regressiontest 0.0.1

data/.document

@@ -0,0 +1,5 @@
+lib/**/*.rb
+bin/*
+- 
+features/**/*.feature
+LICENSE.txt

data/.travis.yml

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+language: ruby
+rvm:
+  - 1.9.2
+  - 1.9.3
+  - jruby-19mode # JRuby in 1.9 mode
+  - rbx-19mode
+#  - 1.8.7
+#  - jruby-18mode # JRuby in 1.8 mode
+#  - rbx-18mode
+
+# uncomment this line if your project needs to run something other than `rake`:
+# script: bundle exec rspec spec

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 "shoulda", ">= 0"
+  gem "rdoc", "~> 3.12"
+  gem "cucumber", ">= 0"
+  gem "jeweler", "~> 1.8.3"
+  gem "bundler", ">= 1.0.21"
+  gem "bio", ">= 1.4.2"
+  gem "rdoc", "~> 3.12"
+end

data/LICENSE.txt

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+Copyright (c) 2012 Pjotr Prins
+
+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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+# regressiontest
+
+[![Build Status](https://secure.travis-ci.org/pjotrp/regressiontest.png)](http://travis-ci.org/pjotrp/regressiontest)
+
+Full description goes here
+
+Note: this software is under active development!
+
+## Installation
+
+```sh
+    gem install regressiontest
+```
+
+## Usage
+
+```ruby
+    require 'regressiontest'
+```
+
+The API doc is online. For more code examples see the test files in
+the source tree.
+        
+## Project home page
+
+Information on the source tree, documentation, examples, issues and
+how to contribute, see
+
+  http://github.com/pjotrp/regressiontest
+
+The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
+
+## Cite
+
+If you use this software, please cite one of
+  
+* [BioRuby: bioinformatics software for the Ruby programming language](http://dx.doi.org/10.1093/bioinformatics/btq475)
+* [Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics](http://dx.doi.org/10.1093/bioinformatics/bts080)
+
+## Biogems.info
+
+This Biogem is published at [#regressiontest](http://biogems.info/index.html)
+
+## Copyright
+
+Copyright (c) 2012 Pjotr Prins. 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 = "regressiontest"
+  gem.homepage = "http://github.com/pjotrp/regressiontest"
+  gem.license = "MIT"
+  gem.summary = %Q{Functional (regression) testing library}
+  gem.description = %Q{Regression testing for the command line, and library API}
+  gem.email = "pjotr.public01@thebird.nl"
+  gem.authors = ["Pjotr Prins"]
+  # dependencies defined in Gemfile
+end
+Jeweler::RubygemsDotOrgTasks.new
+
+require 'rake/testtask'
+Rake::TestTask.new(:test) do |test|
+  test.libs << 'lib' << 'test'
+  test.pattern = 'test/**/test_*.rb'
+  test.verbose = true
+end
+
+require 'cucumber/rake/task'
+Cucumber::Rake::Task.new(:features)
+
+task :default => :test
+
+require 'rdoc/task'
+Rake::RDocTask.new do |rdoc|
+  version = File.exist?('VERSION') ? File.read('VERSION') : ""
+
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "regressiontest #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/VERSION

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+0.0.1

data/bin/regressiontest

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+#!/usr/bin/env ruby
+#
+# BioRuby regressiontest Plugin BioRegressiontest
+# Author:: Pjotr Prins
+# Copyright:: 2012
+
+USAGE = "Describe regressiontest"
+
+gempath = File.dirname(File.dirname(__FILE__))
+$: << File.join(gempath,'lib')
+
+VERSION_FILENAME=File.join(gempath,'VERSION')
+version = File.new(VERSION_FILENAME).read.chomp
+
+# print banner
+print "regressiontest #{version} by Pjotr Prins 2012\n"
+
+if ARGV.size == 0
+  print USAGE
+end
+
+require 'regressiontest'
+require 'optparse'
+
+# Uncomment when using the bio-logger 
+# require 'bio-logger'
+# log = Bio::Log::LoggerPlus.new 'regressiontest'
+# log.outputters = Bio::Log::Outputter.stderr 
+# Bio::Log::CLI.logger('stderr')
+# Bio::Log::CLI.trace('info')
+
+options = {:example_switch=>false,:show_help=>false}
+opts = OptionParser.new do |o|
+  o.banner = "Usage: #{File.basename($0)} [options] filename\ne.g. #{File.basename($0)} test.txt"
+
+  o.on('--example_parameter [EXAMPLE_PARAMETER]', 'TODO: put a description for the PARAMETER') do |example_parameter|
+    # TODO: your logic here, below an example
+    options[:example_parameter] = 'this is a parameter'
+  end
+  
+  o.separator ""
+  o.on("--switch-example", 'TODO: put a description for the SWITCH') do
+    # TODO: your logic here, below an example
+    self[:example_switch] = true
+  end
+
+  # Uncomment the following when using the bio-logger 
+  # o.separator ""
+  # o.on("--logger filename",String,"Log to file (default stderr)") do | name |
+  #   Bio::Log::CLI.logger(name)
+  # end
+  #
+  # o.on("--trace options",String,"Set log level (default INFO, see bio-logger)") do | s |
+  #   Bio::Log::CLI.trace(s)
+  # end
+  # 
+  # o.on("-q", "--quiet", "Run quietly") do |q|
+  #   Bio::Log::CLI.trace('error')
+  # end
+  # 
+  # o.on("-v", "--verbose", "Run verbosely") do |v|
+  #   Bio::Log::CLI.trace('info')
+  # end
+  # 
+  # o.on("--debug", "Show debug messages") do |v|
+  #   Bio::Log::CLI.trace('debug')
+  # end
+
+  o.separator ""
+  o.on_tail('-h', '--help', 'display this help and exit') do
+    options[:show_help] = true
+  end
+end
+
+begin
+  opts.parse!(ARGV)
+
+  # Uncomment when using the bio-logger
+  # Bio::Log::CLI.configure('regressiontest')
+  # logger = Bio::Log::LoggerPlus['regressiontest']
+  # Log parsed options and remaining arguments in ARGV
+  # logger.info [options, ARGV]
+
+  # TODO: your code here
+  # use options for your logic
+rescue OptionParser::InvalidOption => e
+  options[:invalid_argument] = e.message
+end
+

data/features/bio-regressiontest.feature

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+Feature: something something
+  In order to something something
+  A user something something
+  something something something
+
+  Scenario: something something
+    Given inspiration
+    When I create a sweet new gem
+    Then everyone should see how awesome I am

data/features/support/env.rb

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+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+
+$LOAD_PATH.unshift(File.dirname(__FILE__) + '/../../lib')
+require 'regressiontest'
+
+require 'test/unit/assertions'
+
+World(Test::Unit::Assertions)

data/lib/regressiontest.rb

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+# Please require your code below, respecting the naming conventions in the
+# bioruby directory tree.
+#
+# For example, say you have a plugin named bio-plugin, the only uncommented
+# line in this file would be 
+#
+#   require 'bio/bio-plugin/plugin'
+#
+# In this file only require other files. Avoid other source code.
+
+require 'regressiontest/cli_exec'

data/lib/regressiontest/cli_exec.rb

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+module RegressionTest
+
+  DEFAULT_TESTDIR = "test/data/regression"
+
+  # Regression test runner compares output in ./test/data/regression (by default).
+  # The convention is to have a file with names .ref (reference) and create .new
+  module CliExec
+    def CliExec::exec command, testname, options = {}
+      # ---- Find .ref file
+      fullname = DEFAULT_TESTDIR + "/" + testname 
+      basefn = if File.exist?(testname+".ref")
+                testname 
+              elsif fullname + ".ref"
+                FileUtils.mkdir_p DEFAULT_TESTDIR
+                fullname
+              else
+                raise "Can not find reference file for #{testname} - expected #{fullname}.ref"
+              end
+      outfn = basefn + ".new"
+      reffn = basefn + ".ref"
+      # ---- Create .new file
+      cmd = command + " > #{outfn}"
+      $stderr.print cmd,"\n"
+      if Kernel.system(cmd) == false
+        $stderr.print cmd," returned an error\n"
+        return false 
+      end
+      # ---- Compare the two files
+      compare_files(outfn,reffn)
+    end
+
+    def CliExec::compare_files fn1, fn2
+      cmd = "diff #{fn2} #{fn1}"
+      $stderr.print cmd+"\n"
+      return true if Kernel.system(cmd) == true
+      $stderr.print "If it is correct, execute \"cp #{fn1} {fn2}\", and run again"
+      false
+    end
+  end
+
+end

data/test/helper.rb

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+require 'rubygems'
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+require 'test/unit'
+require 'shoulda'
+
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+$LOAD_PATH.unshift(File.dirname(__FILE__))
+require 'regressiontest'
+
+class Test::Unit::TestCase
+end

data/test/test_bio-regressiontest.rb

@@ -0,0 +1,7 @@
+require 'helper'
+
+class TestBioRegressiontest < Test::Unit::TestCase
+  should "probably rename this file and start testing for real" do
+    flunk "hey buddy, you should probably rename this file and start testing for real"
+  end
+end

metadata

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+--- !ruby/object:Gem::Specification
+name: regressiontest
+version: !ruby/object:Gem::Version
+  version: 0.0.1
+  prerelease: 
+platform: ruby
+authors:
+- Pjotr Prins
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2012-07-27 00:00:00.000000000Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: shoulda
+  requirement: &27821800 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: *27821800
+- !ruby/object:Gem::Dependency
+  name: rdoc
+  requirement: &27820620 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.12'
+  type: :development
+  prerelease: false
+  version_requirements: *27820620
+- !ruby/object:Gem::Dependency
+  name: cucumber
+  requirement: &27819580 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: *27819580
+- !ruby/object:Gem::Dependency
+  name: jeweler
+  requirement: &27818860 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.8.3
+  type: :development
+  prerelease: false
+  version_requirements: *27818860
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: &27818060 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.0.21
+  type: :development
+  prerelease: false
+  version_requirements: *27818060
+- !ruby/object:Gem::Dependency
+  name: bio
+  requirement: &27814360 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.4.2
+  type: :development
+  prerelease: false
+  version_requirements: *27814360
+- !ruby/object:Gem::Dependency
+  name: rdoc
+  requirement: &27807100 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.12'
+  type: :development
+  prerelease: false
+  version_requirements: *27807100
+description: Regression testing for the command line, and library API
+email: pjotr.public01@thebird.nl
+executables:
+- regressiontest
+extensions: []
+extra_rdoc_files:
+- LICENSE.txt
+- README.md
+files:
+- .document
+- .travis.yml
+- Gemfile
+- LICENSE.txt
+- README.md
+- Rakefile
+- VERSION
+- bin/regressiontest
+- features/bio-regressiontest.feature
+- features/step_definitions/bio-regressiontest_steps.rb
+- features/support/env.rb
+- lib/regressiontest.rb
+- lib/regressiontest/cli_exec.rb
+- test/helper.rb
+- test/test_bio-regressiontest.rb
+homepage: http://github.com/pjotrp/regressiontest
+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: 2174228862267285081
+required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 1.8.10
+signing_key: 
+specification_version: 3
+summary: Functional (regression) testing library
+test_files: []