pbs_job 0.0.1

checksums.yaml

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+---
+SHA1:
+  metadata.gz: fc1d00b54a1f3831231d2298367a8d6c04146b27
+  data.tar.gz: d3d52813019b0a936c1cbb679f93db234ffb087a
+SHA512:
+  metadata.gz: b57061cfd8bc858dce808277bbfe3353b663fd72f4a29f572ce8a01fa7aaa1ae4b99a47713a3b6090d03106aa48d39699b652bd1d10ebbd73649d734a893c8e9
+  data.tar.gz: d3ba18b5ae94087a58b85210d55923e7467c89814a7378e098ffad66f39f237c69a6c27f3f9581675afc6cfbfc20f8e2ba5f511366321006996e0194831772ec

data/.gitignore

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+.DS_Store
+results.html
+pkg
+html
+coverage
+Gemfile.lock

data/Gemfile

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+source 'https://rubygems.org'
+
+# Specify your gem's dependencies in pbs_job.gemspec
+gemspec

data/LICENSE.txt

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+Copyright (c) 2013 Dustin Morrill
+
+MIT License
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/README.md

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+# PbsJob 
+
+TODO: Write a gem description
+
+## Installation
+
+Add this line to your application's Gemfile:
+
+    gem 'pbs_job'
+
+And then execute:
+
+    $ bundle
+
+Or install it yourself as:
+
+    $ gem install pbs_job
+
+## Usage
+
+TODO: Write usage instructions here
+
+## Contributing
+
+1. Fork it
+2. Create your feature branch (`git checkout -b my-new-feature`)
+3. Commit your changes (`git commit -am 'Add some feature'`)
+4. Push to the branch (`git push origin my-new-feature`)
+5. Create new Pull Request

data/Rakefile

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+#!/usr/bin/env rake
+require 'bundler'
+
+require 'rake/clean'
+require 'rake/testtask'
+
+include Rake::DSL
+
+Bundler::GemHelper.install_tasks
+
+Rake::TestTask.new do |t|
+  t.libs << "lib" << 'spec/support'
+  t.test_files = FileList['spec/**/*_spec.rb']
+  t.verbose = false
+  t.warning = false # pry-rescue has a lot of warnings
+end
+
+task :default => [:test]

data/bin/pbs_job

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+#!/usr/bin/env ruby
+require "rubygems"
+require 'thor'
+require 'date'
+
+module PbsJob
+  class New < Thor::Group
+    include Thor::Actions
+
+    argument :name, :desc => 'Name of the new job.'
+    argument :email_address, :desc => 'Email to which to send PBS alerts.'
+
+    class_option(
+      :link_results,
+      {
+        :desc => 'Directory to which to redirect results',
+        :default => nil,
+        :aliases => 'r'
+      }
+    )
+    class_option(
+      :script,
+      {
+        :desc => 'Type of script to make the task script',
+        :default => '<script type>',
+        :aliases => 's'
+      }
+    )
+
+    def self.source_root
+      File.expand_path('../../', __FILE__)
+    end
+
+    def gen_root
+      empty_directory full_name
+    end
+
+    def qsub_script
+      create_file_from_template 'job.qsub'
+    end
+
+    def pbs_script
+      create_file_from_template 'job.pbs'
+    end
+
+    def task
+      create_file_from_template 'task'
+    end
+
+    def results
+      results_path = File.join full_name, 'results'
+      if options[:link_results]
+        create_link(results_path, options[:link_results])
+      else
+        empty_directory results_path
+      end
+    end
+
+    def streams
+      empty_directory streams_path
+    end
+
+    private
+
+    def create_file_from_template(file_name)
+      template(
+        "templates/#{file_name}.tt",
+        "#{full_name}/#{file_name}"
+      )
+    end
+
+    # @returns [String] Name with date appended
+    def full_name
+      @full_name ||= -> do
+        today = Date.today
+        month = Date::MONTHNAMES[today.month].downcase
+        "#{name}.#{month}#{today.day}_#{today.year}"
+      end.call
+    end
+
+    def abs_job_root
+      @abs_job_root ||= File.expand_path(full_name)
+    end
+
+    def streams_path
+      @streams_path ||= File.join full_name, 'streams'
+    end
+
+    def abs_stream_prefix
+      @abs_stream_prefix ||= File.join abs_job_root, streams_path, full_name
+    end
+  end
+
+  class PbsJob < Thor
+    map 'n' => :new
+
+    register(
+      New,
+      'new',
+      'new NAME EMAIL_ADDRESS [OPTIONS]',
+      "Creates a new PBS job with the name NAME and arranges for PBS alerts to be sent to EMAIL_ADDRESS, customized by OPTIONS"
+    )
+    tasks["new"].options = New.class_options
+  end
+end
+
+PbsJob::PbsJob.start(ARGV)

data/lib/pbs_job/version.rb

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+module PbsJob 
+  VERSION = "0.0.1"
+end

data/lib/pbs_job.rb

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+require_relative "pbs_job/version"
+
+module PbsJob 
+end

data/pbs_job.gemspec

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+# coding: utf-8
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'pbs_job/version'
+
+Gem::Specification.new do |spec|
+  spec.name          = "pbs_job"
+  spec.version       = PbsJob::VERSION
+  spec.authors       = ["Dustin Morrill"]
+  spec.email         = ["morrill@ualberta.ca"]
+  spec.description   = %q{PBS/Torque job generator}
+  spec.summary       = %q{Creates a directory and file structure for a well organized PBS/Torque job.}
+  spec.homepage      = "https://github.com/dmorrill10/pbs_job"
+  spec.license       = "MIT"
+
+  spec.files         = `git ls-files`.split($/)
+  spec.executables   = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
+  spec.test_files    = spec.files.grep(%r{^(test|spec|features)/})
+  spec.require_paths = ["lib"]
+
+  spec.add_dependency 'thor', '~> 0.18.1'
+
+  spec.add_development_dependency "bundler", '~> 1.3.5'
+  spec.add_development_dependency 'bahia', '~> 0.7.2'
+  spec.add_development_dependency 'rake', '~> 10.1.0'
+  spec.add_development_dependency 'minitest', '~> 5.0.6'
+  spec.add_development_dependency 'awesome_print', '~> 1.1.0'
+  spec.add_development_dependency 'simplecov', '~> 0.7.1'
+end

data/spec/pbs_job_spec.rb

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+require_relative 'support/spec_helper'
+
+require "date"
+require 'tmpdir'
+
+describe 'pbs_job' do
+
+  HELP = <<-HELP
+Commands:
+  pbs_job help [COMMAND]                    # Describe available commands or ...
+  pbs_job new NAME EMAIL_ADDRESS [OPTIONS]  # Creates a new PBS job with the ...
+
+HELP
+  NAME = 'test_job'
+  EMAIL_ADDRESS = 'email@address'
+  TODAY = Date.today
+  MONTH = Date::MONTHNAMES[TODAY.month].downcase
+  JOB_ROOT = "#{NAME}.#{MONTH}#{TODAY.day}_#{TODAY.year}"
+  QSUB_SCRIPT = "#{JOB_ROOT}/job.qsub"
+  PBS_SCRIPT = "#{JOB_ROOT}/job.pbs"
+  TASK = "#{JOB_ROOT}/task"
+  RESULTS = "#{JOB_ROOT}/results"
+  STREAMS = "#{JOB_ROOT}/streams"
+
+  it 'prints usage and options without arguments' do
+    pbs_job
+    stdout.must_equal HELP
+  end
+  it 'prints help' do
+    pbs_job 'help'
+    stdout.must_equal HELP
+  end
+
+  describe 'new' do
+    it 'prints help' do
+      pbs_job 'help new'
+      stdout.must_equal <<-GEN_HELP
+Usage:
+  pbs_job new NAME EMAIL_ADDRESS [OPTIONS]
+
+Options:
+  r, [--link-results=LINK_RESULTS]  # Directory to which to redirect results
+  s, [--script=SCRIPT]              # Type of script to make the task script
+                                    # Default: <script type>
+
+Creates a new PBS job with the name NAME and arranges for PBS alerts to be sent to EMAIL_ADDRESS, customized by OPTIONS
+GEN_HELP
+    end
+    it 'requires name argument' do
+      pbs_job 'new'
+      stderr.must_equal "No value provided for required arguments 'name', 'email_address'\n"
+    end
+    it 'requires an email argument' do
+      pbs_job "new #{NAME}"
+      stderr.must_equal "No value provided for required arguments 'email_address'\n"
+    end
+    it 'creates a file structure for job components' do
+      in_tmp_dir do
+        pbs_job "new #{NAME} #{EMAIL_ADDRESS}"
+        stdout.must_equal <<-DIR
+\e[1m\e[32m      create\e[0m  #{JOB_ROOT}
+\e[1m\e[32m      create\e[0m  #{QSUB_SCRIPT}
+\e[1m\e[32m      create\e[0m  #{PBS_SCRIPT}
+\e[1m\e[32m      create\e[0m  #{TASK}
+\e[1m\e[32m      create\e[0m  #{RESULTS}
+\e[1m\e[32m      create\e[0m  #{STREAMS}
+DIR
+        File.directory?(JOB_ROOT).must_equal true
+        File.file?(QSUB_SCRIPT).must_equal true
+        File.file?(PBS_SCRIPT).must_equal true
+        File.file?(TASK).must_equal true
+        File.directory?(RESULTS).must_equal true
+        File.directory?(STREAMS).must_equal true
+      end
+    end
+  end
+  describe 'script type option' do
+    it '--script allows specification of the script type of task' do
+      in_tmp_dir do
+        pbs_job "new #{NAME} #{EMAIL_ADDRESS} --script=bash"
+        stdout.must_equal <<-DIR
+\e[1m\e[32m      create\e[0m  #{JOB_ROOT}
+\e[1m\e[32m      create\e[0m  #{QSUB_SCRIPT}
+\e[1m\e[32m      create\e[0m  #{PBS_SCRIPT}
+\e[1m\e[32m      create\e[0m  #{TASK}
+\e[1m\e[32m      create\e[0m  #{RESULTS}
+\e[1m\e[32m      create\e[0m  #{STREAMS}
+DIR
+        File.directory?(JOB_ROOT).must_equal true
+        File.file?(QSUB_SCRIPT).must_equal true
+        File.file?(PBS_SCRIPT).must_equal true
+        File.file?(TASK).must_equal true
+        File.directory?(RESULTS).must_equal true
+        File.directory?(STREAMS).must_equal true
+      end
+    end
+  end
+  describe 'results link option' do
+    it '--link-results allows redirection of results' do
+      linked_results = '/scratch/results'
+      in_tmp_dir do
+        pbs_job "new #{NAME} #{EMAIL_ADDRESS} --link-results=#{linked_results}"
+        stdout.must_equal <<-DIR
+\e[1m\e[32m      create\e[0m  #{JOB_ROOT}
+\e[1m\e[32m      create\e[0m  #{QSUB_SCRIPT}
+\e[1m\e[32m      create\e[0m  #{PBS_SCRIPT}
+\e[1m\e[32m      create\e[0m  #{TASK}
+\e[1m\e[32m      create\e[0m  #{RESULTS}
+\e[1m\e[32m      create\e[0m  #{STREAMS}
+DIR
+        File.directory?(JOB_ROOT).must_equal true
+        File.file?(QSUB_SCRIPT).must_equal true
+        File.file?(PBS_SCRIPT).must_equal true
+        File.file?(TASK).must_equal true
+        File.symlink?(RESULTS).must_equal true
+        File.readlink(RESULTS).must_equal linked_results
+        File.directory?(STREAMS).must_equal true
+      end
+    end
+  end
+
+  def in_tmp_dir
+    Dir.mktmpdir do |dir|
+      Dir.chdir dir
+      yield dir if block_given?
+    end
+  end
+end

data/spec/support/spec_helper.rb

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+require 'simplecov'
+SimpleCov.start
+
+require 'minitest/autorun'
+require 'minitest/spec'
+
+begin
+  require 'awesome_print'
+  module Minitest::Assertions
+    def mu_pp(obj)
+      obj.awesome_inspect
+    end
+  end
+rescue LoadError
+end
+
+require 'bahia'
+
+class MiniTest::Spec
+  include Bahia
+end

data/templates/job.pbs.tt

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+#!/usr/bin/env bash
+#PBS -m abe -M <%= email_address %>
+cd <%= abs_job_root %>
+./task > "<%= abs_stream_prefix %>.out" 2> "<%= abs_stream_prefix %>.err"

data/templates/job.qsub.tt

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+#!/usr/bin/env bash
+# This script runs job.pbs with qsub. Customize as necessary
+qsub job.pbs -N "<%= full_name %>" -e "<%= abs_stream_prefix %>.e" -o "<%= abs_stream_prefix %>.o"

data/templates/task.tt

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+#!/usr/bin/env <%= options[:script] %>
+
+# This is the meat of the job.
+# Please place the task you'd like your job to run.
+# For example, this is where you would put
+# experiment logic.

metadata

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+--- !ruby/object:Gem::Specification
+name: pbs_job
+version: !ruby/object:Gem::Version
+  version: 0.0.1
+platform: ruby
+authors:
+- Dustin Morrill
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2013-07-25 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: thor
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.18.1
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.18.1
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.3.5
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.3.5
+- !ruby/object:Gem::Dependency
+  name: bahia
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.7.2
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.7.2
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 10.1.0
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 10.1.0
+- !ruby/object:Gem::Dependency
+  name: minitest
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 5.0.6
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 5.0.6
+- !ruby/object:Gem::Dependency
+  name: awesome_print
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.1.0
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.1.0
+- !ruby/object:Gem::Dependency
+  name: simplecov
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.7.1
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.7.1
+description: PBS/Torque job generator
+email:
+- morrill@ualberta.ca
+executables:
+- pbs_job
+extensions: []
+extra_rdoc_files: []
+files:
+- .gitignore
+- Gemfile
+- LICENSE.txt
+- README.md
+- Rakefile
+- bin/pbs_job
+- lib/pbs_job.rb
+- lib/pbs_job/version.rb
+- pbs_job.gemspec
+- spec/pbs_job_spec.rb
+- spec/support/spec_helper.rb
+- templates/job.pbs.tt
+- templates/job.qsub.tt
+- templates/task.tt
+homepage: https://github.com/dmorrill10/pbs_job
+licenses:
+- MIT
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.0.3
+signing_key: 
+specification_version: 4
+summary: Creates a directory and file structure for a well organized PBS/Torque job.
+test_files:
+- spec/pbs_job_spec.rb
+- spec/support/spec_helper.rb
+has_rdoc: