bio-foo 0.0.0

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+ lib/**/*.rb
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+ bin/*
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+ -
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+ features/**/*.feature
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+ LICENSE.txt
data/Gemfile ADDED
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+ source "http://rubygems.org"
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+ # Add dependencies required to use your gem here.
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+ # Example:
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+ # gem "activesupport", ">= 2.3.5"
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+
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+ # Add dependencies to develop your gem here.
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+ # Include everything needed to run rake, tests, features, etc.
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+ group :development do
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+ gem "shoulda", ">= 0"
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+ gem "bundler", "~> 1.0.0"
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+ gem "jeweler", "~> 1.6.4"
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+ gem "rcov", ">= 0"
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+ gem "bio", ">= 1.4.2"
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+ end
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+ GEM
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+ remote: http://rubygems.org/
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+ specs:
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+ bio (1.4.2)
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+ git (1.2.5)
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+ jeweler (1.6.4)
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+ bundler (~> 1.0)
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+ git (>= 1.2.5)
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+ rake
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+ rake (0.9.2.2)
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+ rcov (0.9.11)
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+ shoulda (2.11.3)
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+
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+ PLATFORMS
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+ ruby
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+
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+ DEPENDENCIES
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+ bio (>= 1.4.2)
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+ bundler (~> 1.0.0)
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+ jeweler (~> 1.6.4)
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+ rcov
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+ shoulda
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+ Copyright (c) 2011 Toshiaki Katayama
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+
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+ Permission is hereby granted, free of charge, to any person obtaining
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+ a copy of this software and associated documentation files (the
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+ "Software"), to deal in the Software without restriction, including
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+ without limitation the rights to use, copy, modify, merge, publish,
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+ distribute, sublicense, and/or sell copies of the Software, and to
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+ permit persons to whom the Software is furnished to do so, subject to
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+ the following conditions:
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+
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+ The above copyright notice and this permission notice shall be
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+ included in all copies or substantial portions of the Software.
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+
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+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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+ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
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+ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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+ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
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+ LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
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+ OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
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+ WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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+ = bio-foo
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+
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+ Description goes here.
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+
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+ == Contributing to bio-foo
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+
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+ * Check out the latest master to make sure the feature hasn't been implemented or the bug hasn't been fixed yet
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+ * Check out the issue tracker to make sure someone already hasn't requested it and/or contributed it
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+ * Fork the project
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+ * Start a feature/bugfix branch
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+ * Commit and push until you are happy with your contribution
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+ * Make sure to add tests for it. This is important so I don't break it in a future version unintentionally.
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+ * Please try not to mess with the Rakefile, version, or history. If you want to have your own version, or is otherwise necessary, that is fine, but please isolate to its own commit so I can cherry-pick around it.
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+
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+ == Copyright
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+
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+ Copyright (c) 2011 Toshiaki Katayama. See LICENSE.txt for
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+ further details.
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+
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+ # encoding: utf-8
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+
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+ require 'rubygems'
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+ require 'bundler'
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+ begin
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+ Bundler.setup(:default, :development)
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+ rescue Bundler::BundlerError => e
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+ $stderr.puts e.message
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+ $stderr.puts "Run `bundle install` to install missing gems"
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+ exit e.status_code
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+ end
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+ require 'rake'
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+
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+ require 'jeweler'
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+ Jeweler::Tasks.new do |gem|
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+ # gem is a Gem::Specification... see http://docs.rubygems.org/read/chapter/20 for more options
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+ gem.name = "bio-foo"
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+ gem.homepage = "http://github.com/ktym/bioruby-foo"
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+ gem.license = "MIT"
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+ gem.summary = %Q{one-line summary of your gem}
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+ gem.description = %Q{longer description of your gem}
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+ gem.email = "k@bioruby.org"
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+ gem.authors = ["Toshiaki Katayama"]
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+ # dependencies defined in Gemfile
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+ end
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+ Jeweler::RubygemsDotOrgTasks.new
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+
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+ require 'rake/testtask'
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+ Rake::TestTask.new(:test) do |test|
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+ test.libs << 'lib' << 'test'
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+ test.pattern = 'test/**/test_*.rb'
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+ test.verbose = true
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+ end
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+
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+ require 'rcov/rcovtask'
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+ Rcov::RcovTask.new do |test|
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+ test.libs << 'test'
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+ test.pattern = 'test/**/test_*.rb'
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+ test.verbose = true
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+ test.rcov_opts << '--exclude "gems/*"'
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+ end
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+
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+ task :default => :test
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+
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+ require 'rake/rdoctask'
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+ Rake::RDocTask.new do |rdoc|
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+ version = File.exist?('VERSION') ? File.read('VERSION') : ""
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+
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+ rdoc.rdoc_dir = 'rdoc'
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+ rdoc.title = "bio-foo #{version}"
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+ rdoc.rdoc_files.include('README*')
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+ rdoc.rdoc_files.include('lib/**/*.rb')
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+ end
data/VERSION ADDED
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+ 0.0.0
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+ # Generated by jeweler
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+ # DO NOT EDIT THIS FILE DIRECTLY
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+ # Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
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+ # -*- encoding: utf-8 -*-
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+
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+ Gem::Specification.new do |s|
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+ s.name = %q{bio-foo}
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+ s.version = "0.0.0"
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+
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+ s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
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+ s.authors = ["Toshiaki Katayama"]
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+ s.date = %q{2011-11-02}
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+ s.description = %q{longer description of your gem}
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+ s.email = %q{k@bioruby.org}
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+ s.extra_rdoc_files = [
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+ "LICENSE.txt",
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+ "README.rdoc"
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+ ]
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+ s.files = [
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+ ".document",
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+ "Gemfile",
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+ "Gemfile.lock",
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+ "LICENSE.txt",
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+ "README.rdoc",
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+ "Rakefile",
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+ "VERSION",
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+ "bio-foo.gemspec",
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+ "lib/bio-foo.rb",
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+ "test/helper.rb",
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+ "test/test_bio-foo.rb"
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+ ]
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+ s.homepage = %q{http://github.com/ktym/bioruby-foo}
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+ s.licenses = ["MIT"]
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+ s.require_paths = ["lib"]
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+ s.rubygems_version = %q{1.6.2}
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+ s.summary = %q{one-line summary of your gem}
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+
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+ if s.respond_to? :specification_version then
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+ s.specification_version = 3
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+
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+ if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
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+ s.add_development_dependency(%q<shoulda>, [">= 0"])
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+ s.add_development_dependency(%q<bundler>, ["~> 1.0.0"])
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+ s.add_development_dependency(%q<jeweler>, ["~> 1.6.4"])
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+ s.add_development_dependency(%q<rcov>, [">= 0"])
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+ s.add_development_dependency(%q<bio>, [">= 1.4.2"])
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+ else
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+ s.add_dependency(%q<shoulda>, [">= 0"])
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+ s.add_dependency(%q<bundler>, ["~> 1.0.0"])
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+ s.add_dependency(%q<jeweler>, ["~> 1.6.4"])
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+ s.add_dependency(%q<rcov>, [">= 0"])
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+ s.add_dependency(%q<bio>, [">= 1.4.2"])
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+ end
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+ else
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+ s.add_dependency(%q<shoulda>, [">= 0"])
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+ s.add_dependency(%q<bundler>, ["~> 1.0.0"])
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+ s.add_dependency(%q<jeweler>, ["~> 1.6.4"])
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+ s.add_dependency(%q<rcov>, [">= 0"])
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+ s.add_dependency(%q<bio>, [">= 1.4.2"])
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+ end
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+ end
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+
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+ # Please require your code below, respecting the bioruby directory tree.
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+ # For instance, perhaps the only uncommented line in this file might
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+ # be something like this:
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+ #
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+ # require 'bio/sequence/awesome_sequence_plugin_thingy'
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+ #
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+ # and then create the ruby file 'lib/bio/sequence/awesome_sequence_thingy.rb'
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+ # and put your plugin's code there. It is bad practice to write other code
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+ # directly into this file, because doing so causes confusion if this biogem
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+ # was ever to get merged into the main bioruby tree.
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+ require 'rubygems'
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+ require 'bundler'
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+ begin
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+ Bundler.setup(:default, :development)
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+ rescue Bundler::BundlerError => e
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+ $stderr.puts e.message
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+ $stderr.puts "Run `bundle install` to install missing gems"
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+ exit e.status_code
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+ end
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+ require 'test/unit'
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+ require 'shoulda'
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+
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+ $LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
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+ $LOAD_PATH.unshift(File.dirname(__FILE__))
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+ require 'bio-foo'
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+
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+ class Test::Unit::TestCase
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+ end
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+ require 'helper'
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+
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+ class TestBioFoo < Test::Unit::TestCase
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+ should "probably rename this file and start testing for real" do
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+ flunk "hey buddy, you should probably rename this file and start testing for real"
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+ end
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+ end
metadata ADDED
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+ --- !ruby/object:Gem::Specification
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+ name: bio-foo
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+ version: !ruby/object:Gem::Version
4
+ hash: 31
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+ prerelease:
6
+ segments:
7
+ - 0
8
+ - 0
9
+ - 0
10
+ version: 0.0.0
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+ platform: ruby
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+ authors:
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+ - Toshiaki Katayama
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+ autorequire:
15
+ bindir: bin
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+ cert_chain: []
17
+
18
+ date: 2011-11-02 00:00:00 +09:00
19
+ default_executable:
20
+ dependencies:
21
+ - !ruby/object:Gem::Dependency
22
+ prerelease: false
23
+ type: :development
24
+ requirement: &id001 !ruby/object:Gem::Requirement
25
+ none: false
26
+ requirements:
27
+ - - ">="
28
+ - !ruby/object:Gem::Version
29
+ hash: 3
30
+ segments:
31
+ - 0
32
+ version: "0"
33
+ name: shoulda
34
+ version_requirements: *id001
35
+ - !ruby/object:Gem::Dependency
36
+ prerelease: false
37
+ type: :development
38
+ requirement: &id002 !ruby/object:Gem::Requirement
39
+ none: false
40
+ requirements:
41
+ - - ~>
42
+ - !ruby/object:Gem::Version
43
+ hash: 23
44
+ segments:
45
+ - 1
46
+ - 0
47
+ - 0
48
+ version: 1.0.0
49
+ name: bundler
50
+ version_requirements: *id002
51
+ - !ruby/object:Gem::Dependency
52
+ prerelease: false
53
+ type: :development
54
+ requirement: &id003 !ruby/object:Gem::Requirement
55
+ none: false
56
+ requirements:
57
+ - - ~>
58
+ - !ruby/object:Gem::Version
59
+ hash: 7
60
+ segments:
61
+ - 1
62
+ - 6
63
+ - 4
64
+ version: 1.6.4
65
+ name: jeweler
66
+ version_requirements: *id003
67
+ - !ruby/object:Gem::Dependency
68
+ prerelease: false
69
+ type: :development
70
+ requirement: &id004 !ruby/object:Gem::Requirement
71
+ none: false
72
+ requirements:
73
+ - - ">="
74
+ - !ruby/object:Gem::Version
75
+ hash: 3
76
+ segments:
77
+ - 0
78
+ version: "0"
79
+ name: rcov
80
+ version_requirements: *id004
81
+ - !ruby/object:Gem::Dependency
82
+ prerelease: false
83
+ type: :development
84
+ requirement: &id005 !ruby/object:Gem::Requirement
85
+ none: false
86
+ requirements:
87
+ - - ">="
88
+ - !ruby/object:Gem::Version
89
+ hash: 3
90
+ segments:
91
+ - 1
92
+ - 4
93
+ - 2
94
+ version: 1.4.2
95
+ name: bio
96
+ version_requirements: *id005
97
+ description: longer description of your gem
98
+ email: k@bioruby.org
99
+ executables: []
100
+
101
+ extensions: []
102
+
103
+ extra_rdoc_files:
104
+ - LICENSE.txt
105
+ - README.rdoc
106
+ files:
107
+ - .document
108
+ - Gemfile
109
+ - Gemfile.lock
110
+ - LICENSE.txt
111
+ - README.rdoc
112
+ - Rakefile
113
+ - VERSION
114
+ - bio-foo.gemspec
115
+ - lib/bio-foo.rb
116
+ - test/helper.rb
117
+ - test/test_bio-foo.rb
118
+ has_rdoc: true
119
+ homepage: http://github.com/ktym/bioruby-foo
120
+ licenses:
121
+ - MIT
122
+ post_install_message:
123
+ rdoc_options: []
124
+
125
+ require_paths:
126
+ - lib
127
+ required_ruby_version: !ruby/object:Gem::Requirement
128
+ none: false
129
+ requirements:
130
+ - - ">="
131
+ - !ruby/object:Gem::Version
132
+ hash: 3
133
+ segments:
134
+ - 0
135
+ version: "0"
136
+ required_rubygems_version: !ruby/object:Gem::Requirement
137
+ none: false
138
+ requirements:
139
+ - - ">="
140
+ - !ruby/object:Gem::Version
141
+ hash: 3
142
+ segments:
143
+ - 0
144
+ version: "0"
145
+ requirements: []
146
+
147
+ rubyforge_project:
148
+ rubygems_version: 1.6.2
149
+ signing_key:
150
+ specification_version: 3
151
+ summary: one-line summary of your gem
152
+ test_files: []
153
+