jeweler to bundler and adding badges

.gitignore

@@ -4,3 +4,4 @@ doc/output/*
 .*.swp
 *.gemspec
 playing_around_with
+coverage

.travis.yml

@@ -0,0 +1,6 @@
+language: ruby
+rvm:
+  - 2.0.0
+  - 1.9.3
+  - jruby-19mode # JRuby in 1.9 mode
+  - rbx-19mode

Gemfile

@@ -0,0 +1,4 @@
+source 'https://rubygems.org'
+
+# Specify your gem's dependencies in mspire.gemspec
+gemspec

README.md

@@ -1,5 +1,11 @@
 # mspire
 
+[![Gem Version][GV img]][Gem Version]
+[![Build Status][BS img]][Build Status]
+[![Dependency Status][DS img]][Dependency Status]
+[![Code Climate][CC img]][Code Climate]
+[![Coverage Status][CS img]][Coverage Status]
+
 Mspire is a full featured library for working with mass spectrometry data,
 particularly proteomic, metabolomic and lipidomic data sets.  It aims to be
 fast, robust, and beautiful.
@@ -159,3 +165,16 @@ trypsin.digest("AACCKDDEERFFKPGG") # => ["AACCK", "DDEER", "FFKPGG"]
 ## Copyright
 
 MIT license.  See LICENSE for details.
+
+[Gem Version]: https://rubygems.org/gems/mspire
+[Build Status]: https://travis-ci.org/princelab/mspire
+[travis pull requests]: https://travis-ci.org/princelab/mspire/pull_requests
+[Dependency Status]: https://gemnasium.com/princelab/mspire
+[Code Climate]: https://codeclimate.com/github/princelab/mspire
+[Coverage Status]: https://coveralls.io/r/princelab/mspire
+
+[GV img]: https://badge.fury.io/rb/mspire.png
+[BS img]: https://travis-ci.org/princelab/mspire.png
+[DS img]: https://gemnasium.com/princelab/mspire.png
+[CC img]: https://codeclimate.com/github/princelab/mspire.png
+[CS img]: https://coveralls.io/repos/princelab/mspire/badge.png?branch=master

Rakefile

@@ -1,65 +1,19 @@
-require 'rubygems'
-require 'rake'
-require 'rspec/core/rake_task'
-require 'yard'
-
-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 = "mspire"
-  gem.homepage = "http://github.com/princelab/mspire"
-  gem.license = "MIT"
-  gem.summary = %Q{mass spectrometry proteomics, lipidomics, and tools}
-  gem.description = %Q{mass spectrometry proteomics, lipidomics, and tools, a rewrite of mspire, merging of ms-* gems}
-  gem.email = "jtprince@gmail.com"
-  gem.authors = ["John T. Prince", "Simon Chiang"]
-  gem.add_dependency "nokogiri", "~> 1.5.9"
-  gem.add_dependency "bsearch", ">= 1.5.0"
-  gem.add_dependency "andand", ">= 1.3.3"
-  gem.add_dependency "obo", ">= 0.1.3"
-  gem.add_dependency "builder", "~> 3.2.0"
-  gem.add_dependency "bio", "~> 1.4.3"
-  gem.add_dependency "trollop", "~> 2.0.0"
-  # this should be a real dependency, but need to document getting this
-  # working on windows first!
-  gem.add_development_dependency "fftw3", "~> 0.3"
-  gem.add_development_dependency "rspec", "~> 2.13"
-  gem.add_development_dependency "jeweler", "~> 1.8.4"
-  #gem.add_development_dependency "rcov", ">= 0"
-end
-Jeweler::RubygemsDotOrgTasks.new
+require "bundler/gem_tasks"
 
 require 'rspec/core'
 require 'rspec/core/rake_task'
 RSpec::Core::RakeTask.new(:spec) do |spec|
   spec.pattern = FileList['spec/**/*_spec.rb']
 end
 
-YARD::Rake::YardocTask.new do |t|
-  t.files   = ['lib/**/*.rb', 'obo/**/*', 'README.md', 'script/**/*']   # optional
-  #t.options = ['--any', '--extra', '--opts'] # optional
-end
-
-RSpec::Core::RakeTask.new(:rcov) do |spec|
-  spec.pattern = 'spec/**/*_spec.rb'
-  spec.rcov = true
-end
-
-#require 'rcov/rcovtask'
-#Rcov::RcovTask.new do |spec|
-#  spec.libs << 'spec'
-#  spec.pattern = 'spec/**/*_spec.rb'
-#  spec.verbose = true
-#end
-
 task :default => :spec
 
 require 'rdoc/task'
 Rake::RDocTask.new do |rdoc|
   version = File.exist?('VERSION') ? File.read('VERSION') : ""
 
   rdoc.rdoc_dir = 'rdoc'
-  rdoc.title = "mspire #{version}"
+  rdoc.title = "rubabel #{version}"
   rdoc.rdoc_files.include('README*')
   rdoc.rdoc_files.include('lib/**/*.rb')
 end

lib/mspire.rb

@@ -1,7 +1,5 @@
-
-require 'mspire/mass/aa' # requires mspire/mass & therefore mspire/molecular_formula
+require 'mspire/version'
 
 module Mspire
-  VERSION = IO.read(File.join(File.dirname(__FILE__), '..', 'VERSION')).chomp
   CITE = "Prince JT, Marcotte EM. mspire: mass spectrometry proteomics in Ruby. Bioinformatics. 2008. 24(23):2796-7."
 end

lib/mspire/version.rb

@@ -0,0 +1,3 @@
+module Mspire
+  VERSION = "0.8.6.2"
+end

spec/spec_helper.rb

@@ -1,8 +1,11 @@
-$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
-$LOAD_PATH.unshift(File.dirname(__FILE__))
+#$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+#$LOAD_PATH.unshift(File.dirname(__FILE__))
+
+require 'coveralls'
+Coveralls.wear!
 
-require 'rubygems'
 require 'rspec'
+require 'spec_utilities'
 
 TESTFILES = File.dirname(__FILE__) + '/testfiles'
 
@@ -19,47 +22,3 @@
 end
 
 
-def benchmark(*args, &block)
-  if ENV['BENCHMARK']
-    Benchmark.bmbm(*args, &block)
-  end
-end
-
-# given "filename.ext" returns "filename.CHECK.ext
-# block can be given to sanitize each string
-def file_check(filename, delete=true, &block)
-  ext = File.extname(filename)
-  base = filename.chomp(ext)
-  checkfile = base + ".CHECK" + ext
-  File.exist?(filename).should be_true
-  fstring = IO.read(filename)
-  cstring = IO.read(checkfile)
-  if block
-    (fstring, cstring) = [fstring, cstring].map do |string|
-      block.call(string)
-    end
-  end
-  fstring.should == cstring
-  File.unlink(filename) if delete
-end
-
-def sanitize_mspire_version_xml(string)
-  string.gsub(/"mspire(_[\d\.]+)?" version="([\.\d]+)"/, %Q{"mspire" version="X.X.X"})
-  .gsub(/softwareRef="mspire_[\d\.]+/, 'softwareRef="mspire_X.X.X')
-end
-
-require 'stringio'
-
-module Kernel
-
-  def capture_stdout
-    out = StringIO.new
-    $stdout = out
-    yield
-    out.string
-  ensure
-    $stdout = STDOUT
-  end
-
-end
-

spec/spec_utilities.rb

@@ -0,0 +1,45 @@
+
+def benchmark(*args, &block)
+  if ENV['BENCHMARK']
+    Benchmark.bmbm(*args, &block)
+  end
+end
+
+# given "filename.ext" returns "filename.CHECK.ext
+# block can be given to sanitize each string
+def file_check(filename, delete=true, &block)
+  ext = File.extname(filename)
+  base = filename.chomp(ext)
+  checkfile = base + ".CHECK" + ext
+  File.exist?(filename).should be_true
+  fstring = IO.read(filename)
+  cstring = IO.read(checkfile)
+  if block
+    (fstring, cstring) = [fstring, cstring].map do |string|
+      block.call(string)
+    end
+  end
+  fstring.should == cstring
+  File.unlink(filename) if delete
+end
+
+def sanitize_mspire_version_xml(string)
+  string.gsub(/"mspire(_[\d\.]+)?" version="([\.\d]+)"/, %Q{"mspire" version="X.X.X"})
+  .gsub(/softwareRef="mspire_[\d\.]+/, 'softwareRef="mspire_X.X.X')
+end
+
+require 'stringio'
+
+module Kernel
+
+  def capture_stdout
+    out = StringIO.new
+    $stdout = out
+    yield
+    out.string
+  ensure
+    $stdout = STDOUT
+  end
+
+end
+