genfrag 0.0.0.1

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Files changed (47) hide show
  1. data/.bnsignore +16 -0
  2. data/History.txt +4 -0
  3. data/LICENSE.txt +58 -0
  4. data/README.rdoc +40 -0
  5. data/Rakefile +53 -0
  6. data/bin/genfrag +8 -0
  7. data/lib/genfrag.rb +129 -0
  8. data/lib/genfrag/app.rb +105 -0
  9. data/lib/genfrag/app/command.rb +145 -0
  10. data/lib/genfrag/app/index_command.rb +227 -0
  11. data/lib/genfrag/app/index_command/db.rb +105 -0
  12. data/lib/genfrag/app/search_command.rb +298 -0
  13. data/lib/genfrag/app/search_command/match.rb +165 -0
  14. data/lib/genfrag/app/search_command/process_file.rb +125 -0
  15. data/lib/genfrag/app/search_command/trim.rb +121 -0
  16. data/lib/genfrag/debug.rb +0 -0
  17. data/spec/data/index_command/in/a.fasta +109 -0
  18. data/spec/data/index_command/out/1-a_lookup.tdf +4 -0
  19. data/spec/data/index_command/out/2-a_lookup.db +0 -0
  20. data/spec/data/index_command/out/3-a_lookup.tdf +2 -0
  21. data/spec/data/index_command/out/4-a_lookup.db +0 -0
  22. data/spec/data/index_command/out/5-a_lookup.tdf +4 -0
  23. data/spec/data/index_command/out/6-a_lookup.db +0 -0
  24. data/spec/data/index_command/out/a.fasta.db +0 -0
  25. data/spec/data/index_command/out/a.fasta.tdf +6 -0
  26. data/spec/genfrag/app/command_spec.rb +55 -0
  27. data/spec/genfrag/app/index_command_spec.rb +258 -0
  28. data/spec/genfrag/app/search_command/match_spec.rb +77 -0
  29. data/spec/genfrag/app/search_command/process_file_spec.rb +185 -0
  30. data/spec/genfrag/app/search_command/trim_spec.rb +75 -0
  31. data/spec/genfrag/app/search_command_spec.rb +260 -0
  32. data/spec/genfrag/app_spec.rb +77 -0
  33. data/spec/genfrag_spec.rb +87 -0
  34. data/spec/spec_helper.rb +56 -0
  35. data/tasks/ann.rake +80 -0
  36. data/tasks/bones.rake +20 -0
  37. data/tasks/gem.rake +201 -0
  38. data/tasks/git.rake +40 -0
  39. data/tasks/notes.rake +27 -0
  40. data/tasks/post_load.rake +34 -0
  41. data/tasks/rdoc.rake +50 -0
  42. data/tasks/rubyforge.rake +55 -0
  43. data/tasks/setup.rb +300 -0
  44. data/tasks/spec.rake +54 -0
  45. data/tasks/svn.rake +47 -0
  46. data/tasks/test.rake +40 -0
  47. metadata +136 -0
@@ -0,0 +1,50 @@
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+
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+ require 'rake/rdoctask'
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+
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+ namespace :doc do
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+
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+ desc 'Generate RDoc documentation'
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+ Rake::RDocTask.new do |rd|
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+ rdoc = PROJ.rdoc
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+ rd.main = rdoc.main
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+ rd.rdoc_dir = rdoc.dir
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+
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+ incl = Regexp.new(rdoc.include.join('|'))
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+ excl = Regexp.new(rdoc.exclude.join('|'))
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+ files = PROJ.gem.files.find_all do |fn|
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+ case fn
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+ when excl; false
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+ when incl; true
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+ else false end
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+ end
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+ rd.rdoc_files.push(*files)
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+
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+ title = "#{PROJ.name}-#{PROJ.version} Documentation"
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+
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+ rf_name = PROJ.rubyforge.name
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+ title = "#{rf_name}'s " + title if rf_name.valid? and rf_name != title
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+
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+ rd.options << "-t #{title}"
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+ rd.options.concat(rdoc.opts)
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+ end
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+
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+ desc 'Generate ri locally for testing'
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+ task :ri => :clobber_ri do
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+ sh "#{RDOC} --ri -o ri ."
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+ end
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+
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+ task :clobber_ri do
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+ rm_r 'ri' rescue nil
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+ end
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+
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+ end # namespace :doc
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+
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+ desc 'Alias to doc:rdoc'
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+ task :doc => 'doc:rdoc'
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+
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+ desc 'Remove all build products'
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+ task :clobber => %w(doc:clobber_rdoc doc:clobber_ri)
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+
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+ remove_desc_for_task %w(doc:clobber_rdoc)
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+
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+ # EOF
@@ -0,0 +1,55 @@
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+
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+ if PROJ.rubyforge.name.valid? && HAVE_RUBYFORGE
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+
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+ require 'rubyforge'
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+ require 'rake/contrib/sshpublisher'
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+
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+ namespace :gem do
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+ desc 'Package and upload to RubyForge'
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+ task :release => [:clobber, 'gem'] do |t|
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+ v = ENV['VERSION'] or abort 'Must supply VERSION=x.y.z'
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+ abort "Versions don't match #{v} vs #{PROJ.version}" if v != PROJ.version
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+ pkg = "pkg/#{PROJ.gem._spec.full_name}"
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+
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+ if $DEBUG then
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+ puts "release_id = rf.add_release #{PROJ.rubyforge.name.inspect}, #{PROJ.name.inspect}, #{PROJ.version.inspect}, \"#{pkg}.tgz\""
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+ puts "rf.add_file #{PROJ.rubyforge.name.inspect}, #{PROJ.name.inspect}, release_id, \"#{pkg}.gem\""
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+ end
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+
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+ rf = RubyForge.new
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+ rf.configure rescue nil
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+ puts 'Logging in'
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+ rf.login
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+
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+ c = rf.userconfig
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+ c['release_notes'] = PROJ.description if PROJ.description
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+ c['release_changes'] = PROJ.changes if PROJ.changes
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+ c['preformatted'] = true
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+
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+ files = Dir.glob("#{pkg}*.*")
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+
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+ puts "Releasing #{PROJ.name} v. #{PROJ.version}"
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+ rf.add_release PROJ.rubyforge.name, PROJ.name, PROJ.version, *files
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+ end
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+ end # namespace :gem
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+
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+
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+ namespace :doc do
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+ desc "Publish RDoc to RubyForge"
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+ task :release => %w(doc:clobber_rdoc doc:rdoc) do
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+ config = YAML.load(
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+ File.read(File.expand_path('~/.rubyforge/user-config.yml'))
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+ )
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+
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+ host = "#{config['username']}@rubyforge.org"
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+ remote_dir = "/var/www/gforge-projects/#{PROJ.rubyforge.name}/"
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+ remote_dir << PROJ.rdoc.remote_dir if PROJ.rdoc.remote_dir
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+ local_dir = PROJ.rdoc.dir
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+
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+ Rake::SshDirPublisher.new(host, remote_dir, local_dir).upload
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+ end
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+ end # namespace :doc
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+
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+ end # if HAVE_RUBYFORGE
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+
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+ # EOF
@@ -0,0 +1,300 @@
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+
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+ require 'rubygems'
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+ require 'rake'
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+ require 'rake/clean'
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+ require 'fileutils'
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+ require 'ostruct'
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+ require 'find'
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+
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+ class OpenStruct; undef :gem; end
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+
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+ # TODO: make my own openstruct type object that includes descriptions
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+ # TODO: use the descriptions to output help on the available bones options
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+
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+ PROJ = OpenStruct.new(
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+ # Project Defaults
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+ :name => nil,
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+ :summary => nil,
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+ :description => nil,
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+ :changes => nil,
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+ :authors => nil,
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+ :email => nil,
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+ :url => "\000",
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+ :version => ENV['VERSION'] || '0.0.0',
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+ :exclude => %w(tmp$ bak$ ~$ CVS \.svn/ \.git/ ^pkg/),
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+ :release_name => ENV['RELEASE'],
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+
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+ # System Defaults
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+ :ruby_opts => %w(-w),
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+ :libs => [],
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+ :history_file => 'History.txt',
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+ :readme_file => 'README.txt',
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+ :ignore_file => '.bnsignore',
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+
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+ # Announce
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+ :ann => OpenStruct.new(
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+ :file => 'announcement.txt',
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+ :text => nil,
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+ :paragraphs => [],
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+ :email => {
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+ :from => nil,
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+ :to => %w(ruby-talk@ruby-lang.org),
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+ :server => 'localhost',
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+ :port => 25,
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+ :domain => ENV['HOSTNAME'],
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+ :acct => nil,
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+ :passwd => nil,
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+ :authtype => :plain
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+ }
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+ ),
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+
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+ # Gem Packaging
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+ :gem => OpenStruct.new(
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+ :dependencies => [],
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+ :development_dependencies => [],
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+ :executables => nil,
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+ :extensions => FileList['ext/**/extconf.rb'],
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+ :files => nil,
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+ :need_tar => true,
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+ :need_zip => false,
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+ :extras => {}
61
+ ),
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+
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+ # File Annotations
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+ :notes => OpenStruct.new(
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+ :exclude => %w(^tasks/setup\.rb$),
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+ :extensions => %w(.txt .rb .erb .rdoc) << '',
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+ :tags => %w(FIXME OPTIMIZE TODO)
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+ ),
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+
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+ # Rcov
71
+ :rcov => OpenStruct.new(
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+ :dir => 'coverage',
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+ :opts => %w[--sort coverage -T],
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+ :threshold => 90.0,
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+ :threshold_exact => false
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+ ),
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+
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+ # Rdoc
79
+ :rdoc => OpenStruct.new(
80
+ :opts => [],
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+ :include => %w(^lib/ ^bin/ ^ext/ \.txt$ \.rdoc$),
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+ :exclude => %w(extconf\.rb$),
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+ :main => nil,
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+ :dir => 'doc',
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+ :remote_dir => nil
86
+ ),
87
+
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+ # Rubyforge
89
+ :rubyforge => OpenStruct.new(
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+ :name => "\000"
91
+ ),
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+
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+ # Rspec
94
+ :spec => OpenStruct.new(
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+ :files => FileList['spec/**/*_spec.rb'],
96
+ :opts => []
97
+ ),
98
+
99
+ # Subversion Repository
100
+ :svn => OpenStruct.new(
101
+ :root => nil,
102
+ :path => '',
103
+ :trunk => 'trunk',
104
+ :tags => 'tags',
105
+ :branches => 'branches'
106
+ ),
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+
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+ # Test::Unit
109
+ :test => OpenStruct.new(
110
+ :files => FileList['test/**/test_*.rb'],
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+ :file => 'test/all.rb',
112
+ :opts => []
113
+ )
114
+ )
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+
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+ # Load the other rake files in the tasks folder
117
+ tasks_dir = File.expand_path(File.dirname(__FILE__))
118
+ post_load_fn = File.join(tasks_dir, 'post_load.rake')
119
+ rakefiles = Dir.glob(File.join(tasks_dir, '*.rake')).sort
120
+ rakefiles.unshift(rakefiles.delete(post_load_fn)).compact!
121
+ import(*rakefiles)
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+
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+ # Setup the project libraries
124
+ %w(lib ext).each {|dir| PROJ.libs << dir if test ?d, dir}
125
+
126
+ # Setup some constants
127
+ WIN32 = %r/djgpp|(cyg|ms|bcc)win|mingw/ =~ RUBY_PLATFORM unless defined? WIN32
128
+
129
+ DEV_NULL = WIN32 ? 'NUL:' : '/dev/null'
130
+
131
+ def quiet( &block )
132
+ io = [STDOUT.dup, STDERR.dup]
133
+ STDOUT.reopen DEV_NULL
134
+ STDERR.reopen DEV_NULL
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+ block.call
136
+ ensure
137
+ STDOUT.reopen io.first
138
+ STDERR.reopen io.last
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+ $stdout, $stderr = STDOUT, STDERR
140
+ end
141
+
142
+ DIFF = if WIN32 then 'diff.exe'
143
+ else
144
+ if quiet {system "gdiff", __FILE__, __FILE__} then 'gdiff'
145
+ else 'diff' end
146
+ end unless defined? DIFF
147
+
148
+ SUDO = if WIN32 then ''
149
+ else
150
+ if quiet {system 'which sudo'} then 'sudo'
151
+ else '' end
152
+ end
153
+
154
+ RCOV = WIN32 ? 'rcov.bat' : 'rcov'
155
+ RDOC = WIN32 ? 'rdoc.bat' : 'rdoc'
156
+ GEM = WIN32 ? 'gem.bat' : 'gem'
157
+
158
+ %w(rcov spec/rake/spectask rubyforge bones facets/ansicode).each do |lib|
159
+ begin
160
+ require lib
161
+ Object.instance_eval {const_set "HAVE_#{lib.tr('/','_').upcase}", true}
162
+ rescue LoadError
163
+ Object.instance_eval {const_set "HAVE_#{lib.tr('/','_').upcase}", false}
164
+ end
165
+ end
166
+ HAVE_SVN = (Dir.entries(Dir.pwd).include?('.svn') and
167
+ system("svn --version 2>&1 > #{DEV_NULL}"))
168
+ HAVE_GIT = (Dir.entries(Dir.pwd).include?('.git') and
169
+ system("git --version 2>&1 > #{DEV_NULL}"))
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+
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+ # Add bones as a development dependency
172
+ #
173
+ if HAVE_BONES
174
+ PROJ.gem.development_dependencies << ['bones', ">= #{Bones::VERSION}"]
175
+ end
176
+
177
+ # Reads a file at +path+ and spits out an array of the +paragraphs+
178
+ # specified.
179
+ #
180
+ # changes = paragraphs_of('History.txt', 0..1).join("\n\n")
181
+ # summary, *description = paragraphs_of('README.txt', 3, 3..8)
182
+ #
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+ def paragraphs_of( path, *paragraphs )
184
+ title = String === paragraphs.first ? paragraphs.shift : nil
185
+ ary = File.read(path).delete("\r").split(/\n\n+/)
186
+
187
+ result = if title
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+ tmp, matching = [], false
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+ rgxp = %r/^=+\s*#{Regexp.escape(title)}/i
190
+ paragraphs << (0..-1) if paragraphs.empty?
191
+
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+ ary.each do |val|
193
+ if val =~ rgxp
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+ break if matching
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+ matching = true
196
+ rgxp = %r/^=+/i
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+ elsif matching
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+ tmp << val
199
+ end
200
+ end
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+ tmp
202
+ else ary end
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+
204
+ result.values_at(*paragraphs)
205
+ end
206
+
207
+ # Adds the given gem _name_ to the current project's dependency list. An
208
+ # optional gem _version_ can be given. If omitted, the newest gem version
209
+ # will be used.
210
+ #
211
+ def depend_on( name, version = nil )
212
+ spec = Gem.source_index.find_name(name).last
213
+ version = spec.version.to_s if version.nil? and !spec.nil?
214
+
215
+ PROJ.gem.dependencies << case version
216
+ when nil; [name]
217
+ when %r/^\d/; [name, ">= #{version}"]
218
+ else [name, version] end
219
+ end
220
+
221
+ # Adds the given arguments to the include path if they are not already there
222
+ #
223
+ def ensure_in_path( *args )
224
+ args.each do |path|
225
+ path = File.expand_path(path)
226
+ $:.unshift(path) if test(?d, path) and not $:.include?(path)
227
+ end
228
+ end
229
+
230
+ # Find a rake task using the task name and remove any description text. This
231
+ # will prevent the task from being displayed in the list of available tasks.
232
+ #
233
+ def remove_desc_for_task( names )
234
+ Array(names).each do |task_name|
235
+ task = Rake.application.tasks.find {|t| t.name == task_name}
236
+ next if task.nil?
237
+ task.instance_variable_set :@comment, nil
238
+ end
239
+ end
240
+
241
+ # Change working directories to _dir_, call the _block_ of code, and then
242
+ # change back to the original working directory (the current directory when
243
+ # this method was called).
244
+ #
245
+ def in_directory( dir, &block )
246
+ curdir = pwd
247
+ begin
248
+ cd dir
249
+ return block.call
250
+ ensure
251
+ cd curdir
252
+ end
253
+ end
254
+
255
+ # Scans the current working directory and creates a list of files that are
256
+ # candidates to be in the manifest.
257
+ #
258
+ def manifest
259
+ files = []
260
+ exclude = PROJ.exclude.dup
261
+ comment = %r/^\s*#/
262
+
263
+ # process the ignore file and add the items there to the exclude list
264
+ if test(?f, PROJ.ignore_file)
265
+ ary = []
266
+ File.readlines(PROJ.ignore_file).each do |line|
267
+ next if line =~ comment
268
+ line.chomp!
269
+ line.strip!
270
+ next if line.nil? or line.empty?
271
+
272
+ glob = line =~ %r/\*\./ ? File.join('**', line) : line
273
+ Dir.glob(glob).each {|fn| ary << "^#{Regexp.escape(fn)}"}
274
+ end
275
+ exclude.concat ary
276
+ end
277
+
278
+ # generate a regular expression from the exclude list
279
+ exclude = Regexp.new(exclude.join('|'))
280
+
281
+ Find.find '.' do |path|
282
+ path.sub! %r/^(\.\/|\/)/o, ''
283
+ next unless test ?f, path
284
+ next if path =~ exclude
285
+ files << path
286
+ end
287
+ files.sort!
288
+ end
289
+
290
+ # We need a "valid" method thtat determines if a string is suitable for use
291
+ # in the gem specification.
292
+ #
293
+ class Object
294
+ def valid?
295
+ return !(self.empty? or self == "\000") if self.respond_to?(:to_str)
296
+ return false
297
+ end
298
+ end
299
+
300
+ # EOF
@@ -0,0 +1,54 @@
1
+
2
+ if HAVE_SPEC_RAKE_SPECTASK and not PROJ.spec.files.to_a.empty?
3
+ require 'spec/rake/verify_rcov'
4
+
5
+ namespace :spec do
6
+
7
+ desc 'Run all specs with basic output'
8
+ Spec::Rake::SpecTask.new(:run) do |t|
9
+ t.ruby_opts = PROJ.ruby_opts
10
+ t.spec_opts = PROJ.spec.opts
11
+ t.spec_files = PROJ.spec.files
12
+ t.libs += PROJ.libs
13
+ end
14
+
15
+ desc 'Run all specs with text output'
16
+ Spec::Rake::SpecTask.new(:specdoc) do |t|
17
+ t.ruby_opts = PROJ.ruby_opts
18
+ t.spec_opts = PROJ.spec.opts + ['--format', 'specdoc']
19
+ t.spec_files = PROJ.spec.files
20
+ t.libs += PROJ.libs
21
+ end
22
+
23
+ if HAVE_RCOV
24
+ desc 'Run all specs with RCov'
25
+ Spec::Rake::SpecTask.new(:rcov) do |t|
26
+ t.ruby_opts = PROJ.ruby_opts
27
+ t.spec_opts = PROJ.spec.opts
28
+ t.spec_files = PROJ.spec.files
29
+ t.libs += PROJ.libs
30
+ t.rcov = true
31
+ t.rcov_dir = PROJ.rcov.dir
32
+ t.rcov_opts = PROJ.rcov.opts + ['--exclude', 'spec']
33
+ end
34
+
35
+ RCov::VerifyTask.new(:verify) do |t|
36
+ t.threshold = PROJ.rcov.threshold
37
+ t.index_html = File.join(PROJ.rcov.dir, 'index.html')
38
+ t.require_exact_threshold = PROJ.rcov.threshold_exact
39
+ end
40
+
41
+ task :verify => :rcov
42
+ remove_desc_for_task %w(spec:clobber_rcov)
43
+ end
44
+
45
+ end # namespace :spec
46
+
47
+ desc 'Alias to spec:run'
48
+ task :spec => 'spec:run'
49
+
50
+ task :clobber => 'spec:clobber_rcov' if HAVE_RCOV
51
+
52
+ end # if HAVE_SPEC_RAKE_SPECTASK
53
+
54
+ # EOF