pbs_job 0.0.1

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data/.gitignore ADDED
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+ .DS_Store
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+ results.html
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+ pkg
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+ html
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+ coverage
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+ Gemfile.lock
data/Gemfile ADDED
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+ source 'https://rubygems.org'
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+
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+ # Specify your gem's dependencies in pbs_job.gemspec
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+ gemspec
data/LICENSE.txt ADDED
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+ Copyright (c) 2013 Dustin Morrill
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+
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+ MIT License
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+
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+ Permission is hereby granted, free of charge, to any person obtaining
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+ a copy of this software and associated documentation files (the
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+ "Software"), to deal in the Software without restriction, including
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+ without limitation the rights to use, copy, modify, merge, publish,
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+ distribute, sublicense, and/or sell copies of the Software, and to
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+ permit persons to whom the Software is furnished to do so, subject to
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+ the following conditions:
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+
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+ The above copyright notice and this permission notice shall be
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+ included in all copies or substantial portions of the Software.
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+
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+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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+ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
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+ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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+ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
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+ LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
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+ OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
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+ WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
data/README.md ADDED
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+ # PbsJob
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+
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+ TODO: Write a gem description
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+
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+ ## Installation
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+
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+ Add this line to your application's Gemfile:
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+
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+ gem 'pbs_job'
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+
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+ And then execute:
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+
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+ $ bundle
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+
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+ Or install it yourself as:
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+
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+ $ gem install pbs_job
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+
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+ ## Usage
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+
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+ TODO: Write usage instructions here
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+
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+ ## Contributing
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+
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+ 1. Fork it
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+ 2. Create your feature branch (`git checkout -b my-new-feature`)
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+ 3. Commit your changes (`git commit -am 'Add some feature'`)
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+ 4. Push to the branch (`git push origin my-new-feature`)
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+ 5. Create new Pull Request
data/Rakefile ADDED
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+ #!/usr/bin/env rake
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+ require 'bundler'
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+
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+ require 'rake/clean'
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+ require 'rake/testtask'
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+
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+ include Rake::DSL
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+
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+ Bundler::GemHelper.install_tasks
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+
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+ Rake::TestTask.new do |t|
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+ t.libs << "lib" << 'spec/support'
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+ t.test_files = FileList['spec/**/*_spec.rb']
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+ t.verbose = false
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+ t.warning = false # pry-rescue has a lot of warnings
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+ end
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+
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+ task :default => [:test]
data/bin/pbs_job ADDED
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+ #!/usr/bin/env ruby
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+ require "rubygems"
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+ require 'thor'
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+ require 'date'
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+
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+ module PbsJob
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+ class New < Thor::Group
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+ include Thor::Actions
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+
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+ argument :name, :desc => 'Name of the new job.'
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+ argument :email_address, :desc => 'Email to which to send PBS alerts.'
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+
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+ class_option(
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+ :link_results,
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+ {
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+ :desc => 'Directory to which to redirect results',
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+ :default => nil,
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+ :aliases => 'r'
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+ }
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+ )
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+ class_option(
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+ :script,
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+ {
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+ :desc => 'Type of script to make the task script',
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+ :default => '<script type>',
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+ :aliases => 's'
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+ }
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+ )
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+
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+ def self.source_root
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+ File.expand_path('../../', __FILE__)
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+ end
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+
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+ def gen_root
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+ empty_directory full_name
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+ end
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+
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+ def qsub_script
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+ create_file_from_template 'job.qsub'
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+ end
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+
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+ def pbs_script
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+ create_file_from_template 'job.pbs'
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+ end
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+
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+ def task
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+ create_file_from_template 'task'
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+ end
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+
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+ def results
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+ results_path = File.join full_name, 'results'
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+ if options[:link_results]
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+ create_link(results_path, options[:link_results])
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+ else
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+ empty_directory results_path
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+ end
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+ end
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+
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+ def streams
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+ empty_directory streams_path
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+ end
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+
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+ private
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+
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+ def create_file_from_template(file_name)
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+ template(
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+ "templates/#{file_name}.tt",
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+ "#{full_name}/#{file_name}"
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+ )
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+ end
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+
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+ # @returns [String] Name with date appended
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+ def full_name
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+ @full_name ||= -> do
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+ today = Date.today
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+ month = Date::MONTHNAMES[today.month].downcase
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+ "#{name}.#{month}#{today.day}_#{today.year}"
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+ end.call
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+ end
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+
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+ def abs_job_root
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+ @abs_job_root ||= File.expand_path(full_name)
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+ end
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+
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+ def streams_path
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+ @streams_path ||= File.join full_name, 'streams'
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+ end
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+
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+ def abs_stream_prefix
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+ @abs_stream_prefix ||= File.join abs_job_root, streams_path, full_name
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+ end
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+ end
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+
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+ class PbsJob < Thor
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+ map 'n' => :new
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+
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+ register(
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+ New,
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+ 'new',
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+ 'new NAME EMAIL_ADDRESS [OPTIONS]',
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+ "Creates a new PBS job with the name NAME and arranges for PBS alerts to be sent to EMAIL_ADDRESS, customized by OPTIONS"
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+ )
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+ tasks["new"].options = New.class_options
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+ end
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+ end
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+
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+ PbsJob::PbsJob.start(ARGV)
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+ module PbsJob
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+ VERSION = "0.0.1"
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+ end
data/lib/pbs_job.rb ADDED
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+ require_relative "pbs_job/version"
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+
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+ module PbsJob
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+ end
data/pbs_job.gemspec ADDED
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+ # coding: utf-8
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+ lib = File.expand_path('../lib', __FILE__)
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+ $LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
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+ require 'pbs_job/version'
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+
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+ Gem::Specification.new do |spec|
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+ spec.name = "pbs_job"
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+ spec.version = PbsJob::VERSION
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+ spec.authors = ["Dustin Morrill"]
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+ spec.email = ["morrill@ualberta.ca"]
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+ spec.description = %q{PBS/Torque job generator}
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+ spec.summary = %q{Creates a directory and file structure for a well organized PBS/Torque job.}
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+ spec.homepage = "https://github.com/dmorrill10/pbs_job"
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+ spec.license = "MIT"
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+
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+ spec.files = `git ls-files`.split($/)
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+ spec.executables = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
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+ spec.test_files = spec.files.grep(%r{^(test|spec|features)/})
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+ spec.require_paths = ["lib"]
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+
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+ spec.add_dependency 'thor', '~> 0.18.1'
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+
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+ spec.add_development_dependency "bundler", '~> 1.3.5'
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+ spec.add_development_dependency 'bahia', '~> 0.7.2'
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+ spec.add_development_dependency 'rake', '~> 10.1.0'
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+ spec.add_development_dependency 'minitest', '~> 5.0.6'
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+ spec.add_development_dependency 'awesome_print', '~> 1.1.0'
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+ spec.add_development_dependency 'simplecov', '~> 0.7.1'
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+ end
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+ require_relative 'support/spec_helper'
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+
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+ require "date"
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+ require 'tmpdir'
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+
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+ describe 'pbs_job' do
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+
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+ HELP = <<-HELP
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+ Commands:
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+ pbs_job help [COMMAND] # Describe available commands or ...
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+ pbs_job new NAME EMAIL_ADDRESS [OPTIONS] # Creates a new PBS job with the ...
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+
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+ HELP
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+ NAME = 'test_job'
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+ EMAIL_ADDRESS = 'email@address'
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+ TODAY = Date.today
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+ MONTH = Date::MONTHNAMES[TODAY.month].downcase
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+ JOB_ROOT = "#{NAME}.#{MONTH}#{TODAY.day}_#{TODAY.year}"
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+ QSUB_SCRIPT = "#{JOB_ROOT}/job.qsub"
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+ PBS_SCRIPT = "#{JOB_ROOT}/job.pbs"
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+ TASK = "#{JOB_ROOT}/task"
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+ RESULTS = "#{JOB_ROOT}/results"
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+ STREAMS = "#{JOB_ROOT}/streams"
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+
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+ it 'prints usage and options without arguments' do
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+ pbs_job
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+ stdout.must_equal HELP
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+ end
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+ it 'prints help' do
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+ pbs_job 'help'
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+ stdout.must_equal HELP
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+ end
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+
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+ describe 'new' do
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+ it 'prints help' do
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+ pbs_job 'help new'
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+ stdout.must_equal <<-GEN_HELP
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+ Usage:
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+ pbs_job new NAME EMAIL_ADDRESS [OPTIONS]
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+
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+ Options:
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+ r, [--link-results=LINK_RESULTS] # Directory to which to redirect results
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+ s, [--script=SCRIPT] # Type of script to make the task script
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+ # Default: <script type>
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+
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+ Creates a new PBS job with the name NAME and arranges for PBS alerts to be sent to EMAIL_ADDRESS, customized by OPTIONS
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+ GEN_HELP
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+ end
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+ it 'requires name argument' do
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+ pbs_job 'new'
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+ stderr.must_equal "No value provided for required arguments 'name', 'email_address'\n"
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+ end
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+ it 'requires an email argument' do
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+ pbs_job "new #{NAME}"
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+ stderr.must_equal "No value provided for required arguments 'email_address'\n"
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+ end
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+ it 'creates a file structure for job components' do
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+ in_tmp_dir do
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+ pbs_job "new #{NAME} #{EMAIL_ADDRESS}"
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+ stdout.must_equal <<-DIR
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+ \e[1m\e[32m create\e[0m #{JOB_ROOT}
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+ \e[1m\e[32m create\e[0m #{QSUB_SCRIPT}
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+ \e[1m\e[32m create\e[0m #{PBS_SCRIPT}
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+ \e[1m\e[32m create\e[0m #{TASK}
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+ \e[1m\e[32m create\e[0m #{RESULTS}
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+ \e[1m\e[32m create\e[0m #{STREAMS}
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+ DIR
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+ File.directory?(JOB_ROOT).must_equal true
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+ File.file?(QSUB_SCRIPT).must_equal true
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+ File.file?(PBS_SCRIPT).must_equal true
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+ File.file?(TASK).must_equal true
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+ File.directory?(RESULTS).must_equal true
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+ File.directory?(STREAMS).must_equal true
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+ end
75
+ end
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+ end
77
+ describe 'script type option' do
78
+ it '--script allows specification of the script type of task' do
79
+ in_tmp_dir do
80
+ pbs_job "new #{NAME} #{EMAIL_ADDRESS} --script=bash"
81
+ stdout.must_equal <<-DIR
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+ \e[1m\e[32m create\e[0m #{JOB_ROOT}
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+ \e[1m\e[32m create\e[0m #{QSUB_SCRIPT}
84
+ \e[1m\e[32m create\e[0m #{PBS_SCRIPT}
85
+ \e[1m\e[32m create\e[0m #{TASK}
86
+ \e[1m\e[32m create\e[0m #{RESULTS}
87
+ \e[1m\e[32m create\e[0m #{STREAMS}
88
+ DIR
89
+ File.directory?(JOB_ROOT).must_equal true
90
+ File.file?(QSUB_SCRIPT).must_equal true
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+ File.file?(PBS_SCRIPT).must_equal true
92
+ File.file?(TASK).must_equal true
93
+ File.directory?(RESULTS).must_equal true
94
+ File.directory?(STREAMS).must_equal true
95
+ end
96
+ end
97
+ end
98
+ describe 'results link option' do
99
+ it '--link-results allows redirection of results' do
100
+ linked_results = '/scratch/results'
101
+ in_tmp_dir do
102
+ pbs_job "new #{NAME} #{EMAIL_ADDRESS} --link-results=#{linked_results}"
103
+ stdout.must_equal <<-DIR
104
+ \e[1m\e[32m create\e[0m #{JOB_ROOT}
105
+ \e[1m\e[32m create\e[0m #{QSUB_SCRIPT}
106
+ \e[1m\e[32m create\e[0m #{PBS_SCRIPT}
107
+ \e[1m\e[32m create\e[0m #{TASK}
108
+ \e[1m\e[32m create\e[0m #{RESULTS}
109
+ \e[1m\e[32m create\e[0m #{STREAMS}
110
+ DIR
111
+ File.directory?(JOB_ROOT).must_equal true
112
+ File.file?(QSUB_SCRIPT).must_equal true
113
+ File.file?(PBS_SCRIPT).must_equal true
114
+ File.file?(TASK).must_equal true
115
+ File.symlink?(RESULTS).must_equal true
116
+ File.readlink(RESULTS).must_equal linked_results
117
+ File.directory?(STREAMS).must_equal true
118
+ end
119
+ end
120
+ end
121
+
122
+ def in_tmp_dir
123
+ Dir.mktmpdir do |dir|
124
+ Dir.chdir dir
125
+ yield dir if block_given?
126
+ end
127
+ end
128
+ end
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+ require 'simplecov'
2
+ SimpleCov.start
3
+
4
+ require 'minitest/autorun'
5
+ require 'minitest/spec'
6
+
7
+ begin
8
+ require 'awesome_print'
9
+ module Minitest::Assertions
10
+ def mu_pp(obj)
11
+ obj.awesome_inspect
12
+ end
13
+ end
14
+ rescue LoadError
15
+ end
16
+
17
+ require 'bahia'
18
+
19
+ class MiniTest::Spec
20
+ include Bahia
21
+ end
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+ #!/usr/bin/env bash
2
+ #PBS -m abe -M <%= email_address %>
3
+ cd <%= abs_job_root %>
4
+ ./task > "<%= abs_stream_prefix %>.out" 2> "<%= abs_stream_prefix %>.err"
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+ #!/usr/bin/env bash
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+ # This script runs job.pbs with qsub. Customize as necessary
3
+ qsub job.pbs -N "<%= full_name %>" -e "<%= abs_stream_prefix %>.e" -o "<%= abs_stream_prefix %>.o"
data/templates/task.tt ADDED
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+ #!/usr/bin/env <%= options[:script] %>
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+
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+ # This is the meat of the job.
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+ # Please place the task you'd like your job to run.
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+ # For example, this is where you would put
6
+ # experiment logic.
metadata ADDED
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+ --- !ruby/object:Gem::Specification
2
+ name: pbs_job
3
+ version: !ruby/object:Gem::Version
4
+ version: 0.0.1
5
+ platform: ruby
6
+ authors:
7
+ - Dustin Morrill
8
+ autorequire:
9
+ bindir: bin
10
+ cert_chain: []
11
+ date: 2013-07-25 00:00:00.000000000 Z
12
+ dependencies:
13
+ - !ruby/object:Gem::Dependency
14
+ name: thor
15
+ requirement: !ruby/object:Gem::Requirement
16
+ requirements:
17
+ - - ~>
18
+ - !ruby/object:Gem::Version
19
+ version: 0.18.1
20
+ type: :runtime
21
+ prerelease: false
22
+ version_requirements: !ruby/object:Gem::Requirement
23
+ requirements:
24
+ - - ~>
25
+ - !ruby/object:Gem::Version
26
+ version: 0.18.1
27
+ - !ruby/object:Gem::Dependency
28
+ name: bundler
29
+ requirement: !ruby/object:Gem::Requirement
30
+ requirements:
31
+ - - ~>
32
+ - !ruby/object:Gem::Version
33
+ version: 1.3.5
34
+ type: :development
35
+ prerelease: false
36
+ version_requirements: !ruby/object:Gem::Requirement
37
+ requirements:
38
+ - - ~>
39
+ - !ruby/object:Gem::Version
40
+ version: 1.3.5
41
+ - !ruby/object:Gem::Dependency
42
+ name: bahia
43
+ requirement: !ruby/object:Gem::Requirement
44
+ requirements:
45
+ - - ~>
46
+ - !ruby/object:Gem::Version
47
+ version: 0.7.2
48
+ type: :development
49
+ prerelease: false
50
+ version_requirements: !ruby/object:Gem::Requirement
51
+ requirements:
52
+ - - ~>
53
+ - !ruby/object:Gem::Version
54
+ version: 0.7.2
55
+ - !ruby/object:Gem::Dependency
56
+ name: rake
57
+ requirement: !ruby/object:Gem::Requirement
58
+ requirements:
59
+ - - ~>
60
+ - !ruby/object:Gem::Version
61
+ version: 10.1.0
62
+ type: :development
63
+ prerelease: false
64
+ version_requirements: !ruby/object:Gem::Requirement
65
+ requirements:
66
+ - - ~>
67
+ - !ruby/object:Gem::Version
68
+ version: 10.1.0
69
+ - !ruby/object:Gem::Dependency
70
+ name: minitest
71
+ requirement: !ruby/object:Gem::Requirement
72
+ requirements:
73
+ - - ~>
74
+ - !ruby/object:Gem::Version
75
+ version: 5.0.6
76
+ type: :development
77
+ prerelease: false
78
+ version_requirements: !ruby/object:Gem::Requirement
79
+ requirements:
80
+ - - ~>
81
+ - !ruby/object:Gem::Version
82
+ version: 5.0.6
83
+ - !ruby/object:Gem::Dependency
84
+ name: awesome_print
85
+ requirement: !ruby/object:Gem::Requirement
86
+ requirements:
87
+ - - ~>
88
+ - !ruby/object:Gem::Version
89
+ version: 1.1.0
90
+ type: :development
91
+ prerelease: false
92
+ version_requirements: !ruby/object:Gem::Requirement
93
+ requirements:
94
+ - - ~>
95
+ - !ruby/object:Gem::Version
96
+ version: 1.1.0
97
+ - !ruby/object:Gem::Dependency
98
+ name: simplecov
99
+ requirement: !ruby/object:Gem::Requirement
100
+ requirements:
101
+ - - ~>
102
+ - !ruby/object:Gem::Version
103
+ version: 0.7.1
104
+ type: :development
105
+ prerelease: false
106
+ version_requirements: !ruby/object:Gem::Requirement
107
+ requirements:
108
+ - - ~>
109
+ - !ruby/object:Gem::Version
110
+ version: 0.7.1
111
+ description: PBS/Torque job generator
112
+ email:
113
+ - morrill@ualberta.ca
114
+ executables:
115
+ - pbs_job
116
+ extensions: []
117
+ extra_rdoc_files: []
118
+ files:
119
+ - .gitignore
120
+ - Gemfile
121
+ - LICENSE.txt
122
+ - README.md
123
+ - Rakefile
124
+ - bin/pbs_job
125
+ - lib/pbs_job.rb
126
+ - lib/pbs_job/version.rb
127
+ - pbs_job.gemspec
128
+ - spec/pbs_job_spec.rb
129
+ - spec/support/spec_helper.rb
130
+ - templates/job.pbs.tt
131
+ - templates/job.qsub.tt
132
+ - templates/task.tt
133
+ homepage: https://github.com/dmorrill10/pbs_job
134
+ licenses:
135
+ - MIT
136
+ metadata: {}
137
+ post_install_message:
138
+ rdoc_options: []
139
+ require_paths:
140
+ - lib
141
+ required_ruby_version: !ruby/object:Gem::Requirement
142
+ requirements:
143
+ - - '>='
144
+ - !ruby/object:Gem::Version
145
+ version: '0'
146
+ required_rubygems_version: !ruby/object:Gem::Requirement
147
+ requirements:
148
+ - - '>='
149
+ - !ruby/object:Gem::Version
150
+ version: '0'
151
+ requirements: []
152
+ rubyforge_project:
153
+ rubygems_version: 2.0.3
154
+ signing_key:
155
+ specification_version: 4
156
+ summary: Creates a directory and file structure for a well organized PBS/Torque job.
157
+ test_files:
158
+ - spec/pbs_job_spec.rb
159
+ - spec/support/spec_helper.rb
160
+ has_rdoc: