bio-gem 1.3.4 → 1.3.5

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA1:
+  metadata.gz: d51d946c9198261b369526a545153ea8f4806e55
+  data.tar.gz: 2f5aca2b0c51a7a7c512be9bcd253d705c9f7295
+SHA512:
+  metadata.gz: 381baf735d2b2f95b1291ec3f867f50c7d9f9c8c1fc172ed55245339650fcef80e988066651e8b319b9f6b43159654e4a82a0f29eff31339df20af7de0c75469
+  data.tar.gz: 1c8d0e431d34e6e14f3ea3e93c610aba48ebdd2f9e1769cdc7b0bf03a6faa36b900a4d5aa96293288e1fd685b5b0393dc4024efacc1af0403cc9ac62ddc53215

data/.travis.yml

@@ -3,7 +3,7 @@ rvm:
   - 1.9.2
   - 1.9.3
   - jruby-19mode # JRuby in 1.9 mode
-  - rbx-19mode # rvm install rbx -- --enable-version=1.9,1.8 --default-version=1.9
+#  - rbx-19mode # rvm install rbx -- --enable-version=1.9,1.8 --default-version=1.9
 #  - 1.8.7
 #  - jruby-18mode # JRuby in 1.8 mode
 #  - rbx-18mode

data/Gemfile

@@ -3,7 +3,7 @@ source "http://rubygems.org"
 # Example:
 #   gem "activesupport", ">= 2.3.5"
 gem "bundler", ">= 1.0.21"
-gem "jeweler"
+gem "jeweler", :git => 'https://github.com/technicalpickles/jeweler.git'
 gem "rdoc"
 
 # Add dependencies to develop your gem here.

data/Rakefile

@@ -24,7 +24,7 @@ Jeweler::Tasks.new do |gem|
   # and development dependencies are only needed for development (ie running rake tasks, tests, etc)
   #gem.version='0.0.1'
   gem.rdoc_options << '--main' << 'README' << '--line-numbers'
-  gem.required_ruby_version = "~>1.9"
+  gem.required_ruby_version = ">= 1.9"
   gem.extra_rdoc_files = ['LICENSE.txt', 'README.rdoc','Tutorial.rdoc']
 end
 

data/Tutorial.rdoc

@@ -204,20 +204,29 @@ In bioinformatics is very common to presents data using a web application, and o
 To example this Biogem's features we want to create a Rails application which provides a form to users. Data are submitted to TogoWS http://togows.dbcls.jp/ and the result is returned in a web page. In the mean time we want to store suers queries and return them in the page of TogoWS' result. We'll create a Rails application and a separated Biogem to store queries and provide connection to TogoWS, following "man in the middle" pattern.
 
     $ biogem --with-engine Foo foo
+    $ cd bioruby-foo
+    $ rake version:write
+    $ bundle install
 
 Note: a database is automatically configure for the newly created gem
 
-    $ rails new Webfoo
+Create a completely new Rails web application NOT inside the newly create biogem, so rememner to 
 
-You can test your application just inserting into Rails application Gemfile the newly created gem:
+    $ cd ..
 
-    gem 'bio-foo', :path=>'path_gem_dir'
+and then create a new web app
+
+    $ rails new Webfoo
 
 update the installation running:
 
      cd Webfoo
      bundle install
 
+You can test your application just inserting into Rails application Gemfile the newly created gem:
+
+    gem 'bio-foo', :path=>'path_gem_dir'
+
 Enable the route for the added gem (in biouby-foo/config/routes.rb) uncomment:
 
     yourPathToTheControllerFiles = 'foopath'
@@ -291,8 +300,8 @@ This is Gemfile's content
    # Include everything needed to run rake, tests, features, etc.
    group :development do
      gem "shoulda", ">= 0"
-     gem "bundler", "~> 1.0.0"
-     gem "jeweler", "~> 1.6.4"
+     gem "bundler", "> 1.0.0"
+     gem "jeweler", "> 1.6.4"
      gem "rcov", ">= 0"
      gem "bio", ">= 1.4.2"
    end

data/VERSION

@@ -1 +1 @@
-1.3.4
+1.3.5

data/bin/biogem

@@ -10,33 +10,40 @@ require 'rake'
 
 orig_argv = ARGV.clone
 # application_exit[:exit] exists, application_exit[:options] it depends.
-application_exit = Bio::Gem::Generator::Application.run!(*ARGV)
-options = application_exit[:options]
+exit Bio::Gem::Generator::Application.run!(*ARGV)
 
-if (application_exit[:exit]==0)
-  pwd = FileUtils.pwd
-  FileUtils.cd "bioruby-#{application_exit[:options][:project_name]}"
-  ARGV.clear << "install"
+#run
+## bundle install
+## rake version:write
+## rake gemspec
 
-  Bundler::CLI.start
-  #TODO: call rake directly not from shell
+# application_exit = Bio::Gem::Generator::Application.run!(*ARGV)
+# options = application_exit[:options]
+
+# if (application_exit[:exit]==0)
+#   pwd = FileUtils.pwd
+#   FileUtils.cd "bioruby-#{application_exit[:options][:project_name]}"
+#   ARGV.clear << "install"
+
+#   Bundler::CLI.start
+#   #TODO: call rake directly not from shell
  
-  if options[:testing_framework] == :rspec
-    # Don't remove the following warning, as it may be encountered by anyone running
-    # biogem from source (especially with the --with-rspec switch)!
-    print "
-    WARNING: if rake gives an (rspec) error try running biogem from a directly 
-             installed gem instead:
-     bundle exec rake install
-     biogem [options] 
-    "
-  end
-  print "\trake version:write\n"
-  sh "rake version:write"
-  print "\trake gemspec\n"
-  sh "rake gemspec"
-  print "Done!\n"
-else
-  $stderr.print "\nERROR: Biogem failed!\n"
-end
+#   if options[:testing_framework] == :rspec
+#     # Don't remove the following warning, as it may be encountered by anyone running
+#     # biogem from source (especially with the --with-rspec switch)!
+#     print "
+#     WARNING: if rake gives an (rspec) error try running biogem from a directly 
+#              installed gem instead:
+#      bundle exec rake install
+#      biogem [options] 
+#     "
+#   end
+#   print "\trake version:write\n"
+#   sh "rake version:write"
+#   print "\trake gemspec\n"
+#   sh "rake gemspec"
+#   print "Done!\n"
+# else
+#   $stderr.print "\nERROR: Biogem failed!\n"
+# end
 

data/bio-gem.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = "bio-gem"
-  s.version = "1.3.4"
+  s.version = "1.3.5"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Raoul J.P. Bonnal", "Pjotr Prins"]
-  s.date = "2012-04-18"
+  s.date = "2013-07-24"
   s.description = "Biogem is a software generator for those bioinformaticans who want to start coding an application or a library for using/extending BioRuby core library and sharing it through rubygems.org .\n  The basic idea is to simplify and promote a modular approach to bioinformatics software development"
   s.email = "ilpuccio.febo@gmail.com"
   s.executables = ["biogem"]
@@ -23,7 +23,6 @@ Gem::Specification.new do |s|
     ".travis.yml",
     ".yardopts",
     "Gemfile",
-    "Gemfile.lock",
     "LICENSE.txt",
     "README.rdoc",
     "Rakefile",
@@ -71,12 +70,12 @@ Gem::Specification.new do |s|
   s.licenses = ["MIT"]
   s.rdoc_options = ["--main", "README", "--line-numbers"]
   s.require_paths = ["lib"]
-  s.required_ruby_version = Gem::Requirement.new("~> 1.9")
-  s.rubygems_version = "1.8.10"
+  s.required_ruby_version = Gem::Requirement.new(">= 1.9")
+  s.rubygems_version = "2.0.0"
   s.summary = "Biogem is a software generator for Ruby in bioinformatics"
 
   if s.respond_to? :specification_version then
-    s.specification_version = 3
+    s.specification_version = 4
 
     if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
       s.add_runtime_dependency(%q<bundler>, [">= 1.0.21"])

data/lib/bio-gem/application.rb

@@ -4,52 +4,63 @@ module Bio
     class Generator
       class Application
         class << self
-          # Return an hash with :exit=>(0|1) and optionally and :options which is another hash
-          # This function has been stolen from Jeweler and mdified with the return hash, the original class returns just 0|1
-          # the problem is that I need to identify the name of the project_name from outside to use bundler.
+          include Shellwords 
           def run!(*arguments)
-            env_opts = if ENV['JEWELER_OPTS']
-              Jeweler::Generator::Options.new(ENV['JEWELER_OPTS'].split(' '))
-            end
-            options = Jeweler::Generator::Options.new(arguments)
-            options = options.merge(env_opts) if env_opts
 
-            if options[:invalid_argument]
-              $stderr.puts options[:invalid_argument]
-              options[:show_help] = true
-            end
+          options = build_options(arguments)
 
-            if options[:show_help]
-              $stderr.puts options.opts
-              return {:exit=>1}
-            end
+          if options[:invalid_argument]
+            $stderr.puts options[:invalid_argument]
+            options[:show_help] = true
+          end
 
-            if options[:project_name].nil? || options[:project_name].squeeze.strip == ""
-              $stderr.puts options.opts
-              return {:exit=>1}
-            end
+          if options[:show_version]
+            $stderr.puts "Version: #{Jeweler::Version::STRING}"
+            return 1
+          end
+
+          if options[:show_help]
+            $stderr.puts options.opts
+            return 1
+          end
 
-            begin
+          if options[:project_name].nil? || options[:project_name].squeeze.strip == ""
+            $stderr.puts options.opts
+            return 1
+          end
+
+          begin
+            if options[:directory]!='.'
+              FileUtils.mkdir_p options[:directory]
+            end
+            FileUtils.cd options[:directory] do 
               generator = Jeweler::Generator.new(options)
               generator.run
-              return {:exit=>0, :options=>options}
-            rescue Jeweler::NoGitUserName
-              $stderr.puts %Q{No user.name found in ~/.gitconfig. Please tell git about yourself (see http://help.github.com/git-email-settings/ for details). For example: git config --global user.name "mad voo"}
-              return {:exit=>1}
-            rescue Jeweler::NoGitUserEmail
-              $stderr.puts %Q{No user.email found in ~/.gitconfig. Please tell git about yourself (see http://help.github.com/git-email-settings/ for details). For example: git config --global user.email mad.vooo@gmail.com}
-              return {:exit=>1}
-            rescue Jeweler::NoGitHubUser
-              $stderr.puts %Q{No github.user found in ~/.gitconfig. Please tell git about your GitHub account (see http://github.com/blog/180-local-github-config for details). For example: git config --global github.user defunkt}
-              return {:exit=>1}
-            rescue Jeweler::NoGitHubToken
-              $stderr.puts %Q{No github.token found in ~/.gitconfig. Please tell git about your GitHub account (see http://github.com/blog/180-local-github-config for details). For example: git config --global github.token 6ef8395fecf207165f1a82178ae1b984}
-              return {:exit=>1}
-            rescue Jeweler::FileInTheWay
-              $stderr.puts "The directory for #{options[:project_name]} already exists. Maybe move it out of the way before continuing?"
-              return {:exit=>1}
+              return 0
             end
+          rescue Jeweler::NoGitUserName
+            $stderr.puts %Q{No user.name found in ~/.gitconfig. Please tell git about yourself (see http://help.github.com/git-email-settings/ for details). For example: git config --global user.name "mad voo"}
+            return 1
+          rescue Jeweler::NoGitUserEmail
+            $stderr.puts %Q{No user.email found in ~/.gitconfig. Please tell git about yourself (see http://help.github.com/git-email-settings/ for details). For example: git config --global user.email mad.vooo@gmail.com}
+            return 1
+          rescue Jeweler::NoGitHubUser
+            $stderr.puts %Q{Please specify --github-username or set github.user in ~/.gitconfig (see http://github.com/blog/180-local-github-config for details). For example: git config --global github.user defunkt}
+            return 1
+          rescue Jeweler::FileInTheWay
+            $stderr.puts "The directory #{options[:project_name]} already exists. Maybe move it out of the way before continuing?"
+            return 1
+          end
           end #run!
+
+        def build_options(arguments)
+          env_opts_string = ENV['JEWELER_OPTS'] || ""
+          env_opts        = Jeweler::Generator::Options.new(shellwords(env_opts_string))
+          argument_opts   = Jeweler::Generator::Options.new(arguments)
+
+          env_opts.merge(argument_opts)
+        end
+
         end #self
       end #Application
     end #Generator

data/lib/bio-gem/generator/render.rb

@@ -3,7 +3,7 @@
 
 module Biogem
   module Render
-    # new hook for removing stuff
+    # new hook for removing stuff (FIXME: could use a test!!)
     def after_render_template(source,buf)
       if source == 'other_tasks.erb'
         $stdout.puts "\tremove jeweler rcov lines"
@@ -92,12 +92,17 @@ module Biogem
       mkdir_in_target bin_dir
       output_template_in_target_generic path('bin/bio-plugin'), path(bin_dir, bin_name)
       # TODO: set the file as executable (Windows?)
-      File.chmod 0655, path(target_dir, bin_dir, bin_name)
+      File.chmod 0755, path(target_dir, bin_dir, bin_name)
     end
 
     def create_test_data
       mkdir_in_target("test") unless File.exists? "#{target_dir}/test"
-      mkdir_in_target test_data_dir  
+      #TODO use and iterator ...
+      mkdir_in_target test_data_dir
+      mkdir_in_target 'test/data/input'
+      mkdir_in_target 'test/data/regression'
+      mkdir_in_target 'test/data/rspec'
+      mkdir_in_target 'test/data/cucumber'
     end
 
     def create_ffi_structure

data/lib/bio-gem/mod/jeweler.rb

@@ -19,6 +19,11 @@ class Jeweler
       original_initialize(options)
       # RCov is not properly supported in Ruby 1.9.2, so we remove it
       development_dependencies.delete_if { |k,v| k == "rcov" }
+      # Jeweler has a bug for bundler
+      development_dependencies.delete_if { |k,v| k == "bundler" }
+      development_dependencies.delete_if { |k,v| k == "jeweler" }
+      development_dependencies << ["jeweler",'~> 1.8.4", :git => "https://github.com/technicalpickles/jeweler.git']
+      development_dependencies << ["bundler", ">= 1.0.21"]
       # development_dependencies << ["bio-logger"]
       development_dependencies << ["bio", ">= 1.4.2"]
       # we add rdoc because of an upgrade of rake RDocTask causing errors
@@ -28,6 +33,7 @@ class Jeweler
         development_dependencies << ["activesupport", ">= 3.0.7"]
         development_dependencies << ["sqlite3", ">= 1.3.3"]
       end
+      development_dependencies << ['systemu', '>=2.5.2'] if options[:wrapper]
     end
 
     alias original_project_name project_name  
@@ -69,20 +75,20 @@ class Jeweler
     end
 
     def create_and_push_repo
-      return if $UNITTEST  # skip github create when testing
-      begin 
-        Net::HTTP.post_form URI.parse('http://github.com/api/v2/yaml/repos/create'),
-        'login' => github_username,
-        'token' => github_token,
-        'description' => summary,
-        'name' => github_repo_name
-        # BY DEFAULT THE REPO IS CREATED
-        # DO NOT PUSH THE REPO BECAUSE USER MUST ADD INFO TO CONFIGURATION FILES
-        # TODO do a HEAD request to see when it's ready?
-        #@repo.push('origin')
-      rescue  SocketError => se
-        puts_template_message("Seems you are not connected to Internet, can't create a remote repository. Do not forget to create it by hand, from GitHub, and sync it with this project.")
+      puts "Please provide your Github password to create the Github repository"
+      begin
+        login = github_username
+        password = ask("Password: ") { |q| q.echo = false }
+        github = Github.new(:login => login.strip, :password => password.strip)
+        github.repos.create(:name => github_repo_name, :description => summary)
+      rescue Github::Error::Unauthorized
+        puts "Wrong login/password! Please try again"
+        retry
+      rescue Github::Error::UnprocessableEntity
+        raise GitRepoCreationFailed, "Can't create that repo. Does it already exist?"
       end
+      # TODO do a HEAD request to see when it's ready?
+      @repo.push('origin')
     end
   end #Generator
 end #Jeweler

data/lib/bio-gem/mod/jeweler/options.rb

@@ -24,6 +24,7 @@ class Jeweler
 
         require 'optparse'
         @opts = OptionParser.new do |o|
+          self[:directory]='.'
           o.banner = "Usage: #{File.basename($0)} [options] reponame\ne.g. #{File.basename($0)} the-perfect-gem"
 
           o.on('--directory [DIRECTORY]', 'specify the directory to generate into') do |directory|
@@ -62,6 +63,10 @@ class Jeweler
             self[:biogem_db] = true
           end
           
+          o.on('--with-wrapper', 'setup the biogem to be a wrapper around a command line application') do
+            self[:wrapper] = true
+          end
+          
           o.separator ""
           
           o.separator "These options are for Jeweler"

data/lib/bio-gem/templates/README.md

@@ -9,13 +9,13 @@ Note: this software is under active development!
 ## Installation
 
 ```sh
-    gem install <%= project_name %>
+gem install <%= project_name %>
 ```
 
 ## Usage
 
 ```ruby
-    require '<%= project_name %>'
+require '<%= project_name %>'
 ```
 
 The API doc is online. For more code examples see the test files in
@@ -39,7 +39,7 @@ If you use this software, please cite one of
 
 ## Biogems.info
 
-This Biogem is published at [#<%= project_name %>](http://biogems.info/index.html)
+This Biogem is published at (http://biogems.info/index.html#<%= project_name %>)
 
 ## Copyright
 

data/lib/bio-gem/templates/bin/bio-plugin

@@ -4,7 +4,16 @@
 # Author:: <%= user_name %>
 # Copyright:: <%= Time.now.year %>
 
- USAGE = "Describe <%= bin_name %>"
+USAGE = "Describe <%= bin_name %>"
+
+gempath = File.dirname(File.dirname(__FILE__))
+$: << File.join(gempath,'lib')
+
+VERSION_FILENAME=File.join(gempath,'VERSION')
+version = File.new(VERSION_FILENAME).read.chomp
+
+# print banner
+print "<%= bin_name %> #{version} by <%= user_name %> <%= Time.now.year %>\n"
 
 if ARGV.size == 0
   print USAGE

data/lib/bio-gem/templates/lib/plugin.rb

@@ -1,3 +1,19 @@
-module <%= constant_name %>
+<% if options[:wrapper] %>require 'systemu'
+<% end %>
 
+module <%= constant_name %>
+<% if options[:wrapper] %>
+  class Wrapper
+    def run
+      command = "some_application arguments"
+      status, stdout, stderr = systemu command, 0 => 'dummy stdin'
+      if status.exitstatus != 0
+         $stderr.puts "Failed to run wrapping command correctly, as non-zero exit status "+
+           "#{status.exitstatus} detected. Command run was `#{command}'"
+      else
+        # All good. Now to something useful with the stdout..
+      end
+    end
+  end
+<% end %>
 end

data/lib/bio-gem/templates/travis.yml

@@ -3,7 +3,8 @@ rvm:
   - 1.9.2
   - 1.9.3
   - jruby-19mode # JRuby in 1.9 mode
-  - rbx-19mode
+
+# - rbx-19mode
 #  - 1.8.7
 #  - jruby-18mode # JRuby in 1.8 mode
 #  - rbx-18mode

data/test/test_bio-gem.rb

@@ -5,10 +5,18 @@ $UNITTEST=true   # prevents github push
 
 class TestBiorubyGem < Test::Unit::TestCase
   TEST_DIR = 'test/bioruby-biogem-test'
+  def basic_generated_files(project_name)
+    %W(Gemfile lib lib/bio-#{project_name}.rb LICENSE.txt Rakefile README.rdoc test test/helper.rb test/test_bio-#{project_name}.rb).map do |file_name_to_test|
+      File.join("bioruby-#{project_name}",file_name_to_test)
+    end
+  end
+  
   def setup
     # check and create test directory
-     FileUtils.rm_rf(TEST_DIR) if Dir.exist?(TEST_DIR)
-     Dir.mkdir TEST_DIR
+    `git config --global user.email "git@example.com"` if `git config user.email`.empty?
+    `git config --global user.name "GitExample"` if `git config user.name`.empty?
+    FileUtils.rm_rf(TEST_DIR) if Dir.exist?(TEST_DIR)
+    Dir.mkdir TEST_DIR
   end
   
   def teardown
@@ -21,11 +29,23 @@ class TestBiorubyGem < Test::Unit::TestCase
     project_name = "biogem-test"
     Dir.chdir(TEST_DIR) do
       application_exit = Bio::Gem::Generator::Application.run!("--no-create-repo", "--user-name=\"fake_name\"", "--user-email=\"fake_email\"", "--github-username=\"fake_github_user\"","#{project_name}")
-      files_tested = %W(Gemfile lib lib/bio-#{project_name}.rb LICENSE.txt Rakefile README.rdoc test test/helper.rb test/test_bio-#{project_name}.rb).map do |file_name_to_test|
-        File.exist?(File.join("bioruby-#{project_name}",file_name_to_test))
+      basic_generated_files(project_name).each do |path| 
+        assert File.exist?(path), path
       end
-      assert_equal [true, true, true, true, true, true, true, true, true], files_tested
     end
 
   end
+  
+  def test_create_wrapper_project
+    project_name = "biogem-test2"
+    Dir.chdir(TEST_DIR) do
+      application_exit = Bio::Gem::Generator::Application.run!('--with-wrapper',"--no-create-repo", "--user-name=\"fake_name\"", "--user-email=\"fake_email\"", "--github-username=\"fake_github_user\"","#{project_name}")
+      basic_generated_files(project_name).each do |path| 
+        assert File.exist?(path), path
+      end
+      assert File.read(File.join("bioruby-#{project_name}",'lib',"bio-#{project_name}","#{project_name}.rb")).match(/require 'systemu'/)
+      assert File.read(File.join("bioruby-#{project_name}",'lib',"bio-#{project_name}","#{project_name}.rb")).match(/systemu command/)
+      assert File.read(File.join("bioruby-#{project_name}",'Gemfile')).match(/gem "systemu"/)
+    end    
+  end
 end

metadata

@@ -1,8 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-gem
 version: !ruby/object:Gem::Version
-  version: 1.3.4
-  prerelease: 
+  version: 1.3.5
 platform: ruby
 authors:
 - Raoul J.P. Bonnal
@@ -10,56 +9,67 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-04-18 00:00:00.000000000 Z
+date: 2013-07-24 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &2160322920 !ruby/object:Gem::Requirement
-    none: false
+  requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: 1.0.21
   type: :runtime
   prerelease: false
-  version_requirements: *2160322920
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: 1.0.21
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &2160321780 !ruby/object:Gem::Requirement
-    none: false
+  requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *2160321780
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: rdoc
-  requirement: &2160320080 !ruby/object:Gem::Requirement
-    none: false
+  requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *2160320080
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: shoulda
-  requirement: &2160335520 !ruby/object:Gem::Requirement
-    none: false
+  requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2160335520
-description: ! "Biogem is a software generator for those bioinformaticans who want
-  to start coding an application or a library for using/extending BioRuby core library
-  and sharing it through rubygems.org .\n  The basic idea is to simplify and promote
-  a modular approach to bioinformatics software development"
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+description: |-
+  Biogem is a software generator for those bioinformaticans who want to start coding an application or a library for using/extending BioRuby core library and sharing it through rubygems.org .
+    The basic idea is to simplify and promote a modular approach to bioinformatics software development
 email: ilpuccio.febo@gmail.com
 executables:
 - biogem
@@ -73,7 +83,6 @@ files:
 - .travis.yml
 - .yardopts
 - Gemfile
-- Gemfile.lock
 - LICENSE.txt
 - README.rdoc
 - Rakefile
@@ -119,6 +128,7 @@ files:
 homepage: http://github.com/helios/bioruby-gem
 licenses:
 - MIT
+metadata: {}
 post_install_message: 
 rdoc_options:
 - --main
@@ -127,21 +137,19 @@ rdoc_options:
 require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
-  - - ~>
+  - - '>='
     - !ruby/object:Gem::Version
       version: '1.9'
 required_rubygems_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
-  - - ! '>='
+  - - '>='
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.8.10
+rubygems_version: 2.0.0
 signing_key: 
-specification_version: 3
+specification_version: 4
 summary: Biogem is a software generator for Ruby in bioinformatics
 test_files: []

data/Gemfile.lock

@@ -1,29 +0,0 @@
-GEM
-  remote: http://rubygems.org/
-  specs:
-    git (1.2.5)
-    jeweler (1.8.3)
-      bundler (~> 1.0)
-      git (>= 1.2.5)
-      rake
-      rdoc
-    json (1.6.5)
-    json (1.6.5-java)
-    rake (0.9.2.2)
-    rdoc (3.12)
-      json (~> 1.4)
-    shoulda (3.0.1)
-      shoulda-context (~> 1.0.0)
-      shoulda-matchers (~> 1.0.0)
-    shoulda-context (1.0.0)
-    shoulda-matchers (1.0.0)
-
-PLATFORMS
-  java
-  ruby
-
-DEPENDENCIES
-  bundler (>= 1.0.21)
-  jeweler
-  rdoc
-  shoulda