From 2e4220bb7fb893c1cd8360221bce84b569fab699 Mon Sep 17 00:00:00 2001 From: Ben J Woodcroft Date: Fri, 25 May 2012 09:54:51 +1000 Subject: [PATCH] Initial commit to bio-ipcress. --- .document | 5 ++++ .gitignore | 52 ++++++++++++++++++++++++++++++++++++++ .travis.yml | 12 +++++++++ Gemfile | 15 +++++++++++ LICENSE.txt | 20 +++++++++++++++ README.md | 47 ++++++++++++++++++++++++++++++++++ README.rdoc | 48 +++++++++++++++++++++++++++++++++++ Rakefile | 45 +++++++++++++++++++++++++++++++++ lib/bio-ipcress.rb | 12 +++++++++ lib/bio-ipcress/ipcress.rb | 3 +++ test/helper.rb | 18 +++++++++++++ test/test_bio-ipcress.rb | 7 +++++ 12 files changed, 284 insertions(+) create mode 100644 .document create mode 100644 .gitignore create mode 100644 .travis.yml create mode 100644 Gemfile create mode 100644 LICENSE.txt create mode 100644 README.md create mode 100644 README.rdoc create mode 100644 Rakefile create mode 100644 lib/bio-ipcress.rb create mode 100644 lib/bio-ipcress/ipcress.rb create mode 100644 test/helper.rb create mode 100644 test/test_bio-ipcress.rb diff --git a/.document b/.document new file mode 100644 index 0000000..3d618dd --- /dev/null +++ b/.document @@ -0,0 +1,5 @@ +lib/**/*.rb +bin/* +- +features/**/*.feature +LICENSE.txt diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..59b0c07 --- /dev/null +++ b/.gitignore @@ -0,0 +1,52 @@ +# rcov generated +coverage +coverage.data + +# rdoc generated +rdoc + +# yard generated +doc +.yardoc + +# bundler +.bundle + +# jeweler generated +pkg + +# 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 + +# For TextMate +#*.tmproj +#tmtags + +# For emacs: +#*~ +#\#* +#.\#* + +# For vim: +#*.swp + +# For redcar: +#.redcar + +# 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 diff --git a/.travis.yml b/.travis.yml new file mode 100644 index 0000000..0a48c4d --- /dev/null +++ b/.travis.yml @@ -0,0 +1,12 @@ +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 diff --git a/Gemfile b/Gemfile new file mode 100644 index 0000000..aa6049e --- /dev/null +++ b/Gemfile @@ -0,0 +1,15 @@ +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 "jeweler", "~> 1.8.3" + gem "bundler", ">= 1.0.21" + gem "bio", ">= 1.4.2" + gem "rdoc", "~> 3.12" +end diff --git a/LICENSE.txt b/LICENSE.txt new file mode 100644 index 0000000..0d8e3c8 --- /dev/null +++ b/LICENSE.txt @@ -0,0 +1,20 @@ +Copyright (c) 2012 Ben J Woodcroft + +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. diff --git a/README.md b/README.md new file mode 100644 index 0000000..719d689 --- /dev/null +++ b/README.md @@ -0,0 +1,47 @@ +# bio-ipcress + +[![Build Status](https://secure.travis-ci.org/wwood/bioruby-ipcress.png)](http://travis-ci.org/wwood/bioruby-ipcress) + +Full description goes here + +Note: this software is under active development! + +## Installation + +```sh + gem install bio-ipcress +``` + +## Usage + +```ruby + require 'bio-ipcress' +``` + +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/wwood/bioruby-ipcress + +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 [#bio-ipcress](http://biogems.info/index.html) + +## Copyright + +Copyright (c) 2012 Ben J Woodcroft. See LICENSE.txt for further details. + diff --git a/README.rdoc b/README.rdoc new file mode 100644 index 0000000..ad375a3 --- /dev/null +++ b/README.rdoc @@ -0,0 +1,48 @@ += bio-ipcress + +{}[http://travis-ci.org/#!/wwood/bioruby-ipcress] + +Full description goes here + +Note: this software is under active development! + +== Installation + + gem install bio-ipcress + +== Usage + +== Developers + +To use the library + + require 'bio-ipcress' + +The API doc is online. For more code examples see also the test files in +the source tree. + +== Project home page + +Information on the source tree, documentation, issues and how to contribute, see + + http://github.com/wwood/bioruby-ipcress + +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 http://biogems.info/index.html#bio-ipcress + +== Copyright + +Copyright (c) 2012 Ben J Woodcroft. See LICENSE.txt for further details. + diff --git a/Rakefile b/Rakefile new file mode 100644 index 0000000..c79aa0c --- /dev/null +++ b/Rakefile @@ -0,0 +1,45 @@ +# 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 = "bio-ipcress" + gem.homepage = "http://github.com/wwood/bioruby-ipcress" + gem.license = "MIT" + gem.summary = %Q{TODO: one-line summary of your gem} + gem.description = %Q{TODO: longer description of your gem} + gem.email = "gmail.com after donttrustben" + gem.authors = ["Ben J Woodcroft"] + # 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 + +task :default => :test + +require 'rdoc/task' +Rake::RDocTask.new do |rdoc| + version = File.exist?('VERSION') ? File.read('VERSION') : "" + + rdoc.rdoc_dir = 'rdoc' + rdoc.title = "bio-ipcress #{version}" + rdoc.rdoc_files.include('README*') + rdoc.rdoc_files.include('lib/**/*.rb') +end \ No newline at end of file diff --git a/lib/bio-ipcress.rb b/lib/bio-ipcress.rb new file mode 100644 index 0000000..ef995b1 --- /dev/null +++ b/lib/bio-ipcress.rb @@ -0,0 +1,12 @@ +# 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 'bio-ipcress/ipcress.rb' + diff --git a/lib/bio-ipcress/ipcress.rb b/lib/bio-ipcress/ipcress.rb new file mode 100644 index 0000000..4617ad6 --- /dev/null +++ b/lib/bio-ipcress/ipcress.rb @@ -0,0 +1,3 @@ +module BioIpcress + +end diff --git a/test/helper.rb b/test/helper.rb new file mode 100644 index 0000000..d9cfdb1 --- /dev/null +++ b/test/helper.rb @@ -0,0 +1,18 @@ +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 'bio-ipcress' + +class Test::Unit::TestCase +end diff --git a/test/test_bio-ipcress.rb b/test/test_bio-ipcress.rb new file mode 100644 index 0000000..2677416 --- /dev/null +++ b/test/test_bio-ipcress.rb @@ -0,0 +1,7 @@ +require 'helper' + +class TestBioIpcress < 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