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Initial commit to bio-chembl.

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0 parents commit a34b012e1a396955f11cec0b8ed61a3d0f5123ea @nakao committed Jun 9, 2012
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  1. +5 −0 .document
  2. +52 −0 .gitignore
  3. +12 −0 .travis.yml
  4. +15 −0 Gemfile
  5. +20 −0 LICENSE.txt
  6. +47 −0 README.md
  7. +48 −0 README.rdoc
  8. +45 −0 Rakefile
  9. +12 −0 lib/bio-chembl.rb
  10. +3 −0 lib/bio-chembl/chembl.rb
  11. +18 −0 test/helper.rb
  12. +7 −0 test/test_bio-chembl.rb
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+lib/**/*.rb
+bin/*
+-
+features/**/*.feature
+LICENSE.txt
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+# 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
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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
15 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 "bundler", "~> 1.0.0"
+ gem "jeweler", "~> 1.8.3"
+ gem "bio", ">= 1.4.2"
+ gem "rdoc", "~> 3.12"
+end
@@ -0,0 +1,20 @@
+Copyright (c) 2012 Mitsuteru Nakao
+
+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.
@@ -0,0 +1,47 @@
+# bio-chembl
+
+[![Build Status](https://secure.travis-ci.org/nakao/bioruby-chembl.png)](http://travis-ci.org/nakao/bioruby-chembl)
+
+Full description goes here
+
+Note: this software is under active development!
+
+## Installation
+
+```sh
+ gem install bio-chembl
+```
+
+## Usage
+
+```ruby
+ require 'bio-chembl'
+```
+
+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/nakao/bioruby-chembl
+
+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-chembl](http://biogems.info/index.html)
+
+## Copyright
+
+Copyright (c) 2012 Mitsuteru Nakao. See LICENSE.txt for further details.
+
@@ -0,0 +1,48 @@
+= bio-chembl
+
+{<img
+src="https://secure.travis-ci.org/nakao/bioruby-chembl.png"
+/>}[http://travis-ci.org/#!/nakao/bioruby-chembl]
+
+Full description goes here
+
+Note: this software is under active development!
+
+== Installation
+
+ gem install bio-chembl
+
+== Usage
+
+== Developers
+
+To use the library
+
+ require 'bio-chembl'
+
+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/nakao/bioruby-chembl
+
+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-chembl
+
+== Copyright
+
+Copyright (c) 2012 Mitsuteru Nakao. See LICENSE.txt for further details.
+
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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 = "bio-chembl"
+ gem.homepage = "http://github.com/nakao/bioruby-chembl"
+ gem.license = "MIT"
+ gem.summary = %Q{TODO: one-line summary of your gem}
+ gem.description = %Q{TODO: longer description of your gem}
+ gem.email = "mitsuteru.nakao@gmail.com"
+ gem.authors = ["Mitsuteru Nakao"]
+ # 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-chembl #{version}"
+ rdoc.rdoc_files.include('README*')
+ rdoc.rdoc_files.include('lib/**/*.rb')
+end
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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 'bio-chembl/chembl.rb'
+
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+module BioChembl
+
+end
@@ -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-chembl'
+
+class Test::Unit::TestCase
+end
@@ -0,0 +1,7 @@
+require 'helper'
+
+class TestBioChembl < 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

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