bio-gem 1.3.4 → 1.3.5

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@@ -0,0 +1,7 @@
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+ ---
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+ SHA1:
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+ metadata.gz: d51d946c9198261b369526a545153ea8f4806e55
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+ data.tar.gz: 2f5aca2b0c51a7a7c512be9bcd253d705c9f7295
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+ SHA512:
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+ metadata.gz: 381baf735d2b2f95b1291ec3f867f50c7d9f9c8c1fc172ed55245339650fcef80e988066651e8b319b9f6b43159654e4a82a0f29eff31339df20af7de0c75469
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+ data.tar.gz: 1c8d0e431d34e6e14f3ea3e93c610aba48ebdd2f9e1769cdc7b0bf03a6faa36b900a4d5aa96293288e1fd685b5b0393dc4024efacc1af0403cc9ac62ddc53215
@@ -3,7 +3,7 @@ rvm:
3
3
  - 1.9.2
4
4
  - 1.9.3
5
5
  - jruby-19mode # JRuby in 1.9 mode
6
- - rbx-19mode # rvm install rbx -- --enable-version=1.9,1.8 --default-version=1.9
6
+ # - rbx-19mode # rvm install rbx -- --enable-version=1.9,1.8 --default-version=1.9
7
7
  # - 1.8.7
8
8
  # - jruby-18mode # JRuby in 1.8 mode
9
9
  # - rbx-18mode
data/Gemfile CHANGED
@@ -3,7 +3,7 @@ source "http://rubygems.org"
3
3
  # Example:
4
4
  # gem "activesupport", ">= 2.3.5"
5
5
  gem "bundler", ">= 1.0.21"
6
- gem "jeweler"
6
+ gem "jeweler", :git => 'https://github.com/technicalpickles/jeweler.git'
7
7
  gem "rdoc"
8
8
 
9
9
  # Add dependencies to develop your gem here.
data/Rakefile CHANGED
@@ -24,7 +24,7 @@ Jeweler::Tasks.new do |gem|
24
24
  # and development dependencies are only needed for development (ie running rake tasks, tests, etc)
25
25
  #gem.version='0.0.1'
26
26
  gem.rdoc_options << '--main' << 'README' << '--line-numbers'
27
- gem.required_ruby_version = "~>1.9"
27
+ gem.required_ruby_version = ">= 1.9"
28
28
  gem.extra_rdoc_files = ['LICENSE.txt', 'README.rdoc','Tutorial.rdoc']
29
29
  end
30
30
 
@@ -204,20 +204,29 @@ In bioinformatics is very common to presents data using a web application, and o
204
204
  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.
205
205
 
206
206
  $ biogem --with-engine Foo foo
207
+ $ cd bioruby-foo
208
+ $ rake version:write
209
+ $ bundle install
207
210
 
208
211
  Note: a database is automatically configure for the newly created gem
209
212
 
210
- $ rails new Webfoo
213
+ Create a completely new Rails web application NOT inside the newly create biogem, so rememner to
211
214
 
212
- You can test your application just inserting into Rails application Gemfile the newly created gem:
215
+ $ cd ..
213
216
 
214
- gem 'bio-foo', :path=>'path_gem_dir'
217
+ and then create a new web app
218
+
219
+ $ rails new Webfoo
215
220
 
216
221
  update the installation running:
217
222
 
218
223
  cd Webfoo
219
224
  bundle install
220
225
 
226
+ You can test your application just inserting into Rails application Gemfile the newly created gem:
227
+
228
+ gem 'bio-foo', :path=>'path_gem_dir'
229
+
221
230
  Enable the route for the added gem (in biouby-foo/config/routes.rb) uncomment:
222
231
 
223
232
  yourPathToTheControllerFiles = 'foopath'
@@ -291,8 +300,8 @@ This is Gemfile's content
291
300
  # Include everything needed to run rake, tests, features, etc.
292
301
  group :development do
293
302
  gem "shoulda", ">= 0"
294
- gem "bundler", "~> 1.0.0"
295
- gem "jeweler", "~> 1.6.4"
303
+ gem "bundler", "> 1.0.0"
304
+ gem "jeweler", "> 1.6.4"
296
305
  gem "rcov", ">= 0"
297
306
  gem "bio", ">= 1.4.2"
298
307
  end
data/VERSION CHANGED
@@ -1 +1 @@
1
- 1.3.4
1
+ 1.3.5
data/bin/biogem CHANGED
@@ -10,33 +10,40 @@ require 'rake'
10
10
 
11
11
  orig_argv = ARGV.clone
12
12
  # application_exit[:exit] exists, application_exit[:options] it depends.
13
- application_exit = Bio::Gem::Generator::Application.run!(*ARGV)
14
- options = application_exit[:options]
13
+ exit Bio::Gem::Generator::Application.run!(*ARGV)
15
14
 
16
- if (application_exit[:exit]==0)
17
- pwd = FileUtils.pwd
18
- FileUtils.cd "bioruby-#{application_exit[:options][:project_name]}"
19
- ARGV.clear << "install"
15
+ #run
16
+ ## bundle install
17
+ ## rake version:write
18
+ ## rake gemspec
20
19
 
21
- Bundler::CLI.start
22
- #TODO: call rake directly not from shell
20
+ # application_exit = Bio::Gem::Generator::Application.run!(*ARGV)
21
+ # options = application_exit[:options]
22
+
23
+ # if (application_exit[:exit]==0)
24
+ # pwd = FileUtils.pwd
25
+ # FileUtils.cd "bioruby-#{application_exit[:options][:project_name]}"
26
+ # ARGV.clear << "install"
27
+
28
+ # Bundler::CLI.start
29
+ # #TODO: call rake directly not from shell
23
30
 
24
- if options[:testing_framework] == :rspec
25
- # Don't remove the following warning, as it may be encountered by anyone running
26
- # biogem from source (especially with the --with-rspec switch)!
27
- print "
28
- WARNING: if rake gives an (rspec) error try running biogem from a directly
29
- installed gem instead:
30
- bundle exec rake install
31
- biogem [options]
32
- "
33
- end
34
- print "\trake version:write\n"
35
- sh "rake version:write"
36
- print "\trake gemspec\n"
37
- sh "rake gemspec"
38
- print "Done!\n"
39
- else
40
- $stderr.print "\nERROR: Biogem failed!\n"
41
- end
31
+ # if options[:testing_framework] == :rspec
32
+ # # Don't remove the following warning, as it may be encountered by anyone running
33
+ # # biogem from source (especially with the --with-rspec switch)!
34
+ # print "
35
+ # WARNING: if rake gives an (rspec) error try running biogem from a directly
36
+ # installed gem instead:
37
+ # bundle exec rake install
38
+ # biogem [options]
39
+ # "
40
+ # end
41
+ # print "\trake version:write\n"
42
+ # sh "rake version:write"
43
+ # print "\trake gemspec\n"
44
+ # sh "rake gemspec"
45
+ # print "Done!\n"
46
+ # else
47
+ # $stderr.print "\nERROR: Biogem failed!\n"
48
+ # end
42
49
 
@@ -5,11 +5,11 @@
5
5
 
6
6
  Gem::Specification.new do |s|
7
7
  s.name = "bio-gem"
8
- s.version = "1.3.4"
8
+ s.version = "1.3.5"
9
9
 
10
10
  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
11
11
  s.authors = ["Raoul J.P. Bonnal", "Pjotr Prins"]
12
- s.date = "2012-04-18"
12
+ s.date = "2013-07-24"
13
13
  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"
14
14
  s.email = "ilpuccio.febo@gmail.com"
15
15
  s.executables = ["biogem"]
@@ -23,7 +23,6 @@ Gem::Specification.new do |s|
23
23
  ".travis.yml",
24
24
  ".yardopts",
25
25
  "Gemfile",
26
- "Gemfile.lock",
27
26
  "LICENSE.txt",
28
27
  "README.rdoc",
29
28
  "Rakefile",
@@ -71,12 +70,12 @@ Gem::Specification.new do |s|
71
70
  s.licenses = ["MIT"]
72
71
  s.rdoc_options = ["--main", "README", "--line-numbers"]
73
72
  s.require_paths = ["lib"]
74
- s.required_ruby_version = Gem::Requirement.new("~> 1.9")
75
- s.rubygems_version = "1.8.10"
73
+ s.required_ruby_version = Gem::Requirement.new(">= 1.9")
74
+ s.rubygems_version = "2.0.0"
76
75
  s.summary = "Biogem is a software generator for Ruby in bioinformatics"
77
76
 
78
77
  if s.respond_to? :specification_version then
79
- s.specification_version = 3
78
+ s.specification_version = 4
80
79
 
81
80
  if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
82
81
  s.add_runtime_dependency(%q<bundler>, [">= 1.0.21"])
@@ -4,52 +4,63 @@ module Bio
4
4
  class Generator
5
5
  class Application
6
6
  class << self
7
- # Return an hash with :exit=>(0|1) and optionally and :options which is another hash
8
- # This function has been stolen from Jeweler and mdified with the return hash, the original class returns just 0|1
9
- # the problem is that I need to identify the name of the project_name from outside to use bundler.
7
+ include Shellwords
10
8
  def run!(*arguments)
11
- env_opts = if ENV['JEWELER_OPTS']
12
- Jeweler::Generator::Options.new(ENV['JEWELER_OPTS'].split(' '))
13
- end
14
- options = Jeweler::Generator::Options.new(arguments)
15
- options = options.merge(env_opts) if env_opts
16
9
 
17
- if options[:invalid_argument]
18
- $stderr.puts options[:invalid_argument]
19
- options[:show_help] = true
20
- end
10
+ options = build_options(arguments)
21
11
 
22
- if options[:show_help]
23
- $stderr.puts options.opts
24
- return {:exit=>1}
25
- end
12
+ if options[:invalid_argument]
13
+ $stderr.puts options[:invalid_argument]
14
+ options[:show_help] = true
15
+ end
26
16
 
27
- if options[:project_name].nil? || options[:project_name].squeeze.strip == ""
28
- $stderr.puts options.opts
29
- return {:exit=>1}
30
- end
17
+ if options[:show_version]
18
+ $stderr.puts "Version: #{Jeweler::Version::STRING}"
19
+ return 1
20
+ end
21
+
22
+ if options[:show_help]
23
+ $stderr.puts options.opts
24
+ return 1
25
+ end
31
26
 
32
- begin
27
+ if options[:project_name].nil? || options[:project_name].squeeze.strip == ""
28
+ $stderr.puts options.opts
29
+ return 1
30
+ end
31
+
32
+ begin
33
+ if options[:directory]!='.'
34
+ FileUtils.mkdir_p options[:directory]
35
+ end
36
+ FileUtils.cd options[:directory] do
33
37
  generator = Jeweler::Generator.new(options)
34
38
  generator.run
35
- return {:exit=>0, :options=>options}
36
- rescue Jeweler::NoGitUserName
37
- $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"}
38
- return {:exit=>1}
39
- rescue Jeweler::NoGitUserEmail
40
- $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}
41
- return {:exit=>1}
42
- rescue Jeweler::NoGitHubUser
43
- $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}
44
- return {:exit=>1}
45
- rescue Jeweler::NoGitHubToken
46
- $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}
47
- return {:exit=>1}
48
- rescue Jeweler::FileInTheWay
49
- $stderr.puts "The directory for #{options[:project_name]} already exists. Maybe move it out of the way before continuing?"
50
- return {:exit=>1}
39
+ return 0
51
40
  end
41
+ rescue Jeweler::NoGitUserName
42
+ $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"}
43
+ return 1
44
+ rescue Jeweler::NoGitUserEmail
45
+ $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}
46
+ return 1
47
+ rescue Jeweler::NoGitHubUser
48
+ $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}
49
+ return 1
50
+ rescue Jeweler::FileInTheWay
51
+ $stderr.puts "The directory #{options[:project_name]} already exists. Maybe move it out of the way before continuing?"
52
+ return 1
53
+ end
52
54
  end #run!
55
+
56
+ def build_options(arguments)
57
+ env_opts_string = ENV['JEWELER_OPTS'] || ""
58
+ env_opts = Jeweler::Generator::Options.new(shellwords(env_opts_string))
59
+ argument_opts = Jeweler::Generator::Options.new(arguments)
60
+
61
+ env_opts.merge(argument_opts)
62
+ end
63
+
53
64
  end #self
54
65
  end #Application
55
66
  end #Generator
@@ -3,7 +3,7 @@
3
3
 
4
4
  module Biogem
5
5
  module Render
6
- # new hook for removing stuff
6
+ # new hook for removing stuff (FIXME: could use a test!!)
7
7
  def after_render_template(source,buf)
8
8
  if source == 'other_tasks.erb'
9
9
  $stdout.puts "\tremove jeweler rcov lines"
@@ -92,12 +92,17 @@ module Biogem
92
92
  mkdir_in_target bin_dir
93
93
  output_template_in_target_generic path('bin/bio-plugin'), path(bin_dir, bin_name)
94
94
  # TODO: set the file as executable (Windows?)
95
- File.chmod 0655, path(target_dir, bin_dir, bin_name)
95
+ File.chmod 0755, path(target_dir, bin_dir, bin_name)
96
96
  end
97
97
 
98
98
  def create_test_data
99
99
  mkdir_in_target("test") unless File.exists? "#{target_dir}/test"
100
- mkdir_in_target test_data_dir
100
+ #TODO use and iterator ...
101
+ mkdir_in_target test_data_dir
102
+ mkdir_in_target 'test/data/input'
103
+ mkdir_in_target 'test/data/regression'
104
+ mkdir_in_target 'test/data/rspec'
105
+ mkdir_in_target 'test/data/cucumber'
101
106
  end
102
107
 
103
108
  def create_ffi_structure
@@ -19,6 +19,11 @@ class Jeweler
19
19
  original_initialize(options)
20
20
  # RCov is not properly supported in Ruby 1.9.2, so we remove it
21
21
  development_dependencies.delete_if { |k,v| k == "rcov" }
22
+ # Jeweler has a bug for bundler
23
+ development_dependencies.delete_if { |k,v| k == "bundler" }
24
+ development_dependencies.delete_if { |k,v| k == "jeweler" }
25
+ development_dependencies << ["jeweler",'~> 1.8.4", :git => "https://github.com/technicalpickles/jeweler.git']
26
+ development_dependencies << ["bundler", ">= 1.0.21"]
22
27
  # development_dependencies << ["bio-logger"]
23
28
  development_dependencies << ["bio", ">= 1.4.2"]
24
29
  # we add rdoc because of an upgrade of rake RDocTask causing errors
@@ -28,6 +33,7 @@ class Jeweler
28
33
  development_dependencies << ["activesupport", ">= 3.0.7"]
29
34
  development_dependencies << ["sqlite3", ">= 1.3.3"]
30
35
  end
36
+ development_dependencies << ['systemu', '>=2.5.2'] if options[:wrapper]
31
37
  end
32
38
 
33
39
  alias original_project_name project_name
@@ -69,20 +75,20 @@ class Jeweler
69
75
  end
70
76
 
71
77
  def create_and_push_repo
72
- return if $UNITTEST # skip github create when testing
73
- begin
74
- Net::HTTP.post_form URI.parse('http://github.com/api/v2/yaml/repos/create'),
75
- 'login' => github_username,
76
- 'token' => github_token,
77
- 'description' => summary,
78
- 'name' => github_repo_name
79
- # BY DEFAULT THE REPO IS CREATED
80
- # DO NOT PUSH THE REPO BECAUSE USER MUST ADD INFO TO CONFIGURATION FILES
81
- # TODO do a HEAD request to see when it's ready?
82
- #@repo.push('origin')
83
- rescue SocketError => se
84
- 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.")
78
+ puts "Please provide your Github password to create the Github repository"
79
+ begin
80
+ login = github_username
81
+ password = ask("Password: ") { |q| q.echo = false }
82
+ github = Github.new(:login => login.strip, :password => password.strip)
83
+ github.repos.create(:name => github_repo_name, :description => summary)
84
+ rescue Github::Error::Unauthorized
85
+ puts "Wrong login/password! Please try again"
86
+ retry
87
+ rescue Github::Error::UnprocessableEntity
88
+ raise GitRepoCreationFailed, "Can't create that repo. Does it already exist?"
85
89
  end
90
+ # TODO do a HEAD request to see when it's ready?
91
+ @repo.push('origin')
86
92
  end
87
93
  end #Generator
88
94
  end #Jeweler
@@ -24,6 +24,7 @@ class Jeweler
24
24
 
25
25
  require 'optparse'
26
26
  @opts = OptionParser.new do |o|
27
+ self[:directory]='.'
27
28
  o.banner = "Usage: #{File.basename($0)} [options] reponame\ne.g. #{File.basename($0)} the-perfect-gem"
28
29
 
29
30
  o.on('--directory [DIRECTORY]', 'specify the directory to generate into') do |directory|
@@ -62,6 +63,10 @@ class Jeweler
62
63
  self[:biogem_db] = true
63
64
  end
64
65
 
66
+ o.on('--with-wrapper', 'setup the biogem to be a wrapper around a command line application') do
67
+ self[:wrapper] = true
68
+ end
69
+
65
70
  o.separator ""
66
71
 
67
72
  o.separator "These options are for Jeweler"
@@ -9,13 +9,13 @@ Note: this software is under active development!
9
9
  ## Installation
10
10
 
11
11
  ```sh
12
- gem install <%= project_name %>
12
+ gem install <%= project_name %>
13
13
  ```
14
14
 
15
15
  ## Usage
16
16
 
17
17
  ```ruby
18
- require '<%= project_name %>'
18
+ require '<%= project_name %>'
19
19
  ```
20
20
 
21
21
  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
39
39
 
40
40
  ## Biogems.info
41
41
 
42
- This Biogem is published at [#<%= project_name %>](http://biogems.info/index.html)
42
+ This Biogem is published at (http://biogems.info/index.html#<%= project_name %>)
43
43
 
44
44
  ## Copyright
45
45
 
@@ -4,7 +4,16 @@
4
4
  # Author:: <%= user_name %>
5
5
  # Copyright:: <%= Time.now.year %>
6
6
 
7
- USAGE = "Describe <%= bin_name %>"
7
+ USAGE = "Describe <%= bin_name %>"
8
+
9
+ gempath = File.dirname(File.dirname(__FILE__))
10
+ $: << File.join(gempath,'lib')
11
+
12
+ VERSION_FILENAME=File.join(gempath,'VERSION')
13
+ version = File.new(VERSION_FILENAME).read.chomp
14
+
15
+ # print banner
16
+ print "<%= bin_name %> #{version} by <%= user_name %> <%= Time.now.year %>\n"
8
17
 
9
18
  if ARGV.size == 0
10
19
  print USAGE
@@ -1,3 +1,19 @@
1
- module <%= constant_name %>
1
+ <% if options[:wrapper] %>require 'systemu'
2
+ <% end %>
2
3
 
4
+ module <%= constant_name %>
5
+ <% if options[:wrapper] %>
6
+ class Wrapper
7
+ def run
8
+ command = "some_application arguments"
9
+ status, stdout, stderr = systemu command, 0 => 'dummy stdin'
10
+ if status.exitstatus != 0
11
+ $stderr.puts "Failed to run wrapping command correctly, as non-zero exit status "+
12
+ "#{status.exitstatus} detected. Command run was `#{command}'"
13
+ else
14
+ # All good. Now to something useful with the stdout..
15
+ end
16
+ end
17
+ end
18
+ <% end %>
3
19
  end
@@ -3,7 +3,8 @@ rvm:
3
3
  - 1.9.2
4
4
  - 1.9.3
5
5
  - jruby-19mode # JRuby in 1.9 mode
6
- - rbx-19mode
6
+
7
+ # - rbx-19mode
7
8
  # - 1.8.7
8
9
  # - jruby-18mode # JRuby in 1.8 mode
9
10
  # - rbx-18mode
@@ -5,10 +5,18 @@ $UNITTEST=true # prevents github push
5
5
 
6
6
  class TestBiorubyGem < Test::Unit::TestCase
7
7
  TEST_DIR = 'test/bioruby-biogem-test'
8
+ def basic_generated_files(project_name)
9
+ %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|
10
+ File.join("bioruby-#{project_name}",file_name_to_test)
11
+ end
12
+ end
13
+
8
14
  def setup
9
15
  # check and create test directory
10
- FileUtils.rm_rf(TEST_DIR) if Dir.exist?(TEST_DIR)
11
- Dir.mkdir TEST_DIR
16
+ `git config --global user.email "git@example.com"` if `git config user.email`.empty?
17
+ `git config --global user.name "GitExample"` if `git config user.name`.empty?
18
+ FileUtils.rm_rf(TEST_DIR) if Dir.exist?(TEST_DIR)
19
+ Dir.mkdir TEST_DIR
12
20
  end
13
21
 
14
22
  def teardown
@@ -21,11 +29,23 @@ class TestBiorubyGem < Test::Unit::TestCase
21
29
  project_name = "biogem-test"
22
30
  Dir.chdir(TEST_DIR) do
23
31
  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}")
24
- 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|
25
- File.exist?(File.join("bioruby-#{project_name}",file_name_to_test))
32
+ basic_generated_files(project_name).each do |path|
33
+ assert File.exist?(path), path
26
34
  end
27
- assert_equal [true, true, true, true, true, true, true, true, true], files_tested
28
35
  end
29
36
 
30
37
  end
38
+
39
+ def test_create_wrapper_project
40
+ project_name = "biogem-test2"
41
+ Dir.chdir(TEST_DIR) do
42
+ 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}")
43
+ basic_generated_files(project_name).each do |path|
44
+ assert File.exist?(path), path
45
+ end
46
+ assert File.read(File.join("bioruby-#{project_name}",'lib',"bio-#{project_name}","#{project_name}.rb")).match(/require 'systemu'/)
47
+ assert File.read(File.join("bioruby-#{project_name}",'lib',"bio-#{project_name}","#{project_name}.rb")).match(/systemu command/)
48
+ assert File.read(File.join("bioruby-#{project_name}",'Gemfile')).match(/gem "systemu"/)
49
+ end
50
+ end
31
51
  end
metadata CHANGED
@@ -1,8 +1,7 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: bio-gem
3
3
  version: !ruby/object:Gem::Version
4
- version: 1.3.4
5
- prerelease:
4
+ version: 1.3.5
6
5
  platform: ruby
7
6
  authors:
8
7
  - Raoul J.P. Bonnal
@@ -10,56 +9,67 @@ authors:
10
9
  autorequire:
11
10
  bindir: bin
12
11
  cert_chain: []
13
- date: 2012-04-18 00:00:00.000000000 Z
12
+ date: 2013-07-24 00:00:00.000000000 Z
14
13
  dependencies:
15
14
  - !ruby/object:Gem::Dependency
16
15
  name: bundler
17
- requirement: &2160322920 !ruby/object:Gem::Requirement
18
- none: false
16
+ requirement: !ruby/object:Gem::Requirement
19
17
  requirements:
20
- - - ! '>='
18
+ - - '>='
21
19
  - !ruby/object:Gem::Version
22
20
  version: 1.0.21
23
21
  type: :runtime
24
22
  prerelease: false
25
- version_requirements: *2160322920
23
+ version_requirements: !ruby/object:Gem::Requirement
24
+ requirements:
25
+ - - '>='
26
+ - !ruby/object:Gem::Version
27
+ version: 1.0.21
26
28
  - !ruby/object:Gem::Dependency
27
29
  name: jeweler
28
- requirement: &2160321780 !ruby/object:Gem::Requirement
29
- none: false
30
+ requirement: !ruby/object:Gem::Requirement
30
31
  requirements:
31
- - - ! '>='
32
+ - - '>='
32
33
  - !ruby/object:Gem::Version
33
34
  version: '0'
34
35
  type: :runtime
35
36
  prerelease: false
36
- version_requirements: *2160321780
37
+ version_requirements: !ruby/object:Gem::Requirement
38
+ requirements:
39
+ - - '>='
40
+ - !ruby/object:Gem::Version
41
+ version: '0'
37
42
  - !ruby/object:Gem::Dependency
38
43
  name: rdoc
39
- requirement: &2160320080 !ruby/object:Gem::Requirement
40
- none: false
44
+ requirement: !ruby/object:Gem::Requirement
41
45
  requirements:
42
- - - ! '>='
46
+ - - '>='
43
47
  - !ruby/object:Gem::Version
44
48
  version: '0'
45
49
  type: :runtime
46
50
  prerelease: false
47
- version_requirements: *2160320080
51
+ version_requirements: !ruby/object:Gem::Requirement
52
+ requirements:
53
+ - - '>='
54
+ - !ruby/object:Gem::Version
55
+ version: '0'
48
56
  - !ruby/object:Gem::Dependency
49
57
  name: shoulda
50
- requirement: &2160335520 !ruby/object:Gem::Requirement
51
- none: false
58
+ requirement: !ruby/object:Gem::Requirement
52
59
  requirements:
53
- - - ! '>='
60
+ - - '>='
54
61
  - !ruby/object:Gem::Version
55
62
  version: '0'
56
63
  type: :development
57
64
  prerelease: false
58
- version_requirements: *2160335520
59
- description: ! "Biogem is a software generator for those bioinformaticans who want
60
- to start coding an application or a library for using/extending BioRuby core library
61
- and sharing it through rubygems.org .\n The basic idea is to simplify and promote
62
- a modular approach to bioinformatics software development"
65
+ version_requirements: !ruby/object:Gem::Requirement
66
+ requirements:
67
+ - - '>='
68
+ - !ruby/object:Gem::Version
69
+ version: '0'
70
+ description: |-
71
+ 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 .
72
+ The basic idea is to simplify and promote a modular approach to bioinformatics software development
63
73
  email: ilpuccio.febo@gmail.com
64
74
  executables:
65
75
  - biogem
@@ -73,7 +83,6 @@ files:
73
83
  - .travis.yml
74
84
  - .yardopts
75
85
  - Gemfile
76
- - Gemfile.lock
77
86
  - LICENSE.txt
78
87
  - README.rdoc
79
88
  - Rakefile
@@ -119,6 +128,7 @@ files:
119
128
  homepage: http://github.com/helios/bioruby-gem
120
129
  licenses:
121
130
  - MIT
131
+ metadata: {}
122
132
  post_install_message:
123
133
  rdoc_options:
124
134
  - --main
@@ -127,21 +137,19 @@ rdoc_options:
127
137
  require_paths:
128
138
  - lib
129
139
  required_ruby_version: !ruby/object:Gem::Requirement
130
- none: false
131
140
  requirements:
132
- - - ~>
141
+ - - '>='
133
142
  - !ruby/object:Gem::Version
134
143
  version: '1.9'
135
144
  required_rubygems_version: !ruby/object:Gem::Requirement
136
- none: false
137
145
  requirements:
138
- - - ! '>='
146
+ - - '>='
139
147
  - !ruby/object:Gem::Version
140
148
  version: '0'
141
149
  requirements: []
142
150
  rubyforge_project:
143
- rubygems_version: 1.8.10
151
+ rubygems_version: 2.0.0
144
152
  signing_key:
145
- specification_version: 3
153
+ specification_version: 4
146
154
  summary: Biogem is a software generator for Ruby in bioinformatics
147
155
  test_files: []
@@ -1,29 +0,0 @@
1
- GEM
2
- remote: http://rubygems.org/
3
- specs:
4
- git (1.2.5)
5
- jeweler (1.8.3)
6
- bundler (~> 1.0)
7
- git (>= 1.2.5)
8
- rake
9
- rdoc
10
- json (1.6.5)
11
- json (1.6.5-java)
12
- rake (0.9.2.2)
13
- rdoc (3.12)
14
- json (~> 1.4)
15
- shoulda (3.0.1)
16
- shoulda-context (~> 1.0.0)
17
- shoulda-matchers (~> 1.0.0)
18
- shoulda-context (1.0.0)
19
- shoulda-matchers (1.0.0)
20
-
21
- PLATFORMS
22
- java
23
- ruby
24
-
25
- DEPENDENCIES
26
- bundler (>= 1.0.21)
27
- jeweler
28
- rdoc
29
- shoulda