scaffolder-annotation-locator 0.1.4 → 0.2.0

checksums.yaml

@@ -0,0 +1,15 @@
+---
+!binary "U0hBMQ==":
+  metadata.gz: !binary |-
+    MWMxMDk4YTQzZDFmYTY1OGNmMmRjYjg4ZTA0NGM1MDgxNzM0Yjg0ZA==
+  data.tar.gz: !binary |-
+    Yjc5Y2JjZTJlZjY0ZWQ0YTU3M2YwMGExYjEwYmQ4ZmM0N2U2ZDExOQ==
+!binary "U0hBNTEy":
+  metadata.gz: !binary |-
+    NjEzMDcwYjgzZjFiOGM3YTlmOTI0ZWE2ODQ4OWU0NjU0NmMxNDBjNTk3NTg0
+    MjYwYmRmMTg4YzhiYjY5ZWI1NDAzMTlmOTY0ZjI5YTk1MDhkOTU4YjEwM2E3
+    ZjllOWQ4MTU1NDk1MWE0MDIyMmNmNGIyN2E1ZWI5YmI3Yzc1NWI=
+  data.tar.gz: !binary |-
+    ZTlhM2M2NGRkMTU5YjBmYjY3OGMxY2NkZTJlYmEwZjViMjA5NmJkNzVkOTVj
+    ZjgwYWEyZjU4OGMyZTQ0OTZlYjgxYmQxY2JiYTdlNGY2ZjczNzMzMWY1MTVh
+    YjY2YTFlNjBjYTc1ZmRjYzUwNWI4Zjk5NmEzYTQyOWQ4NWM4OTM=

data/.travis.yml

@@ -1,4 +1,6 @@
 language: ruby
 rvm:
   - 1.8.7
+  - 1.9.2
   - 1.9.3
+  - 2.0.0

data/Gemfile

@@ -1,2 +1,2 @@
-source :rubygems
+source 'https://rubygems.org'
 gemspec

data/Rakefile

@@ -1,14 +1,4 @@
-require 'rubygems'
-require 'bundler'
-begin
-  Bundler.setup(:default, :development)
-rescue Bundler::BundlerError => e
-  $stderr.puts e.message
-  $stderr.puts "Run `bundle install` to install missing gems"
-  exit e.status_code
-end
-require 'rake/dsl_definition'
-require 'rspec/core'
+require "bundler/gem_tasks"
 require 'rspec/core/rake_task'
 require 'cucumber/rake/task'
 

data/VERSION

@@ -1 +1 @@
- 0.1.4
+ 0.2.0

data/lib/scaffolder/annotation_locator.rb

@@ -1,6 +1,7 @@
 require 'delegate'
 require 'scaffolder'
 require 'bio'
+require 'yaml'
 
 require 'scaffolder/extensions'
 

data/scaffolder-annotation-locator.gemspec

@@ -19,14 +19,14 @@ Gem::Specification.new do |s|
   s.files            = `git ls-files`.split("\n")
   s.extra_rdoc_files = %w| LICENSE.txt README.rdoc |
 
-  s.add_dependency "scaffolder", ">= 0.4.3"
+  s.add_dependency "scaffolder", "~> 0.5.0"
   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 "rake",                    "~> 10.1.0"
+  s.add_development_dependency "bundler",                 "~> 1.3.0"
+  s.add_development_dependency "rspec",                   "~> 2.14.0"
+  s.add_development_dependency "cucumber",                "~> 1.3.0"
+  s.add_development_dependency "aruba",                   "~> 0.5.0"
   s.add_development_dependency "scaffolder-test-helpers", "~> 0.4.0"
-  s.add_development_dependency "yard",                    "~> 0.6.0"
+  s.add_development_dependency "yard",                    "~> 0.8.0"
 end

data/spec/scaffolder/annotation_locator_spec.rb

@@ -3,9 +3,14 @@ require File.expand_path(File.join(File.dirname(__FILE__), '..', 'spec_helper'))
 describe Scaffolder::AnnotationLocator do
 
   def relocate(scaffold,records)
+
+    GC.disable
     @scaffold_file, @sequence_file = generate_scaffold_files(scaffold)
-    described_class.new(@scaffold_file.path, @sequence_file.path,
+    c = described_class.new(@scaffold_file.path, @sequence_file.path,
                         generate_gff3_file(records).path)
+
+    GC.enable
+    c
   end
 
   before do

metadata

@@ -1,36 +1,32 @@
 --- !ruby/object:Gem::Specification
 name: scaffolder-annotation-locator
 version: !ruby/object:Gem::Version
-  version: 0.1.4
-  prerelease: 
+  version: 0.2.0
 platform: ruby
 authors:
 - Michael Barton
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-05-31 00:00:00.000000000 Z
+date: 2013-08-13 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: scaffolder
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ~>
       - !ruby/object:Gem::Version
-        version: 0.4.3
+        version: 0.5.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ~>
       - !ruby/object:Gem::Version
-        version: 0.4.3
+        version: 0.5.0
 - !ruby/object:Gem::Dependency
   name: bio
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -38,7 +34,6 @@ dependencies:
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -46,87 +41,76 @@ dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 0.9.0
+        version: 10.1.0
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 0.9.0
+        version: 10.1.0
 - !ruby/object:Gem::Dependency
   name: bundler
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 1.1.0
+        version: 1.3.0
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 1.1.0
+        version: 1.3.0
 - !ruby/object:Gem::Dependency
   name: rspec
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 2.7.0
+        version: 2.14.0
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 2.7.0
+        version: 2.14.0
 - !ruby/object:Gem::Dependency
   name: cucumber
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 1.1.4
+        version: 1.3.0
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 1.1.4
+        version: 1.3.0
 - !ruby/object:Gem::Dependency
   name: aruba
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 0.4.11
+        version: 0.5.0
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 0.4.11
+        version: 0.5.0
 - !ruby/object:Gem::Dependency
   name: scaffolder-test-helpers
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -134,7 +118,6 @@ dependencies:
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -142,19 +125,17 @@ dependencies:
 - !ruby/object:Gem::Dependency
   name: yard
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 0.6.0
+        version: 0.8.0
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 0.6.0
+        version: 0.8.0
 description: Build a genome scaffold using scaffolder and a set of annotated contigs.
   This tool updates the locations of the contig annotations using the scaffold template
   as a base.
@@ -191,29 +172,26 @@ files:
 homepage: http://next.gs
 licenses:
 - MIT
+metadata: {}
 post_install_message: 
 rdoc_options: []
 require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
   - - ! '>='
     - !ruby/object:Gem::Version
       version: '0'
-      segments:
-      - 0
-      hash: 3264369434890404542
 required_rubygems_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
   - - ! '>='
     - !ruby/object:Gem::Version
       version: 1.8.0
 requirements: []
 rubyforge_project: scaffolder-annotation-locator
-rubygems_version: 1.8.23
+rubygems_version: 2.0.3
 signing_key: 
-specification_version: 3
+specification_version: 4
 summary: Update locations of gff3 annotations from a scaffolder template
 test_files: []
+has_rdoc: