comana 0.0.0

data/.document

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+lib/**/*.rb
+bin/*
+- 
+features/**/*.feature
+LICENSE.txt

data/.rspec

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+--color

data/Gemfile

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+source "http://rubygems.org"
+# Add dependencies required to use your gem here.
+# Example:
+#   gem "activesupport", ">= 2.3.5"
+
+# Add dependencies to develop your gem here.
+# Include everything needed to run rake, tests, features, etc.
+group :development do
+  gem "rspec", "~> 2.9.0"
+  gem "rdoc", "~> 3.12"
+  gem "bundler", "~> 1.1.3"
+  gem "jeweler", "~> 1.8.3"
+  gem "simplecov", ">= 0"
+end

data/LICENSE.txt

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+Copyright (c) 2012 ippei94da
+
+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.rdoc

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+= comana
+
+Description goes here.
+
+== Contributing to comana
+ 
+* Check out the latest master to make sure the feature hasn't been implemented or the bug hasn't been fixed yet.
+* Check out the issue tracker to make sure someone already hasn't requested it and/or contributed it.
+* Fork the project.
+* Start a feature/bugfix branch.
+* Commit and push until you are happy with your contribution.
+* Make sure to add tests for it. This is important so I don't break it in a future version unintentionally.
+* Please try not to mess with the Rakefile, version, or history. If you want to have your own version, or is otherwise necessary, that is fine, but please isolate to its own commit so I can cherry-pick around it.
+
+== Copyright
+
+Copyright (c) 2012 ippei94da. See LICENSE.txt for
+further details.
+

data/Rakefile

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+# encoding: utf-8
+
+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'
+
+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 = "comana"
+  gem.homepage = "http://github.com/ippei94da/comana"
+  gem.license = "MIT"
+  gem.summary = %Q{Manager for scientific computing}
+  gem.description = %Q{An aim of this gem is to provide a framework of
+    managing scientific computing.
+    Researchers on computing have to check calculation and
+    generate new calculation and execute, repeatedly.
+    The abstract class that this gem provide would help the work.
+  }
+  gem.email = "ippei94da@gmail.com"
+  gem.authors = ["ippei94da"]
+  # dependencies defined in Gemfile
+end
+Jeweler::RubygemsDotOrgTasks.new
+
+require 'rspec/core'
+require 'rspec/core/rake_task'
+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
+
+task :default => :spec
+
+require 'rdoc/task'
+Rake::RDocTask.new do |rdoc|
+  version = File.exist?('VERSION') ? File.read('VERSION') : ""
+
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "comana #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/VERSION

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+0.0.0

data/lib/comana.rb

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+#! /usr/bin/env ruby
+# coding: utf-8
+
+#
+# Comana: COmputation MANAger
+#
+# This profides a framework of scientific computation.
+# Users have to redefine some methods in subclasses for various computation.
+# 
+class Comana
+  class NotImplementedError < Exception; end
+  class AlreadyStartedError < Exception; end
+
+  #
+  def initialize(dir)
+    @dir = dir
+    set_parameters
+  end
+
+  # Return a symbol which indicate state of calculation.
+  #   :yet           not started
+  #   :started       started, but not ended, including short time from last output
+  #   :terminated    started, but long time no output
+  #   :next          started, normal ended and need next calculation
+  #   :finished      started, normal ended and not need next calculation
+  def state
+    return :finished   if finished?
+    return :next       if normal_ended?
+    return :yet        unless started?
+    return :terminated if (Time.now - latest_modified_time > @alive_time)
+    return :started    
+  end
+
+  # Execute calculation.
+  # If log of Comana exist, raise Comana::AlreadyStartedError,
+  # because the calculation has been done by other process already.
+  def calculate
+    raise AlreadyStartedError if started?
+    File.open(@log, "w")
+    send_command
+  end
+
+  # Generate next calculation and return the computation object.
+  def prepare_next
+    raise NotImplementedError, "#{self.class}::prepare_next need to be redefined"
+  end
+
+  # Return initial state.
+  def initial_state
+    raise NotImplementedError, "#{self.class}::initial_state need to be redefined"
+  end
+
+  # Return latest state.
+  def latest_state
+    raise NotImplementedError, "#{self.class}::latest_state need to be redefined"
+  end
+
+  private
+
+  def send_command
+    raise NotImplementedError, "#{self.class}::send_command need to be redefined"
+  end
+
+  def set_parameters
+    raise NotImplementedError, "#{self.class}::set_parameters need to be redefined"
+
+    # e.g.,
+    #@logfile    = "comana.log"
+    #@alive_time = 3600
+    #@outfiles   = ["output_a", "ouput_b"] # should be use files only to output.
+  end
+
+  # Return latest modified time of files in calc dir recursively.
+  #require "find"
+  def latest_modified_time
+    tmp = Dir.glob("#{@dir}/**/*").max_by do |file|
+      File.mtime(file)
+    end
+    File.mtime(tmp)
+  end
+
+  def started?
+    File.exist?( "#{@dir}/#{@logfile}" )
+  end
+
+  # Return true if the condition is satisfied.
+  # E.g., when calculation output contains orthodox ending sequences.
+  def normal_ended?
+    raise NotImplementedError, "#{self.class}::normal_ended? need to be redefined"
+  end
+
+  # Return true if the condition is satisfied.
+  # E.g., calculation achieve convergence.
+  def finished?
+    raise NotImplementedError, "#{self.class}::finished? need to be redefined"
+  end
+
+end
+

data/spec/comana_spec.rb

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+require "fileutils"
+require File.expand_path(File.dirname(__FILE__) + '/spec_helper')
+
+NOW = Time.now
+CALC_DIR = "spec/dummy"
+LOG = "#{CALC_DIR}/log"
+#OUTFILES = ["output_a"]
+
+class Comana
+  public :latest_modified_time, :started?
+end
+
+class CalcFinished    < Comana
+  def normal_ended?     ; true      ; end
+  def finished?         ; true      ; end
+  def send_command      ;           ; end
+  def prepare_next      ;           ; end
+  def initial_state     ;           ; end
+  def latest_state      ;           ; end
+  def teardown          ;           ; end
+  def set_parameters
+    @logfile    = "log"
+    @alive_time =  500
+  end
+end
+
+describe Comana, "with not calculated" do
+  class CalcYet < Comana
+    def normal_ended?     ; false     ; end
+    def finished?         ; false     ; end
+    def send_command      ;           ; end
+    def prepare_next      ;           ; end
+    def initial_state     ;           ; end
+    def latest_state      ;           ; end
+    def teardown          ;           ; end
+    def set_parameters
+      @logfile    = "log"
+      @alive_time = 3600
+    end
+  end
+  before do
+    @calc = CalcYet .new(CALC_DIR)
+
+    File.utime(NOW - 1000 ,NOW - 1000, "#{CALC_DIR}/input_a")
+    File.utime(NOW - 2000 ,NOW - 2000, "#{CALC_DIR}/input_b")
+    FileUtils.rm(LOG) if File.exist?(LOG)
+  end
+
+  it "should return the state" do
+    @calc.state.should == :yet
+  end
+
+  it "should return latest modified time" do
+    @calc.latest_modified_time.should == (NOW - 1000)
+  end
+
+  it "should return false without log." do
+    @calc.started?.should_not == nil
+    @calc.started?.should be_false
+  end
+
+  it "should return true with log." do
+    File.open(LOG, "w")
+    @calc.started?.should be_true
+  end
+
+  after do
+    FileUtils.rm(LOG) if File.exist?(LOG)
+  end
+end
+
+describe Comana, "with log" do
+  class CalcStarted < Comana
+    def normal_ended?     ; false     ; end
+    def finished?         ; false     ; end
+    def send_command      ;           ; end
+    def prepare_next      ;           ; end
+    def initial_state     ;           ; end
+    def latest_state      ;           ; end
+    def teardown          ;           ; end
+    def set_parameters
+      @logfile    = "log"
+      @alive_time = 5000
+    end
+  end
+
+  before do
+    @calc = CalcStarted   .new(CALC_DIR)
+    File.utime(NOW - 1000 ,NOW - 1000, "#{CALC_DIR}/input_a")
+    File.utime(NOW - 2000 ,NOW - 2000, "#{CALC_DIR}/input_b")
+    File.open(LOG, "w")
+  end
+
+  it "should return :started" do
+    @calc.state.should == :started
+  end
+
+  after do
+    FileUtils.rm(LOG) if File.exist?(LOG)
+  end
+end
+
+#describe Comana, "with output" do
+#  class CalcStarted < Comana
+#    def normal_ended?     ; false     ; end
+#    def finished?         ; false     ; end
+#    def send_command      ;           ; end
+#    def prepare_next      ;           ; end
+#    def initial_state     ;           ; end
+#    def latest_state      ;           ; end
+#    def teardown          ;           ; end
+#    def set_parameters
+#      @logfile    = "log"
+#      @alive_time = 5000
+#    end
+#  end
+#
+#  before do
+#    @calc = CalcStarted   .new(CALC_DIR)
+#    File.utime(NOW - 1000 ,NOW - 1000, "#{CALC_DIR}/input_a")
+#    File.utime(NOW - 2000 ,NOW - 2000, "#{CALC_DIR}/input_b")
+#    #File.open(OUTPUT, "w")
+#  end
+#
+#  it "should return :started"
+#
+#  after do
+#    FileUtils.rm(LOG) if File.exist?(LOG)
+#  end
+#end
+
+describe Comana, "with terminated" do
+  class CalcTerminated < Comana
+    def normal_ended?     ; false     ; end
+    def finished?         ; false     ; end
+    def send_command      ;           ; end
+    def prepare_next      ;           ; end
+    def initial_state     ;           ; end
+    def latest_state      ;           ; end
+    def teardown          ;           ; end
+    def set_parameters
+      @logfile    = "log"
+      @alive_time = 500
+    end
+  end
+
+  before do
+    @calc_terminated   = CalcTerminated.new(CALC_DIR)
+
+    File.utime(NOW - 1000 ,NOW - 1000, "#{CALC_DIR}/input_a")
+    File.utime(NOW - 2000 ,NOW - 2000, "#{CALC_DIR}/input_b")
+    File.open(LOG, "w")
+  end
+
+  it "should return the state" do
+    File.open(LOG, "w")
+    File.utime(NOW - 1000 ,NOW - 1000, LOG)
+    @calc_terminated  .state.should == :terminated
+  end
+
+  after do
+    FileUtils.rm(LOG) if File.exist?(LOG)
+  end
+end
+
+describe Comana, "with next" do
+  class CalcNext < Comana
+    def normal_ended?     ; true      ; end
+    def finished?         ; false     ; end
+    def send_command      ;           ; end
+    def prepare_next      ;           ; end
+    def initial_state     ;           ; end
+    def latest_state      ;           ; end
+    def teardown          ;           ; end
+    def set_parameters
+      @logfile    = "log"
+      @alive_time =  500
+    end
+  end
+
+  before do
+    @calc_next         = CalcNext      .new(CALC_DIR)
+
+    File.utime(NOW - 1000 ,NOW - 1000, "#{CALC_DIR}/input_a")
+    File.utime(NOW - 2000 ,NOW - 2000, "#{CALC_DIR}/input_b")
+    File.open(LOG, "w")
+  end
+
+  it "should return the state" do
+
+    File.open(LOG, "w")
+    File.utime(NOW - 1000 ,NOW - 1000, LOG)
+    @calc_next        .state.should == :next
+  end
+
+  after do
+    FileUtils.rm(LOG) if File.exist?(LOG)
+  end
+end
+
+describe Comana, "with finished" do
+  before do
+    @calc_finished     = CalcFinished  .new(CALC_DIR)
+
+    File.utime(NOW - 1000 ,NOW - 1000, "#{CALC_DIR}/input_a")
+    File.utime(NOW - 2000 ,NOW - 2000, "#{CALC_DIR}/input_b")
+    #FileUtils.rm(LOG) if File.exist?(LOG)
+    File.open(LOG, "w")
+  end
+
+  it "should return the state" do
+
+    File.open(LOG, "w")
+    File.utime(NOW - 1000 ,NOW - 1000, LOG)
+    @calc_finished    .state.should == :finished
+  end
+
+  after do
+    FileUtils.rm(LOG) if File.exist?(LOG)
+  end
+end

data/spec/spec_helper.rb

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+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+$LOAD_PATH.unshift(File.dirname(__FILE__))
+require 'rspec'
+require 'comana'
+
+# Requires supporting files with custom matchers and macros, etc,
+# in ./support/ and its subdirectories.
+Dir["#{File.dirname(__FILE__)}/support/**/*.rb"].each {|f| require f}
+
+RSpec.configure do |config|
+  
+end

metadata

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+--- !ruby/object:Gem::Specification
+name: comana
+version: !ruby/object:Gem::Version
+  version: 0.0.0
+  prerelease: 
+platform: ruby
+authors:
+- ippei94da
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2012-04-03 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 2.9.0
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 2.9.0
+- !ruby/object:Gem::Dependency
+  name: rdoc
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.12'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.12'
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.1.3
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.1.3
+- !ruby/object:Gem::Dependency
+  name: jeweler
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.8.3
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.8.3
+- !ruby/object:Gem::Dependency
+  name: simplecov
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+description: ! "An aim of this gem is to provide a framework of\n    managing scientific
+  computing.\n    Researchers on computing have to check calculation and\n    generate
+  new calculation and execute, repeatedly.\n    The abstract class that this gem provide
+  would help the work.\n  "
+email: ippei94da@gmail.com
+executables: []
+extensions: []
+extra_rdoc_files:
+- LICENSE.txt
+- README.rdoc
+files:
+- .document
+- .rspec
+- Gemfile
+- LICENSE.txt
+- README.rdoc
+- Rakefile
+- VERSION
+- lib/comana.rb
+- spec/comana_spec.rb
+- spec/dummy/input_a
+- spec/dummy/input_b
+- spec/spec_helper.rb
+homepage: http://github.com/ippei94da/comana
+licenses:
+- MIT
+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: 940464947
+required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 1.8.21
+signing_key: 
+specification_version: 3
+summary: Manager for scientific computing
+test_files: []