basil 0.0.4 → 0.1.1

data/Gemfile

@@ -1,7 +1,13 @@
 source :rubygems
 gemspec
+
 gem "dna"
-gem "awesome_print"
 gem "trollop"
-gem "rspec"
-gem "awesome_print"
+
+group :development do
+  gem 'jeweler'
+end
+
+group :test do
+  gem 'rspec'
+end

data/Rakefile

@@ -1 +1,48 @@
-require "bundler/gem_tasks"
+# encoding: utf-8
+
+require 'rubygems'
+require 'bundler'
+
+require './lib/basil/version.rb'
+
+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.name = "basil"
+  gem.homepage = "http://audy.github.com/basil"
+  gem.license = "MIT"
+  gem.summary = "Weapons-grade HTML demultiplexer"
+  gem.description = "Split multiplexed Illumina/454/IonTorrent/etc... output by barcode"
+  gem.email = "harekrishna@gmail.com"
+  gem.authors = ["Austin G. Davis-Richardson"]
+  gem.version = Basil::Version::STRING
+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
+
+task :default => :test
+
+require 'rdoc/task'
+Rake::RDocTask.new do |rdoc|
+
+  version = Basil::Version::STRING
+
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "test #{version}"
+  rdoc.rdoc_files.include('readme.md')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/basil.gemspec

@@ -1,22 +1,78 @@
+# Generated by jeweler
+# DO NOT EDIT THIS FILE DIRECTLY
+# Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
-$:.push File.expand_path("../lib", __FILE__)
-require 'basil/version'
 
 Gem::Specification.new do |s|
-  s.name        = 'basil'
-  s.version     = '0.0.4'
-  s.authors     = ["Austin G. Davis-Richardson"]
-  s.email       = ["harekrishna@gmail.com"]
-  s.homepage    = "http://github.com/audy/basil"
-  s.summary     = 'HTPS demultiplexer'
-  s.description = 'Split multiplexed high-throughput sequencing reads by barcode.'
-  s.rubyforge_project = "basil"
-  s.files         = `git ls-files`.split("\n")
-  s.test_files    = `git ls-files -- {test,spec,features}/*`.split("\n")
-  s.executables   = `git ls-files -- bin/*`.split("\n").map{ |f| File.basename(f) }
+  s.name = "basil"
+  s.version = "0.1.1"
+
+  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
+  s.authors = ["Austin G. Davis-Richardson"]
+  s.date = "2012-09-18"
+  s.description = "Split multiplexed Illumina/454/IonTorrent/etc... output by barcode"
+  s.email = "harekrishna@gmail.com"
+  s.executables = ["basil"]
+  s.files = [
+    ".rspec",
+    ".rvmrc",
+    "Gemfile",
+    "Rakefile",
+    "basil.gemspec",
+    "bin/basil",
+    "lib/basil.rb",
+    "lib/basil/barcodes.rb",
+    "lib/basil/basil.rb",
+    "lib/basil/buffer.rb",
+    "lib/basil/cli.rb",
+    "lib/basil/version.rb",
+    "readme.md",
+    "spec/basil_spec.rb",
+    "spec/buffer_spec.rb",
+    "spec/cli_spec.rb",
+    "spec/data/barcodes.csv",
+    "spec/data/illumina/s_1_1_001_qseq.txt",
+    "spec/data/illumina/s_1_2_001_qseq.txt",
+    "spec/data/illumina/s_1_3_001_qseq.txt",
+    "spec/data/test.fasta",
+    "spec/data/test.fastq",
+    "spec/data/test.qseq",
+    "spec/spec_helper.rb"
+  ]
+  s.homepage = "http://audy.github.com/basil"
+  s.licenses = ["MIT"]
   s.require_paths = ["lib"]
-  s.add_dependency('dna')
-  s.add_dependency('trollop')
-  s.add_dependency('rspec')
-  s.add_dependency('bundler')
+  s.rubygems_version = "1.8.24"
+  s.summary = "Weapons-grade HTML demultiplexer"
+
+  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_runtime_dependency(%q<basil>, [">= 0"])
+      s.add_runtime_dependency(%q<dna>, [">= 0"])
+      s.add_runtime_dependency(%q<trollop>, [">= 0"])
+      s.add_development_dependency(%q<jeweler>, [">= 0"])
+      s.add_development_dependency(%q<jeweler>, [">= 0"])
+      s.add_development_dependency(%q<jeweler>, [">= 0"])
+      s.add_development_dependency(%q<jeweler>, [">= 0"])
+    else
+      s.add_dependency(%q<basil>, [">= 0"])
+      s.add_dependency(%q<dna>, [">= 0"])
+      s.add_dependency(%q<trollop>, [">= 0"])
+      s.add_dependency(%q<jeweler>, [">= 0"])
+      s.add_dependency(%q<jeweler>, [">= 0"])
+      s.add_dependency(%q<jeweler>, [">= 0"])
+      s.add_dependency(%q<jeweler>, [">= 0"])
+    end
+  else
+    s.add_dependency(%q<basil>, [">= 0"])
+    s.add_dependency(%q<dna>, [">= 0"])
+    s.add_dependency(%q<trollop>, [">= 0"])
+    s.add_dependency(%q<jeweler>, [">= 0"])
+    s.add_dependency(%q<jeweler>, [">= 0"])
+    s.add_dependency(%q<jeweler>, [">= 0"])
+    s.add_dependency(%q<jeweler>, [">= 0"])
+  end
 end
+

data/lib/basil/version.rb

@@ -0,0 +1,9 @@
+module Basil
+  module Version
+    MAJOR = 0
+    MINOR = 1
+    PATCH = 1
+
+    STRING = [MAJOR, MINOR, PATCH].join('.')
+  end
+end

data/spec/basil_spec.rb

@@ -19,6 +19,10 @@ describe Basil::Basil do
     barcodes.should_not raise_error TypeError
   end
 
+  it 'has a version number' do
+    Basil::Version::STRING.should_not be_nil
+  end
+
   it 'raises an error if duplicate barcodes are specified' do
     Basil::Basil.new({ 1 => 'gggg', 2 => 'gggg' }).should raise_error
   end
@@ -32,16 +36,16 @@ describe Basil::Basil do
     basil.recognize("NGATC").first.should == 1
   end
 
-  it 'preserves case sensitivity of regexp' do
+  it '#recognize preserves case sensitivity when given regexp' do
     basil = Basil::Basil.new(1 => /^.GATC/)
     basil.recognize("Ngatc").should be_nil
   end
 
-  it '#recognize is case insensitive' do
+  it '#recognize is case sensitive' do
     basil.recognize(dna.upcase!).first.should == 1
   end
 
-  it '#recognize ^ is prepended to barcode regexp if strings are provided' do
+  it '#recognize ^ is automatically prepended to barcode regexp if strings are provided' do
     basil.recognize('aggggaaa').should be_nil
   end
 

data/spec/spec_helper.rb

@@ -1,3 +1,5 @@
 $LOAD_PATH << File.join(File.dirname(__FILE__), 'lib')
 
-require 'basil'
+require 'basil'
+
+Bundler.require :test

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: basil
 version: !ruby/object:Gem::Version 
-  hash: 23
+  hash: 25
   prerelease: 
   segments: 
   - 0
-  - 0
-  - 4
-  version: 0.0.4
+  - 1
+  - 1
+  version: 0.1.1
 platform: ruby
 authors: 
 - Austin G. Davis-Richardson
@@ -15,11 +15,10 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2012-05-15 00:00:00 Z
+date: 2012-09-18 00:00:00 Z
 dependencies: 
 - !ruby/object:Gem::Dependency 
-  name: dna
-  prerelease: false
+  type: :runtime
   requirement: &id001 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
@@ -29,11 +28,11 @@ dependencies:
         segments: 
         - 0
         version: "0"
-  type: :runtime
   version_requirements: *id001
-- !ruby/object:Gem::Dependency 
-  name: trollop
+  name: basil
   prerelease: false
+- !ruby/object:Gem::Dependency 
+  type: :runtime
   requirement: &id002 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
@@ -43,11 +42,11 @@ dependencies:
         segments: 
         - 0
         version: "0"
-  type: :runtime
   version_requirements: *id002
-- !ruby/object:Gem::Dependency 
-  name: rspec
+  name: dna
   prerelease: false
+- !ruby/object:Gem::Dependency 
+  type: :runtime
   requirement: &id003 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
@@ -57,11 +56,11 @@ dependencies:
         segments: 
         - 0
         version: "0"
-  type: :runtime
   version_requirements: *id003
-- !ruby/object:Gem::Dependency 
-  name: bundler
+  name: trollop
   prerelease: false
+- !ruby/object:Gem::Dependency 
+  type: :development
   requirement: &id004 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
@@ -71,11 +70,53 @@ dependencies:
         segments: 
         - 0
         version: "0"
-  type: :runtime
   version_requirements: *id004
-description: Split multiplexed high-throughput sequencing reads by barcode.
-email: 
-- harekrishna@gmail.com
+  name: jeweler
+  prerelease: false
+- !ruby/object:Gem::Dependency 
+  type: :development
+  requirement: &id005 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 3
+        segments: 
+        - 0
+        version: "0"
+  version_requirements: *id005
+  name: jeweler
+  prerelease: false
+- !ruby/object:Gem::Dependency 
+  type: :development
+  requirement: &id006 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 3
+        segments: 
+        - 0
+        version: "0"
+  version_requirements: *id006
+  name: jeweler
+  prerelease: false
+- !ruby/object:Gem::Dependency 
+  type: :development
+  requirement: &id007 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 3
+        segments: 
+        - 0
+        version: "0"
+  version_requirements: *id007
+  name: jeweler
+  prerelease: false
+description: Split multiplexed Illumina/454/IonTorrent/etc... output by barcode
+email: harekrishna@gmail.com
 executables: 
 - basil
 extensions: []
@@ -83,7 +124,6 @@ extensions: []
 extra_rdoc_files: []
 
 files: 
-- .gitignore
 - .rspec
 - .rvmrc
 - Gemfile
@@ -95,6 +135,7 @@ files:
 - lib/basil/basil.rb
 - lib/basil/buffer.rb
 - lib/basil/cli.rb
+- lib/basil/version.rb
 - readme.md
 - spec/basil_spec.rb
 - spec/buffer_spec.rb
@@ -107,9 +148,9 @@ files:
 - spec/data/test.fastq
 - spec/data/test.qseq
 - spec/spec_helper.rb
-homepage: http://github.com/audy/basil
-licenses: []
-
+homepage: http://audy.github.com/basil
+licenses: 
+- MIT
 post_install_message: 
 rdoc_options: []
 
@@ -135,20 +176,10 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: "0"
 requirements: []
 
-rubyforge_project: basil
+rubyforge_project: 
 rubygems_version: 1.8.24
 signing_key: 
 specification_version: 3
-summary: HTPS demultiplexer
-test_files: 
-- spec/basil_spec.rb
-- spec/buffer_spec.rb
-- spec/cli_spec.rb
-- spec/data/barcodes.csv
-- spec/data/illumina/s_1_1_001_qseq.txt
-- spec/data/illumina/s_1_2_001_qseq.txt
-- spec/data/illumina/s_1_3_001_qseq.txt
-- spec/data/test.fasta
-- spec/data/test.fastq
-- spec/data/test.qseq
-- spec/spec_helper.rb
+summary: Weapons-grade HTML demultiplexer
+test_files: []
+

data/.gitignore

@@ -1,2 +0,0 @@
-Gemfile.lock
-pkg/