
-    "Gemfile.lock",
-    "LICENSE.txt",
-    "README.rdoc",
-    "Rakefile",
-    "TODO.txt",
-    "VERSION",
-    "bio-nexml.gemspec",
-    "extconf.rb",
-    "lib/bio-nexml.rb",
-    "lib/bio.rb",
-    "lib/bio/db/nexml.rb",
-    "lib/bio/db/nexml/mapper.rb",
-    "lib/bio/db/nexml/mapper/framework.rb",
-    "lib/bio/db/nexml/mapper/inflection.rb",
-    "lib/bio/db/nexml/mapper/repository.rb",
-    "lib/bio/db/nexml/matrix.rb",
-    "lib/bio/db/nexml/parser.rb",
-    "lib/bio/db/nexml/schema/README.txt",
-    "lib/bio/db/nexml/schema/abstract.xsd",
-    "lib/bio/db/nexml/schema/characters/README.txt",
-    "lib/bio/db/nexml/schema/characters/abstractcharacters.xsd",
-    "lib/bio/db/nexml/schema/characters/characters.xsd",
-    "lib/bio/db/nexml/schema/characters/continuous.xsd",
-    "lib/bio/db/nexml/schema/characters/dna.xsd",
-    "lib/bio/db/nexml/schema/characters/protein.xsd",
-    "lib/bio/db/nexml/schema/characters/restriction.xsd",
-    "lib/bio/db/nexml/schema/characters/rna.xsd",
-    "lib/bio/db/nexml/schema/characters/standard.xsd",
-    "lib/bio/db/nexml/schema/external/sawsdl.xsd",
-    "lib/bio/db/nexml/schema/external/xhtml-datatypes-1.xsd",
-    "lib/bio/db/nexml/schema/external/xlink.xsd",
-    "lib/bio/db/nexml/schema/external/xml.xsd",
-    "lib/bio/db/nexml/schema/meta/README.txt",
-    "lib/bio/db/nexml/schema/meta/annotations.xsd",
-    "lib/bio/db/nexml/schema/meta/meta.xsd",
-    "lib/bio/db/nexml/schema/nexml.xsd",
-    "lib/bio/db/nexml/schema/taxa/README.txt",
-    "lib/bio/db/nexml/schema/taxa/taxa.xsd",
-    "lib/bio/db/nexml/schema/trees/README.txt",
-    "lib/bio/db/nexml/schema/trees/abstracttrees.xsd",
-    "lib/bio/db/nexml/schema/trees/network.xsd",
-    "lib/bio/db/nexml/schema/trees/tree.xsd",
-    "lib/bio/db/nexml/schema/trees/trees.xsd",
-    "lib/bio/db/nexml/taxa.rb",
-    "lib/bio/db/nexml/trees.rb",
-    "lib/bio/db/nexml/writer.rb",
-    "test/data/nexml/test.xml",
-    "test/test_bio-nexml.rb",
-    "test/unit/bio/db/nexml/tc_factory.rb",
-    "test/unit/bio/db/nexml/tc_mapper.rb",
-    "test/unit/bio/db/nexml/tc_matrix.rb",
-    "test/unit/bio/db/nexml/tc_parser.rb",
-    "test/unit/bio/db/nexml/tc_taxa.rb",
-    "test/unit/bio/db/nexml/tc_trees.rb",
-    "test/unit/bio/db/nexml/tc_writer.rb"
-  ]
-  s.homepage = %q{http://github.com/rvosa/bioruby-nexml}
-  s.licenses = ["MIT"]
-  s.require_paths = ["lib"]
-  s.rubygems_version = %q{1.4.2}
-  s.summary = %q{BioRuby plugin for reading and writing NeXML (http://nexml.org)}
-  s.test_files = [
-    "test/test_bio-nexml.rb",
-    "test/unit/bio/db/nexml/tc_factory.rb",
-    "test/unit/bio/db/nexml/tc_mapper.rb",
-    "test/unit/bio/db/nexml/tc_matrix.rb",
-    "test/unit/bio/db/nexml/tc_parser.rb",
-    "test/unit/bio/db/nexml/tc_taxa.rb",
-    "test/unit/bio/db/nexml/tc_trees.rb",
-    "test/unit/bio/db/nexml/tc_writer.rb"
-  ]
-
-  if s.respond_to? :specification_version then
-    s.specification_version = 3
-
-    if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
-      s.add_development_dependency(%q<shoulda>, [">= 0"])
-      s.add_development_dependency(%q<bundler>, ["~> 1.0.0"])
-      s.add_development_dependency(%q<jeweler>, ["~> 1.5.2"])
-      s.add_development_dependency(%q<rcov>, [">= 0"])
-      s.add_development_dependency(%q<bio>, [">= 1.4.1"])
-      s.add_development_dependency(%q<libxml-ruby>, [">= 1.1.4"])
-      s.add_runtime_dependency(%q<libxml-ruby>, ["= 1.1.4"])
-      s.add_development_dependency(%q<libxml-ruby>, ["= 1.1.4"])
-    else
-      s.add_dependency(%q<shoulda>, [">= 0"])
-      s.add_dependency(%q<bundler>, ["~> 1.0.0"])
-      s.add_dependency(%q<jeweler>, ["~> 1.5.2"])
-      s.add_dependency(%q<rcov>, [">= 0"])
-      s.add_dependency(%q<bio>, [">= 1.4.1"])
-      s.add_dependency(%q<libxml-ruby>, [">= 1.1.4"])
-      s.add_dependency(%q<libxml-ruby>, ["= 1.1.4"])
-      s.add_dependency(%q<libxml-ruby>, ["= 1.1.4"])
-    end
-  else
-    s.add_dependency(%q<shoulda>, [">= 0"])
-    s.add_dependency(%q<bundler>, ["~> 1.0.0"])
-    s.add_dependency(%q<jeweler>, ["~> 1.5.2"])
-    s.add_dependency(%q<rcov>, [">= 0"])
-    s.add_dependency(%q<bio>, [">= 1.4.1"])
-    s.add_dependency(%q<libxml-ruby>, [">= 1.1.4"])
-    s.add_dependency(%q<libxml-ruby>, ["= 1.1.4"])
-    s.add_dependency(%q<libxml-ruby>, ["= 1.1.4"])
-  end
-end
-