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base fork: michaelbarton/scaffolder-annotation-locator
base: 0fb5fb6430
...
head fork: michaelbarton/scaffolder-annotation-locator
compare: 8c9278912e
Checking mergeability… Don't worry, you can still create the pull request.
  • 5 commits
  • 6 files changed
  • 0 commit comments
  • 1 contributor
View
5 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.
View
21 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
View
28 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
View
1  lib/scaffolder/annotation_locator.rb
@@ -51,6 +51,7 @@ def initialize(scaffold_file,sequence_file,gff_file)
end
def scaffold
+ YAML::ENGINE.yamler = 'syck'
Scaffolder.new(YAML.load(File.read(@scaffold_file)),@sequence_file)
end
View
3  lib/scaffolder/annotation_locator/version.rb
@@ -0,0 +1,3 @@
+require 'scaffolder/annotation_locator'
+
+Scaffolder::AnnotationLocator::VERSION = '0.1.2'
View
104 scaffolder-annotation-locator.gemspec
@@ -1,86 +1,32 @@
-# Generated by jeweler
-# DO NOT EDIT THIS FILE DIRECTLY
-# Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
# -*- encoding: utf-8 -*-
+require File.expand_path("../lib/scaffolder/annotation_locator/version", __FILE__)
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 = "2012-01-24"
- 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

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