pbs 2.1.0 → 2.2.0

checksums.yaml

@@ -1,7 +1,7 @@
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data/.rspec

@@ -0,0 +1 @@
+--require spec_helper

data/.travis.yml

@@ -0,0 +1,9 @@
+sudo: false
+language: ruby
+rvm:
+  - 2.2.2
+before_install: gem install bundler -v 1.7.8
+notifications:
+  email:
+    on_success: never
+    on_failure: always

data/CHANGELOG.md

@@ -1,41 +1,59 @@
-## Unreleased
+# Changelog
 
-## 2.1.0 (2017-06-02)
+All notable changes to this project will be documented in this file.
 
-Features:
+The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
+and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
 
-  - added helpful scripts to setup and launch console
-  - provide support to get status of selected jobs on batch server
+## [Unreleased]
 
-## 2.0.4 (2017-03-28)
+## [2.2.0] - 2018-04-20
+### Added
+- Added a `Batch#submit` method to submit directly with a `qsub` call.
+  [#29](https://github.com/OSC/pbs-ruby/issues/29)
+- Add Travis CI support.
 
-Bugfixes:
+### Changed
+- Changed the `CHANGELOG.md` formatting.
+- Updated date in `LICENSE.txt`.
 
-  - support reservation id for submitting job with `qsub`
-  - added workaround for users who specify queue in batch script
+### Deprecated
+- Deprecating the old submit methods `Batch#submit_string` and
+  `Batch#submit_script`.
 
-## 2.0.3 (2016-11-04)
+## [2.1.0] - 2017-06-02
+### Added
+- Added helpful scripts to setup and launch console.
+- Provide support to get status of selected jobs on batch server.
 
-Bugfixes:
+## [2.0.4] - 2017-03-28
+### Fixed
+- Support reservation id for submitting job with `qsub`.
+- Added workaround for users who specify queue in batch script.
 
-  - better support `qsub` CLI arguments
+## [2.0.3] - 2016-11-04
+### Fixed
+- Better support `qsub` CLI arguments.
 
-## 2.0.2 (2016-08-17)
+## [2.0.2] - 2016-08-17
+### Fixed
+- Fixes Ruby version requirement to 2.2.0+.
 
-Bugfixes:
+### Removed
+- Removes unused prefix directory option.
 
-  - fixes Ruby version requirement to 2.2.0+
-  - removes unused prefix directory option
+## [2.0.1] - 2016-08-10
+### Changed
+- Batch object can be initialized with lib/bin directories.
 
-## 2.0.1 (2016-08-10)
+## 2.0.0 - 2016-08-05
+### Added
+- Initial release of 2.0.0!
 
-Features:
-
-  - batch object can be initialized with lib/bin directories
-
-## 2.0.0 (2016-08-05)
-
-Features:
-
-  - initial release of v2.0.0
-  - added a changelog
+[Unreleased]: https://github.com/OSC/pbs-ruby/compare/v2.2.0...HEAD
+[2.2.0]: https://github.com/OSC/pbs-ruby/compare/v2.1.0...v2.2.0
+[2.1.0]: https://github.com/OSC/pbs-ruby/compare/v2.0.4...v2.1.0
+[2.0.4]: https://github.com/OSC/pbs-ruby/compare/v2.0.3...v2.0.4
+[2.0.3]: https://github.com/OSC/pbs-ruby/compare/v2.0.2...v2.0.3
+[2.0.2]: https://github.com/OSC/pbs-ruby/compare/v2.0.1...v2.0.2
+[2.0.1]: https://github.com/OSC/pbs-ruby/compare/v2.0.0...v2.0.1

data/LICENSE.txt

@@ -1,4 +1,4 @@
-Copyright (c) 2014-2016 Ohio Supercomputer Center
+Copyright (c) 2014-2018 Ohio Supercomputer Center
 
 MIT License
 

data/README.md

@@ -1,5 +1,9 @@
 # PBS Ruby
 
+[![Build Status](https://travis-ci.org/OSC/pbs-ruby.svg?branch=master)](https://travis-ci.org/OSC/pbs-ruby)
+![GitHub Release](https://img.shields.io/github/release/osc/pbs-ruby.svg)
+[![GitHub License](https://img.shields.io/badge/license-MIT-green.svg)](https://opensource.org/licenses/MIT)
+
 ## Description
 
 Ruby wrapper for the Torque C Library utilizing Ruby-FFI. This has been
@@ -239,3 +243,26 @@ job_id = b.submit_script("/path/to/script", headers: headers, resources: resourc
 # Get job info
 b.get_job(job_id)
 ```
+
+## Development
+
+After checking out the repo, run `bin/setup` to install dependencies. Then, run
+`bundle exec rspec spec` to run the tests. You can also run `bin/console` for
+an interactive prompt that will allow you to experiment.
+
+To install this gem onto your local machine, run `bundle exec rake install`. To
+release a new version, update and commit the version number in `version.rb`,
+and then run `bundle exec rake release`, which will create a git tag for the
+version, push git commits and tags, and push the `.gem` file to
+[rubygems.org](https://rubygems.org).
+
+## Contributing
+
+Bug reports and pull requests are welcome on GitHub at
+https://github.com/OSC/pbs-ruby.
+
+## License
+
+The gem is available as open source under the terms of the [MIT License].
+
+[MIT License]: https://opensource.org/licenses/MIT

data/Rakefile

@@ -1 +1,6 @@
 require "bundler/gem_tasks"
+require "rspec/core/rake_task"
+
+RSpec::Core::RakeTask.new(:spec)
+
+task :default => :spec

data/lib/pbs/batch.rb

@@ -319,6 +319,7 @@ module PBS
     # @param envvars [Hash] pbs environment variables
     # @param qsub [Boolean] whether use library or binary for submission
     # @return [String] the id of the job that was created
+    # @deprecated Use {#submit} instead.
     def submit_script(script, queue: nil, headers: {}, resources: {}, envvars: {}, qsub: true)
       send(qsub ? :qsub_submit : :pbs_submit, script.to_s, queue.to_s, headers, resources, envvars)
     end
@@ -327,6 +328,7 @@ module PBS
     # @param string [#to_s] script as a string
     # @param (see #submit_script)
     # @return [String] the id of the job that was created
+    # @deprecated Use {#submit} instead.
     def submit_string(string, **kwargs)
       Tempfile.open('qsub.') do |f|
         f.write string.to_s
@@ -335,6 +337,17 @@ module PBS
       end
     end
 
+    # Submit a script expanded as a string to the batch server
+    # @param content [#to_s] script as a string
+    # @param args [Array<#to_s>] arguments passed to `qsub` command
+    # @param env [Hash{#to_s => #to_s}] environment variables set
+    # @param chdir [#to_s, nil] working directory where `qsub` is called from
+    # @raise [Error] if `qsub` command exited unsuccessfully
+    # @return [String] the id of the job that was created
+    def submit(content, args: [], env: {}, chdir: nil)
+      call(:qsub, *args, env: env, stdin: content, chdir: chdir).strip
+    end
+
     private
       # Submit a script using Torque library
       def pbs_submit(script, queue, headers, resources, envvars)
@@ -428,5 +441,19 @@ module PBS
         raise PBS::Error, e unless s.success?
         o.chomp
       end
+
+      # Call a forked PBS command for a given host
+      def call(cmd, *args, env: {}, stdin: "", chdir: nil)
+        cmd  = bin.join(cmd.to_s).to_s
+        args = args.map(&:to_s)
+        env  = env.to_h.each_with_object({}) {|(k,v), h| h[k.to_s] = v.to_s}.merge({
+          "PBS_DEFAULT"     => host,
+          "LD_LIBRARY_PATH" => %{#{lib}:#{ENV["LD_LIBRARY_PATH"]}}
+        })
+        stdin = stdin.to_s
+        chdir = chdir && chdir.to_s
+        o, e, s = Open3.capture3(env, cmd, *args, stdin_data: stdin, chdir: chdir)
+        s.success? ? o : raise(PBS::Error, e)
+      end
   end
 end

data/lib/pbs/version.rb

@@ -1,4 +1,4 @@
 module PBS
   # The current version of PBS
-  VERSION = "2.1.0"
+  VERSION = "2.2.0"
 end

data/pbs.gemspec

@@ -25,4 +25,5 @@ Gem::Specification.new do |spec|
   spec.add_development_dependency "bundler", "~> 1.7"
   spec.add_development_dependency "rake", "~> 10.0"
   spec.add_development_dependency "pry", "~> 0.10"
+  spec.add_development_dependency "rspec", "~> 3.7"
 end

data/spec/batch_spec.rb

@@ -0,0 +1,136 @@
+describe PBS::Batch do
+  subject(:batch) { described_class.new(host: host, lib: lib, bin: bin) }
+  let(:host) { double(to_s: "HOST") }
+  let(:bin)  { double(to_s: "BIN")  }
+  let(:lib)  { double(to_s: "LIB")  }
+
+  it { is_expected.to respond_to(:host) }
+  it { is_expected.to respond_to(:bin) }
+  it { is_expected.to respond_to(:lib) }
+  it { is_expected.to respond_to(:submit) }
+
+  describe "#host" do
+    it { expect(subject.host).to eq("HOST") }
+  end
+
+  describe "#bin" do
+    it { expect(subject.bin).to eq(Pathname.new("BIN")) }
+  end
+
+  describe "#lib" do
+    it { expect(subject.lib).to eq(Pathname.new("LIB")) }
+  end
+
+  describe "#submit" do
+    subject { batch.submit(content, args: args, env: env, chdir: chdir) }
+    let(:content) { double(to_s: "CONTENT") }
+    let(:args)    { [] }
+    let(:env)     { {} }
+    let(:chdir)   { nil }
+
+    it "calls the qsub command" do
+      expect(Open3).to receive(:capture3).with(
+        {
+          "PBS_DEFAULT" => "HOST",
+          "LD_LIBRARY_PATH" => %{LIB:#{ENV["LD_LIBRARY_PATH"]}}
+        },
+        "BIN/qsub",
+        stdin_data: "CONTENT",
+        chdir: nil
+      ) do
+        [ "STDOUT", "STDERR", double(success?: true) ]
+      end
+
+      is_expected.to eq("STDOUT")
+    end
+
+    it "strips away whitespace from qsub output" do
+      expect(Open3).to receive(:capture3).with(any_args) do
+        [ "\t  \nSTDOUT  \n\t ", "STDERR", double(success?: true) ]
+      end
+
+      is_expected.to eq("STDOUT")
+    end
+
+    context "when environment variable specified" do
+      let(:env) { { double(to_s: "A") => double(to_s: "B") } }
+
+      it "calls the qsub command with that env var" do
+        expect(Open3).to receive(:capture3).with(
+          {
+            "PBS_DEFAULT" => "HOST",
+            "LD_LIBRARY_PATH" => %{LIB:#{ENV["LD_LIBRARY_PATH"]}},
+            "A" => "B"
+          },
+          "BIN/qsub",
+          stdin_data: "CONTENT",
+          chdir: nil
+        ) do
+          [ "STDOUT", "STDERR", double(success?: true) ]
+        end
+
+        is_expected.to eq("STDOUT")
+      end
+    end
+
+    context "when command line argument specified" do
+      let(:args) { [double(to_s: "a"), double(to_s: "b")] }
+
+      it "calls the qsub command with those arguments" do
+        expect(Open3).to receive(:capture3).with(
+          {
+            "PBS_DEFAULT" => "HOST",
+            "LD_LIBRARY_PATH" => %{LIB:#{ENV["LD_LIBRARY_PATH"]}}
+          },
+          "BIN/qsub",
+          "a",
+          "b",
+          stdin_data: "CONTENT",
+          chdir: nil
+        ) do
+          [ "STDOUT", "STDERR", double(success?: true) ]
+        end
+
+        is_expected.to eq("STDOUT")
+      end
+    end
+
+    context "when workding directory specified" do
+      let(:chdir) { double(to_s: "WORK_DIR") }
+
+      it "calls the qsub command in that working directory" do
+        expect(Open3).to receive(:capture3).with(
+          {
+            "PBS_DEFAULT" => "HOST",
+            "LD_LIBRARY_PATH" => %{LIB:#{ENV["LD_LIBRARY_PATH"]}}
+          },
+          "BIN/qsub",
+          stdin_data: "CONTENT",
+          chdir: "WORK_DIR"
+        ) do
+          [ "STDOUT", "STDERR", double(success?: true) ]
+        end
+
+        is_expected.to eq("STDOUT")
+      end
+    end
+
+    context "when qsub returns unsuccessfully" do
+      it "raises an error with stderr as message" do
+        expect(Open3).to receive(:capture3).with(
+          {
+            "PBS_DEFAULT" => "HOST",
+            "LD_LIBRARY_PATH" => %{LIB:#{ENV["LD_LIBRARY_PATH"]}}
+          },
+          "BIN/qsub",
+          stdin_data: "CONTENT",
+          chdir: nil
+        ) do
+          [ "STDOUT", "STDERR", double(success?: false) ]
+        end
+
+        expect { subject }.to raise_error(PBS::Error, "STDERR")
+      end
+    end
+  end
+end

data/spec/spec_helper.rb

@@ -0,0 +1,102 @@
+require "pbs"
+
+# This file was generated by the `rspec --init` command. Conventionally, all
+# specs live under a `spec` directory, which RSpec adds to the `$LOAD_PATH`.
+# The generated `.rspec` file contains `--require spec_helper` which will cause
+# this file to always be loaded, without a need to explicitly require it in any
+# files.
+#
+# Given that it is always loaded, you are encouraged to keep this file as
+# light-weight as possible. Requiring heavyweight dependencies from this file
+# will add to the boot time of your test suite on EVERY test run, even for an
+# individual file that may not need all of that loaded. Instead, consider making
+# a separate helper file that requires the additional dependencies and performs
+# the additional setup, and require it from the spec files that actually need
+# it.
+#
+# See http://rubydoc.info/gems/rspec-core/RSpec/Core/Configuration
+RSpec.configure do |config|
+  # rspec-expectations config goes here. You can use an alternate
+  # assertion/expectation library such as wrong or the stdlib/minitest
+  # assertions if you prefer.
+  config.expect_with :rspec do |expectations|
+    # This option will default to `true` in RSpec 4. It makes the `description`
+    # and `failure_message` of custom matchers include text for helper methods
+    # defined using `chain`, e.g.:
+    #     be_bigger_than(2).and_smaller_than(4).description
+    #     # => "be bigger than 2 and smaller than 4"
+    # ...rather than:
+    #     # => "be bigger than 2"
+    expectations.include_chain_clauses_in_custom_matcher_descriptions = true
+  end
+
+  # rspec-mocks config goes here. You can use an alternate test double
+  # library (such as bogus or mocha) by changing the `mock_with` option here.
+  config.mock_with :rspec do |mocks|
+    # Prevents you from mocking or stubbing a method that does not exist on
+    # a real object. This is generally recommended, and will default to
+    # `true` in RSpec 4.
+    mocks.verify_partial_doubles = true
+  end
+
+  # This option will default to `:apply_to_host_groups` in RSpec 4 (and will
+  # have no way to turn it off -- the option exists only for backwards
+  # compatibility in RSpec 3). It causes shared context metadata to be
+  # inherited by the metadata hash of host groups and examples, rather than
+  # triggering implicit auto-inclusion in groups with matching metadata.
+  config.shared_context_metadata_behavior = :apply_to_host_groups
+
+# The settings below are suggested to provide a good initial experience
+# with RSpec, but feel free to customize to your heart's content.
+=begin
+  # This allows you to limit a spec run to individual examples or groups
+  # you care about by tagging them with `:focus` metadata. When nothing
+  # is tagged with `:focus`, all examples get run. RSpec also provides
+  # aliases for `it`, `describe`, and `context` that include `:focus`
+  # metadata: `fit`, `fdescribe` and `fcontext`, respectively.
+  config.filter_run_when_matching :focus
+
+  # Allows RSpec to persist some state between runs in order to support
+  # the `--only-failures` and `--next-failure` CLI options. We recommend
+  # you configure your source control system to ignore this file.
+  config.example_status_persistence_file_path = "spec/examples.txt"
+
+  # Limits the available syntax to the non-monkey patched syntax that is
+  # recommended. For more details, see:
+  #   - http://rspec.info/blog/2012/06/rspecs-new-expectation-syntax/
+  #   - http://www.teaisaweso.me/blog/2013/05/27/rspecs-new-message-expectation-syntax/
+  #   - http://rspec.info/blog/2014/05/notable-changes-in-rspec-3/#zero-monkey-patching-mode
+  config.disable_monkey_patching!
+
+  # This setting enables warnings. It's recommended, but in some cases may
+  # be too noisy due to issues in dependencies.
+  config.warnings = true
+
+  # Many RSpec users commonly either run the entire suite or an individual
+  # file, and it's useful to allow more verbose output when running an
+  # individual spec file.
+  if config.files_to_run.one?
+    # Use the documentation formatter for detailed output,
+    # unless a formatter has already been configured
+    # (e.g. via a command-line flag).
+    config.default_formatter = "doc"
+  end
+
+  # Print the 10 slowest examples and example groups at the
+  # end of the spec run, to help surface which specs are running
+  # particularly slow.
+  config.profile_examples = 10
+
+  # Run specs in random order to surface order dependencies. If you find an
+  # order dependency and want to debug it, you can fix the order by providing
+  # the seed, which is printed after each run.
+  #     --seed 1234
+  config.order = :random
+
+  # Seed global randomization in this process using the `--seed` CLI option.
+  # Setting this allows you to use `--seed` to deterministically reproduce
+  # test failures related to randomization by passing the same `--seed` value
+  # as the one that triggered the failure.
+  Kernel.srand config.seed
+=end
+end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: pbs
 version: !ruby/object:Gem::Version
-  version: 2.1.0
+  version: 2.2.0
 platform: ruby
 authors:
 - Jeremy Nicklas
 autorequire: 
 bindir: exe
 cert_chain: []
-date: 2017-07-02 00:00:00.000000000 Z
+date: 2018-04-20 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: ffi
@@ -72,6 +72,20 @@ dependencies:
     - - "~>"
       - !ruby/object:Gem::Version
         version: '0.10'
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.7'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.7'
 description: Ruby wrapper for the Torque C library utilizing Ruby-FFI. This has been
   successfully tested with Torque 4.2.10 and greater. Your mileage may vary.
 email:
@@ -81,6 +95,8 @@ extensions: []
 extra_rdoc_files: []
 files:
 - ".gitignore"
+- ".rspec"
+- ".travis.yml"
 - CHANGELOG.md
 - Gemfile
 - LICENSE.txt
@@ -95,6 +111,8 @@ files:
 - lib/pbs/torque.rb
 - lib/pbs/version.rb
 - pbs.gemspec
+- spec/batch_spec.rb
+- spec/spec_helper.rb
 homepage: https://github.com/OSC/pbs-ruby
 licenses:
 - MIT
@@ -115,9 +133,11 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.4.5
+rubygems_version: 2.4.5.4
 signing_key: 
 specification_version: 4
 summary: Ruby gem that uses FFI to interface with Adaptive Computing's resource manager
   Torque
-test_files: []
+test_files:
+- spec/batch_spec.rb
+- spec/spec_helper.rb