scaffolder-annotation-locator 0.1.1 → 0.1.2

data/.gitignore

@@ -0,0 +1,45 @@
+# Aruba directory
+tmp
+
+# rcov generated
+coverage
+
+# rdoc generated
+rdoc
+
+# yard generated
+doc
+.yardoc
+
+# bundler
+.bundle
+
+# jeweler generated
+pkg
+
+# Have editor/IDE/OS specific files you need to ignore? Consider using a global gitignore: 
+#
+# * Create a file at ~/.gitignore
+# * Include files you want ignored
+# * Run: git config --global core.excludesfile ~/.gitignore
+#
+# After doing this, these files will be ignored in all your git projects,
+# saving you from having to 'pollute' every project you touch with them
+#
+# Not sure what to needs to be ignored for particular editors/OSes? Here's some ideas to get you started. (Remember, remove the leading # of the line)
+#
+# For MacOS:
+#
+#.DS_Store
+#
+# For TextMate
+#*.tmproj
+#tmtags
+#
+# For emacs:
+#*~
+#\#*
+#.\#*
+#
+# For vim:
+#*.swp

data/CHANGELOG.txt

@@ -0,0 +1,5 @@
+0.1.2
+
+  * Remove jeweler from project and use bundler tasks instead.
+  * Update to 1.1.3 version of bundler.
+  * Use syck YAML parser to resolve psych errors.

data/Gemfile

@@ -1,19 +1,2 @@
-source "http://rubygems.org"
-
-group :default do
-  gem "scaffolder", ">= 0.4.3"
-  gem "bio",        "~> 1.4"
-  gem "psych"
-end
-
-group :development do
-  gem "bundler",  "~> 1.0"
-  gem "jeweler",  "~> 1.5"
-
-  gem "rspec",                   "~> 2.4"
-  gem "scaffolder-test-helpers",    "0.3.0"
-  gem "cucumber",                "~> 0.9"
-  gem "aruba",                   "~> 0.2"
-
-  gem "yard",     "~> 0.6"
-end
+source :rubygems
+gemspec

data/Rakefile

@@ -8,36 +8,16 @@ rescue Bundler::BundlerError => e
   exit e.status_code
 end
 require 'rake/dsl_definition'
-require 'rake'
-
-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 = "scaffolder-annotation-locator"
-  gem.homepage = "http://next.gs"
-  gem.license = "MIT"
-  gem.summary = %Q{Update locations of gff3 annotations from a scaffolder template}
-  gem.description = %Q{Build a genome scaffold using scaffolder and a set of annotated contigs. This tool updates the locations of the contig annotations using the scaffolder tempalte as a base.}
-  gem.email = "mail@next.gs"
-  gem.authors = ["Michael Barton"]
-end
-Jeweler::RubygemsDotOrgTasks.new
-
 require 'rspec/core'
 require 'rspec/core/rake_task'
+require 'cucumber/rake/task'
+
+Bundler::GemHelper.install_tasks
+
 RSpec::Core::RakeTask.new(:spec) do |spec|
   spec.pattern = FileList['spec/**/*_spec.rb']
 end
 
-RSpec::Core::RakeTask.new(:rcov) do |spec|
-  spec.pattern = 'spec/**/*_spec.rb'
-  spec.rcov = true
-end
-
-require 'cucumber/rake/task'
 Cucumber::Rake::Task.new(:features)
 
 task :default => :spec
-
-require 'yard'
-YARD::Rake::YardocTask.new

data/lib/scaffolder/annotation_locator.rb

@@ -51,6 +51,7 @@ class Scaffolder::AnnotationLocator < DelegateClass(Array)
   end
 
   def scaffold
+    YAML::ENGINE.yamler = 'syck'
     Scaffolder.new(YAML.load(File.read(@scaffold_file)),@sequence_file)
   end
 

data/lib/scaffolder/annotation_locator/version.rb

@@ -0,0 +1,5 @@
+require 'scaffolder/annotation_locator'
+
+class Scaffolder::AnnotationLocator
+  VERSION = '0.1.2'
+end

data/scaffolder-annotation-locator.gemspec

@@ -1,86 +1,34 @@
-# Generated by jeweler
-# DO NOT EDIT THIS FILE DIRECTLY
-# Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), 'lib'))
+
+require "scaffolder/annotation_locator/version"
 
 Gem::Specification.new do |s|
-  s.name = "scaffolder-annotation-locator"
-  s.version = "0.1.1"
+  s.name        = "scaffolder-annotation-locator"
+  s.version     = Scaffolder::AnnotationLocator::VERSION
+  s.platform    = Gem::Platform::RUBY
+  s.authors     = ["Michael Barton"]
+  s.email       = "mail@next.gs"
+  s.homepage    = "http://next.gs"
+  s.licenses    = ["MIT"]
+  s.summary     = "Update locations of gff3 annotations from a scaffolder template"
+  s.description = "Build a genome scaffold using scaffolder and a set of annotated contigs. This tool updates the locations of the contig annotations using the scaffold template as a base."
 
-  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
-  s.authors = ["Michael Barton"]
-  s.date = "2012-01-26"
-  s.description = "Build a genome scaffold using scaffolder and a set of annotated contigs. This tool updates the locations of the contig annotations using the scaffolder tempalte as a base."
-  s.email = "mail@next.gs"
-  s.extra_rdoc_files = [
-    "LICENSE.txt",
-    "README.rdoc"
-  ]
-  s.files = [
-    ".document",
-    "Gemfile",
-    "LICENSE.txt",
-    "README.rdoc",
-    "Rakefile",
-    "VERSION",
-    "features/inserts.feature",
-    "features/multiple-contigs.feature",
-    "features/single-contig.feature",
-    "features/step_definitions/scaffolder-annotation-locator_steps.rb",
-    "features/support/env.rb",
-    "features/unresolved.feature",
-    "lib/scaffolder/annotation_locator.rb",
-    "lib/scaffolder/extensions.rb",
-    "lib/scaffolder/gff_record_helper.rb",
-    "scaffolder-annotation-locator.gemspec",
-    "spec/scaffolder/annotation_locator_spec.rb",
-    "spec/scaffolder/gff_record_helper_spec.rb",
-    "spec/spec_helper.rb",
-    "spec/support/gff_attribute_matcher.rb"
-  ]
-  s.homepage = "http://next.gs"
-  s.licenses = ["MIT"]
-  s.require_paths = ["lib"]
-  s.rubygems_version = "1.8.11"
-  s.summary = "Update locations of gff3 annotations from a scaffolder template"
+  s.rubyforge_project         = "scaffolder-annotation-locator"
+  s.required_rubygems_version = ">= 1.8.0"
 
-  if s.respond_to? :specification_version then
-    s.specification_version = 3
+  s.require_path     = 'lib'
+  s.files            = `git ls-files`.split("\n")
+  s.extra_rdoc_files = %w| LICENSE.txt README.rdoc |
 
-    if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
-      s.add_runtime_dependency(%q<scaffolder>, [">= 0.4.3"])
-      s.add_runtime_dependency(%q<bio>, ["~> 1.4"])
-      s.add_runtime_dependency(%q<psych>, [">= 0"])
-      s.add_development_dependency(%q<bundler>, ["~> 1.0"])
-      s.add_development_dependency(%q<jeweler>, ["~> 1.5"])
-      s.add_development_dependency(%q<rspec>, ["~> 2.4"])
-      s.add_development_dependency(%q<scaffolder-test-helpers>, ["= 0.3.0"])
-      s.add_development_dependency(%q<cucumber>, ["~> 0.9"])
-      s.add_development_dependency(%q<aruba>, ["~> 0.2"])
-      s.add_development_dependency(%q<yard>, ["~> 0.6"])
-    else
-      s.add_dependency(%q<scaffolder>, [">= 0.4.3"])
-      s.add_dependency(%q<bio>, ["~> 1.4"])
-      s.add_dependency(%q<psych>, [">= 0"])
-      s.add_dependency(%q<bundler>, ["~> 1.0"])
-      s.add_dependency(%q<jeweler>, ["~> 1.5"])
-      s.add_dependency(%q<rspec>, ["~> 2.4"])
-      s.add_dependency(%q<scaffolder-test-helpers>, ["= 0.3.0"])
-      s.add_dependency(%q<cucumber>, ["~> 0.9"])
-      s.add_dependency(%q<aruba>, ["~> 0.2"])
-      s.add_dependency(%q<yard>, ["~> 0.6"])
-    end
-  else
-    s.add_dependency(%q<scaffolder>, [">= 0.4.3"])
-    s.add_dependency(%q<bio>, ["~> 1.4"])
-    s.add_dependency(%q<psych>, [">= 0"])
-    s.add_dependency(%q<bundler>, ["~> 1.0"])
-    s.add_dependency(%q<jeweler>, ["~> 1.5"])
-    s.add_dependency(%q<rspec>, ["~> 2.4"])
-    s.add_dependency(%q<scaffolder-test-helpers>, ["= 0.3.0"])
-    s.add_dependency(%q<cucumber>, ["~> 0.9"])
-    s.add_dependency(%q<aruba>, ["~> 0.2"])
-    s.add_dependency(%q<yard>, ["~> 0.6"])
-  end
-end
+  s.add_dependency "scaffolder", ">= 0.4.3"
+  s.add_dependency "bio",        "~> 1.4.0"
 
+  s.add_development_dependency "rake",                    "~> 0.9.0"
+  s.add_development_dependency "bundler",                 "~> 1.1.0"
+  s.add_development_dependency "rspec",                   "~> 2.7.0"
+  s.add_development_dependency "cucumber",                "~> 1.1.4"
+  s.add_development_dependency "aruba",                   "~> 0.4.11"
+  s.add_development_dependency "scaffolder-test-helpers", "~> 0.4.0"
+  s.add_development_dependency "yard",                    "~> 0.6.0"
+end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: scaffolder-annotation-locator
 version: !ruby/object:Gem::Version
-  version: 0.1.1
+  version: 0.1.2
   prerelease: 
 platform: ruby
 authors:
@@ -9,11 +9,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-01-26 00:00:00.000000000 Z
+date: 2012-04-25 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: scaffolder
-  requirement: &70157864359580 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -21,108 +21,142 @@ dependencies:
         version: 0.4.3
   type: :runtime
   prerelease: false
-  version_requirements: *70157864359580
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 0.4.3
 - !ruby/object:Gem::Dependency
   name: bio
-  requirement: &70157864356600 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: '1.4'
+        version: 1.4.0
   type: :runtime
   prerelease: false
-  version_requirements: *70157864356600
-- !ruby/object:Gem::Dependency
-  name: psych
-  requirement: &70157864369780 !ruby/object:Gem::Requirement
+  version_requirements: !ruby/object:Gem::Requirement
     none: false
     requirements:
-    - - ! '>='
+    - - ~>
       - !ruby/object:Gem::Version
-        version: '0'
-  type: :runtime
-  prerelease: false
-  version_requirements: *70157864369780
+        version: 1.4.0
 - !ruby/object:Gem::Dependency
-  name: bundler
-  requirement: &70157864365900 !ruby/object:Gem::Requirement
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: '1.0'
+        version: 0.9.0
   type: :development
   prerelease: false
-  version_requirements: *70157864365900
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.9.0
 - !ruby/object:Gem::Dependency
-  name: jeweler
-  requirement: &70157864379040 !ruby/object:Gem::Requirement
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: '1.5'
+        version: 1.1.0
   type: :development
   prerelease: false
-  version_requirements: *70157864379040
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.1.0
 - !ruby/object:Gem::Dependency
   name: rspec
-  requirement: &70157864375160 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: '2.4'
+        version: 2.7.0
   type: :development
   prerelease: false
-  version_requirements: *70157864375160
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 2.7.0
 - !ruby/object:Gem::Dependency
-  name: scaffolder-test-helpers
-  requirement: &70157864371800 !ruby/object:Gem::Requirement
+  name: cucumber
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
-    - - =
+    - - ~>
       - !ruby/object:Gem::Version
-        version: 0.3.0
+        version: 1.1.4
   type: :development
   prerelease: false
-  version_requirements: *70157864371800
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.1.4
 - !ruby/object:Gem::Dependency
-  name: cucumber
-  requirement: &70157871937940 !ruby/object:Gem::Requirement
+  name: aruba
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: '0.9'
+        version: 0.4.11
   type: :development
   prerelease: false
-  version_requirements: *70157871937940
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.4.11
 - !ruby/object:Gem::Dependency
-  name: aruba
-  requirement: &70157871936900 !ruby/object:Gem::Requirement
+  name: scaffolder-test-helpers
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: '0.2'
+        version: 0.4.0
   type: :development
   prerelease: false
-  version_requirements: *70157871936900
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.4.0
 - !ruby/object:Gem::Dependency
   name: yard
-  requirement: &70157871935380 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: '0.6'
+        version: 0.6.0
   type: :development
   prerelease: false
-  version_requirements: *70157871935380
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.6.0
 description: Build a genome scaffold using scaffolder and a set of annotated contigs.
-  This tool updates the locations of the contig annotations using the scaffolder tempalte
+  This tool updates the locations of the contig annotations using the scaffold template
   as a base.
 email: mail@next.gs
 executables: []
@@ -132,11 +166,12 @@ extra_rdoc_files:
 - README.rdoc
 files:
 - .document
+- .gitignore
+- CHANGELOG.txt
 - Gemfile
 - LICENSE.txt
 - README.rdoc
 - Rakefile
-- VERSION
 - features/inserts.feature
 - features/multiple-contigs.feature
 - features/single-contig.feature
@@ -144,6 +179,7 @@ files:
 - features/support/env.rb
 - features/unresolved.feature
 - lib/scaffolder/annotation_locator.rb
+- lib/scaffolder/annotation_locator/version.rb
 - lib/scaffolder/extensions.rb
 - lib/scaffolder/gff_record_helper.rb
 - scaffolder-annotation-locator.gemspec
@@ -166,16 +202,16 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: -1068640633611636753
+      hash: -762467383921930214
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements:
   - - ! '>='
     - !ruby/object:Gem::Version
-      version: '0'
+      version: 1.8.0
 requirements: []
-rubyforge_project: 
-rubygems_version: 1.8.11
+rubyforge_project: scaffolder-annotation-locator
+rubygems_version: 1.8.23
 signing_key: 
 specification_version: 3
 summary: Update locations of gff3 annotations from a scaffolder template

data/VERSION

@@ -1 +0,0 @@
-0.1.1