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lib/**/*.rb | ||
bin/* | ||
- | ||
features/**/*.feature | ||
LICENSE.txt |
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# rcov generated | ||
coverage | ||
coverage.data | ||
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# rdoc generated | ||
rdoc | ||
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# yard generated | ||
doc | ||
.yardoc | ||
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# bundler | ||
.bundle | ||
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# jeweler generated | ||
pkg | ||
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# Have editor/IDE/OS specific files you need to ignore? Consider using a global gitignore: | ||
# | ||
# * Create a file at ~/.gitignore | ||
# * Include files you want ignored | ||
# * Run: git config --global core.excludesfile ~/.gitignore | ||
# | ||
# After doing this, these files will be ignored in all your git projects, | ||
# saving you from having to 'pollute' every project you touch with them | ||
# | ||
# Not sure what to needs to be ignored for particular editors/OSes? Here's some ideas to get you started. (Remember, remove the leading # of the line) | ||
# | ||
# For MacOS: | ||
# | ||
#.DS_Store | ||
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# For TextMate | ||
#*.tmproj | ||
#tmtags | ||
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# For emacs: | ||
#*~ | ||
#\#* | ||
#.\#* | ||
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# For vim: | ||
#*.swp | ||
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# For redcar: | ||
#.redcar | ||
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# For rubinius: | ||
#*.rbc | ||
# Ignore Gemfile.lock for gems. See http://yehudakatz.com/2010/12/16/clarifying-the-roles-of-the-gemspec-and-gemfile/ | ||
Gemfile.lock | ||
*.gemspec |
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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 | ||
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# uncomment this line if your project needs to run something other than `rake`: | ||
# script: bundle exec rspec spec |
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source "http://rubygems.org" | ||
# Add dependencies required to use your gem here. | ||
# Example: | ||
# gem "activesupport", ">= 2.3.5" | ||
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# 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 "bundler", "~> 1.0.0" | ||
gem "jeweler", "~> 1.8.4" | ||
gem "bio", ">= 1.4.2" | ||
gem "rdoc", "~> 3.12" | ||
end |
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Copyright (c) 2013 Ankur Goel | ||
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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: | ||
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The above copyright notice and this permission notice shall be | ||
included in all copies or substantial portions of the Software. | ||
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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. |
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# bio-statsample-timeseries | ||
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[![Build Status](https://secure.travis-ci.org/ankurgel/bioruby-statsample-timeseries.png)](http://travis-ci.org/ankurgel/bioruby-statsample-timeseries) | ||
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Full description goes here | ||
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Note: this software is under active development! | ||
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## Installation | ||
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```sh | ||
gem install bio-statsample-timeseries | ||
``` | ||
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## Usage | ||
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```ruby | ||
require 'bio-statsample-timeseries' | ||
``` | ||
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The API doc is online. For more code examples see the test files in | ||
the source tree. | ||
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## Project home page | ||
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Information on the source tree, documentation, examples, issues and | ||
how to contribute, see | ||
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http://github.com/ankurgel/bioruby-statsample-timeseries | ||
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The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby. | ||
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## Cite | ||
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If you use this software, please cite one of | ||
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* [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) | ||
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## Biogems.info | ||
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This Biogem is published at [#bio-statsample-timeseries](http://biogems.info/index.html) | ||
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## Copyright | ||
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Copyright (c) 2013 Ankur Goel. See LICENSE.txt for further details. | ||
|
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= bio-statsample-timeseries | ||
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{<img | ||
src="https://secure.travis-ci.org/ankurgel/bioruby-statsample-timeseries.png" | ||
/>}[http://travis-ci.org/#!/ankurgel/bioruby-statsample-timeseries] | ||
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Full description goes here | ||
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Note: this software is under active development! | ||
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== Installation | ||
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gem install bio-statsample-timeseries | ||
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== Usage | ||
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== Developers | ||
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To use the library | ||
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require 'bio-statsample-timeseries' | ||
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The API doc is online. For more code examples see also the test files in | ||
the source tree. | ||
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== Project home page | ||
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Information on the source tree, documentation, issues and how to contribute, see | ||
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http://github.com/ankurgel/bioruby-statsample-timeseries | ||
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The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby. | ||
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== Cite | ||
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If you use this software, please cite one of | ||
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* [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) | ||
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== Biogems.info | ||
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This Biogem is published at http://biogems.info/index.html#bio-statsample-timeseries | ||
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== Copyright | ||
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Copyright (c) 2013 Ankur Goel. See LICENSE.txt for further details. | ||
|
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# encoding: utf-8 | ||
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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 'rake' | ||
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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 = "bio-statsample-timeseries" | ||
gem.homepage = "http://github.com/ankurgel/bioruby-statsample-timeseries" | ||
gem.license = "MIT" | ||
gem.summary = %Q{TODO: one-line summary of your gem} | ||
gem.description = %Q{TODO: longer description of your gem} | ||
gem.email = "ankurgel@gmail.com" | ||
gem.authors = ["Ankur Goel"] | ||
# dependencies defined in Gemfile | ||
end | ||
Jeweler::RubygemsDotOrgTasks.new | ||
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require 'rake/testtask' | ||
Rake::TestTask.new(:test) do |test| | ||
test.libs << 'lib' << 'test' | ||
test.pattern = 'test/**/test_*.rb' | ||
test.verbose = true | ||
end | ||
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require 'cucumber/rake/task' | ||
Cucumber::Rake::Task.new(:features) | ||
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task :default => :test | ||
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require 'rdoc/task' | ||
Rake::RDocTask.new do |rdoc| | ||
version = File.exist?('VERSION') ? File.read('VERSION') : "" | ||
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rdoc.rdoc_dir = 'rdoc' | ||
rdoc.title = "bio-statsample-timeseries #{version}" | ||
rdoc.rdoc_files.include('README*') | ||
rdoc.rdoc_files.include('lib/**/*.rb') | ||
end |
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#!/usr/bin/env ruby | ||
# | ||
# BioRuby bio-statsample-timeseries Plugin BioStatsampleTimeseries | ||
# Author:: Ankur Goel | ||
# Copyright:: 2013 | ||
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USAGE = "Describe bio-statsample-timeseries" | ||
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if ARGV.size == 0 | ||
print USAGE | ||
end | ||
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require 'bio-statsample-timeseries' | ||
require 'optparse' | ||
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# Uncomment when using the bio-logger | ||
# require 'bio-logger' | ||
# Bio::Log::CLI.logger('stderr') | ||
# Bio::Log::CLI.trace('info') | ||
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options = {:example_switch=>false,:show_help=>false} | ||
opts = OptionParser.new do |o| | ||
o.banner = "Usage: #{File.basename($0)} [options] reponame\ne.g. #{File.basename($0)} the-perfect-gem" | ||
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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 | ||
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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 | ||
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# 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 | ||
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o.separator "" | ||
o.on_tail('-h', '--help', 'display this help and exit') do | ||
options[:show_help] = true | ||
end | ||
end | ||
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begin | ||
opts.parse!(ARGV) | ||
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# Uncomment the following when using the bio-logger | ||
# Bio::Log::CLI.configure('bio-statsample-timeseries') | ||
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# TODO: your code here | ||
# use options for your logic | ||
rescue OptionParser::InvalidOption => e | ||
options[:invalid_argument] = e.message | ||
end |
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Feature: something something | ||
In order to something something | ||
A user something something | ||
something something something | ||
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Scenario: something something | ||
Given inspiration | ||
When I create a sweet new gem | ||
Then everyone should see how awesome I am |
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require 'bundler' | ||
begin | ||
Bundler.setup(:default, :development) | ||
rescue Bundler::BundlerError => e | ||
$stderr.puts e.message | ||
$stderr.puts "Run `bundle install` to install missing gems" | ||
exit e.status_code | ||
end | ||
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$LOAD_PATH.unshift(File.dirname(__FILE__) + '/../../lib') | ||
require 'bio-statsample-timeseries' | ||
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require 'test/unit/assertions' | ||
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World(Test::Unit::Assertions) |
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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. | ||
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require 'bio-statsample-timeseries/statsample-timeseries.rb' | ||
|
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module BioStatsampleTimeseries | ||
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end |
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require 'rubygems' | ||
require 'bundler' | ||
begin | ||
Bundler.setup(:default, :development) | ||
rescue Bundler::BundlerError => e | ||
$stderr.puts e.message | ||
$stderr.puts "Run `bundle install` to install missing gems" | ||
exit e.status_code | ||
end | ||
require 'test/unit' | ||
require 'shoulda' | ||
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$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib')) | ||
$LOAD_PATH.unshift(File.dirname(__FILE__)) | ||
require 'bio-statsample-timeseries' | ||
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class Test::Unit::TestCase | ||
end |
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