bio-gem 1.3.1 → 1.3.2

data/.travis.yml

@@ -3,10 +3,14 @@ rvm:
   - 1.9.2
   - 1.9.3
   - jruby-19mode # JRuby in 1.9 mode
-  - rbx-19mode
+  - 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
 
 # uncomment this line if your project needs to run something other than `rake`:
 # script: bundle exec rspec spec
+
+before_install:
+  - bundle --version
+  - gem env

data/Gemfile

@@ -2,15 +2,12 @@ source "http://rubygems.org"
 # Add dependencies required to use your gem here.
 # Example:
 #   gem "activesupport", ">= 2.3.5"
-gem "bundler", "~> 1.0.18"
-gem "jeweler", ">= 1.7.0"
-
-
+gem "bundler", "~> 1.0.21"
+gem "jeweler"
+gem "rdoc"
 
 # Add dependencies to develop your gem here.
 # Include everything needed to run rake, tests, features, etc.
 group :development do
   gem "shoulda", ">= 0"
-  gem "bundler", "~> 1.0.18"
-  gem "jeweler", ">= 1.7.0"
 end

data/Gemfile.lock

@@ -6,7 +6,12 @@ GEM
       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)
@@ -14,9 +19,11 @@ GEM
     shoulda-matchers (1.0.0)
 
 PLATFORMS
+  java
   ruby
 
 DEPENDENCIES
-  bundler (~> 1.0.18)
-  jeweler (>= 1.7.0)
+  bundler (~> 1.0.21)
+  jeweler
+  rdoc
   shoulda

data/README.rdoc

@@ -1,5 +1,10 @@
 = Biogem
 
+Helios: {<img
+src="https://secure.travis-ci.org/helios/bioruby-gem.png"/>}[http://travis-ci.org/#!/helios/bioruby-gem]
+
+Pjotr: {<img src="https://secure.travis-ci.org/pjotrp/bioruby-gem.png"/>}[http://travis-ci.org/#!/pjotrp/bioruby-gem]
+
 Biogem provides a set of tools for those Bioinformaticans who want to
 start coding an application, or a library for using/extending
 BioRuby's core library and sharing the code as a gem through
@@ -56,6 +61,10 @@ Rubygems will not let you install Biogem in an environment with a Ruby
 interpreter older than 1.9.X. Biogem can create gems for Ruby 1.8.7 -
 but you need a recent version of Ruby and tools to run Biogem itself.
 
+Also it is recommended to install the latest version of bundler using
+
+  $ gem install bundler
+
 === Download
 
 Install the Biogem toolset with

data/VERSION

@@ -1 +1 @@
-1.3.1
+1.3.2

data/bio-gem.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = "bio-gem"
-  s.version = "1.3.1"
+  s.version = "1.3.2"
 
   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 = "2012-03-03"
+  s.date = "2012-03-20"
   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"]
@@ -77,24 +77,21 @@ Gem::Specification.new do |s|
     s.specification_version = 3
 
     if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
-      s.add_runtime_dependency(%q<bundler>, ["~> 1.0.18"])
-      s.add_runtime_dependency(%q<jeweler>, [">= 1.7.0"])
+      s.add_runtime_dependency(%q<bundler>, ["~> 1.0.21"])
+      s.add_runtime_dependency(%q<jeweler>, [">= 0"])
+      s.add_runtime_dependency(%q<rdoc>, [">= 0"])
       s.add_development_dependency(%q<shoulda>, [">= 0"])
-      s.add_development_dependency(%q<bundler>, ["~> 1.0.18"])
-      s.add_development_dependency(%q<jeweler>, [">= 1.7.0"])
     else
-      s.add_dependency(%q<bundler>, ["~> 1.0.18"])
-      s.add_dependency(%q<jeweler>, [">= 1.7.0"])
+      s.add_dependency(%q<bundler>, ["~> 1.0.21"])
+      s.add_dependency(%q<jeweler>, [">= 0"])
+      s.add_dependency(%q<rdoc>, [">= 0"])
       s.add_dependency(%q<shoulda>, [">= 0"])
-      s.add_dependency(%q<bundler>, ["~> 1.0.18"])
-      s.add_dependency(%q<jeweler>, [">= 1.7.0"])
     end
   else
-    s.add_dependency(%q<bundler>, ["~> 1.0.18"])
-    s.add_dependency(%q<jeweler>, [">= 1.7.0"])
+    s.add_dependency(%q<bundler>, ["~> 1.0.21"])
+    s.add_dependency(%q<jeweler>, [">= 0"])
+    s.add_dependency(%q<rdoc>, [">= 0"])
     s.add_dependency(%q<shoulda>, [">= 0"])
-    s.add_dependency(%q<bundler>, ["~> 1.0.18"])
-    s.add_dependency(%q<jeweler>, [">= 1.7.0"])
   end
 end
 

data/test/test_bio-gem.rb

@@ -20,7 +20,7 @@ class TestBiorubyGem < Test::Unit::TestCase
   def test_create_basic_project
     project_name = "biogem-test"
     Dir.chdir(TEST_DIR) do
-      application_exit = Bio::Gem::Generator::Application.run!(project_name)
+      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))
       end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-gem
 version: !ruby/object:Gem::Version
-  version: 1.3.1
+  version: 1.3.2
   prerelease: 
 platform: ruby
 authors:
@@ -10,63 +10,52 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-03-03 00:00:00.000000000 Z
+date: 2012-03-20 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &2169129020 !ruby/object:Gem::Requirement
+  requirement: &2153251320 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 1.0.18
+        version: 1.0.21
   type: :runtime
   prerelease: false
-  version_requirements: *2169129020
+  version_requirements: *2153251320
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &2169125980 !ruby/object:Gem::Requirement
+  requirement: &2153250800 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
       - !ruby/object:Gem::Version
-        version: 1.7.0
+        version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *2169125980
+  version_requirements: *2153250800
 - !ruby/object:Gem::Dependency
-  name: shoulda
-  requirement: &2169124020 !ruby/object:Gem::Requirement
+  name: rdoc
+  requirement: &2153250260 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
       - !ruby/object:Gem::Version
         version: '0'
-  type: :development
-  prerelease: false
-  version_requirements: *2169124020
-- !ruby/object:Gem::Dependency
-  name: bundler
-  requirement: &2169121720 !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - ~>
-      - !ruby/object:Gem::Version
-        version: 1.0.18
-  type: :development
+  type: :runtime
   prerelease: false
-  version_requirements: *2169121720
+  version_requirements: *2153250260
 - !ruby/object:Gem::Dependency
-  name: jeweler
-  requirement: &2169136360 !ruby/object:Gem::Requirement
+  name: shoulda
+  requirement: &2153249360 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
       - !ruby/object:Gem::Version
-        version: 1.7.0
+        version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2169136360
+  version_requirements: *2153249360
 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