bio-gem 1.3.0 → 1.3.1

data/Gemfile

@@ -4,7 +4,7 @@ source "http://rubygems.org"
 #   gem "activesupport", ">= 2.3.5"
 gem "bundler", "~> 1.0.18"
 gem "jeweler", ">= 1.7.0"
-gem "rdoc"
+
 
 
 # Add dependencies to develop your gem here.
@@ -13,5 +13,4 @@ group :development do
   gem "shoulda", ">= 0"
   gem "bundler", "~> 1.0.18"
   gem "jeweler", ">= 1.7.0"
-  gem "rdoc"
 end

data/Gemfile.lock

@@ -2,16 +2,16 @@ GEM
   remote: http://rubygems.org/
   specs:
     git (1.2.5)
-    jeweler (1.7.0)
+    jeweler (1.8.3)
       bundler (~> 1.0)
       git (>= 1.2.5)
       rake
-      rdoc
-    json (1.6.4)
     rake (0.9.2.2)
-    rdoc (3.12)
-      json (~> 1.4)
-    shoulda (2.11.3)
+    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
   ruby
@@ -19,5 +19,4 @@ PLATFORMS
 DEPENDENCIES
   bundler (~> 1.0.18)
   jeweler (>= 1.7.0)
-  rdoc
   shoulda

data/VERSION

@@ -1 +1 @@
-1.3.0
+1.3.1

data/bio-gem.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = "bio-gem"
-  s.version = "1.3.0"
+  s.version = "1.3.1"
 
   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 = "2012-02-28"
+  s.date = "2012-03-03"
   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"]
@@ -79,28 +79,22 @@ Gem::Specification.new do |s|
     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<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"])
-      s.add_development_dependency(%q<rdoc>, [">= 0"])
     else
       s.add_dependency(%q<bundler>, ["~> 1.0.18"])
       s.add_dependency(%q<jeweler>, [">= 1.7.0"])
-      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"])
-      s.add_dependency(%q<rdoc>, [">= 0"])
     end
   else
     s.add_dependency(%q<bundler>, ["~> 1.0.18"])
     s.add_dependency(%q<jeweler>, [">= 1.7.0"])
-    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"])
-    s.add_dependency(%q<rdoc>, [">= 0"])
   end
 end
 

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

@@ -22,7 +22,7 @@ class Jeweler
       # development_dependencies << ["bio-logger"]
       development_dependencies << ["bio", ">= 1.4.2"]
       # we add rdoc because of an upgrade of rake RDocTask causing errors
-      development_dependencies << ["rdoc", ">= 2.4.2"]
+      development_dependencies << ["rdoc","~> 3.12"]
       if options[:biogem_db]
         development_dependencies << ["activerecord", ">= 3.0.7"]
         development_dependencies << ["activesupport", ">= 3.0.7"]

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-gem
 version: !ruby/object:Gem::Version
-  version: 1.3.0
+  version: 1.3.1
   prerelease: 
 platform: ruby
 authors:
@@ -10,11 +10,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-02-28 00:00:00.000000000 Z
+date: 2012-03-03 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &2152477800 !ruby/object:Gem::Requirement
+  requirement: &2169129020 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -22,10 +22,10 @@ dependencies:
         version: 1.0.18
   type: :runtime
   prerelease: false
-  version_requirements: *2152477800
+  version_requirements: *2169129020
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &2152476940 !ruby/object:Gem::Requirement
+  requirement: &2169125980 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -33,21 +33,10 @@ dependencies:
         version: 1.7.0
   type: :runtime
   prerelease: false
-  version_requirements: *2152476940
-- !ruby/object:Gem::Dependency
-  name: rdoc
-  requirement: &2152476160 !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - ! '>='
-      - !ruby/object:Gem::Version
-        version: '0'
-  type: :runtime
-  prerelease: false
-  version_requirements: *2152476160
+  version_requirements: *2169125980
 - !ruby/object:Gem::Dependency
   name: shoulda
-  requirement: &2152490840 !ruby/object:Gem::Requirement
+  requirement: &2169124020 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -55,10 +44,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2152490840
+  version_requirements: *2169124020
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &2152488740 !ruby/object:Gem::Requirement
+  requirement: &2169121720 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -66,10 +55,10 @@ dependencies:
         version: 1.0.18
   type: :development
   prerelease: false
-  version_requirements: *2152488740
+  version_requirements: *2169121720
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &2152486560 !ruby/object:Gem::Requirement
+  requirement: &2169136360 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -77,18 +66,7 @@ dependencies:
         version: 1.7.0
   type: :development
   prerelease: false
-  version_requirements: *2152486560
-- !ruby/object:Gem::Dependency
-  name: rdoc
-  requirement: &2152485000 !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - ! '>='
-      - !ruby/object:Gem::Version
-        version: '0'
-  type: :development
-  prerelease: false
-  version_requirements: *2152485000
+  version_requirements: *2169136360
 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