shaq_lib 0.0.1

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data/.gitignore ADDED
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+ /.bundle/
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+ /.yardoc
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+ /Gemfile.lock
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+ /_yardoc/
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+ /coverage/
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+ /doc/
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+ /pkg/
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+ /spec/reports/
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+ /tmp/
data/.rspec ADDED
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+ --format documentation
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+ --color
data/.ruby-gemset ADDED
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+ shaq_lib
data/.ruby-version ADDED
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+ ruby-2.3.0
data/.travis.yml ADDED
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+ language: ruby
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+ rvm:
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+ - 2.3.0
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+ before_install: gem install bundler -v 1.11.2
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+ # Contributor Code of Conduct
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+
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+ As contributors and maintainers of this project, and in the interest of
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+ fostering an open and welcoming community, we pledge to respect all people who
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+ contribute through reporting issues, posting feature requests, updating
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+ documentation, submitting pull requests or patches, and other activities.
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+
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+ We are committed to making participation in this project a harassment-free
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+ experience for everyone, regardless of level of experience, gender, gender
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+ identity and expression, sexual orientation, disability, personal appearance,
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+ body size, race, ethnicity, age, religion, or nationality.
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+
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+ Examples of unacceptable behavior by participants include:
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+
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+ * The use of sexualized language or imagery
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+ * Personal attacks
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+ * Trolling or insulting/derogatory comments
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+ * Public or private harassment
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+ * Publishing other's private information, such as physical or electronic
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+ addresses, without explicit permission
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+ * Other unethical or unprofessional conduct
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+
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+ Project maintainers have the right and responsibility to remove, edit, or
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+ reject comments, commits, code, wiki edits, issues, and other contributions
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+ that are not aligned to this Code of Conduct, or to ban temporarily or
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+ permanently any contributor for other behaviors that they deem inappropriate,
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+ threatening, offensive, or harmful.
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+
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+ By adopting this Code of Conduct, project maintainers commit themselves to
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+ fairly and consistently applying these principles to every aspect of managing
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+ this project. Project maintainers who do not follow or enforce the Code of
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+ Conduct may be permanently removed from the project team.
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+
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+ This code of conduct applies both within project spaces and in public spaces
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+ when an individual is representing the project or its community.
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+
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+ Instances of abusive, harassing, or otherwise unacceptable behavior may be
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+ reported by contacting a project maintainer at moorer@udel.edu. All
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+ complaints will be reviewed and investigated and will result in a response that
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+ is deemed necessary and appropriate to the circumstances. Maintainers are
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+ obligated to maintain confidentiality with regard to the reporter of an
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+ incident.
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+
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+ This Code of Conduct is adapted from the [Contributor Covenant][homepage],
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+ version 1.3.0, available at
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+ [http://contributor-covenant.org/version/1/3/0/][version]
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+
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+ [homepage]: http://contributor-covenant.org
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+ [version]: http://contributor-covenant.org/version/1/3/0/
data/Gemfile ADDED
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+ source 'https://rubygems.org'
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+
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+ # Specify your gem's dependencies in shaq_lib.gemspec
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+ gemspec
data/README.md ADDED
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+ # ShaqLib #
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+
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+ Library code for the [Shaq](https://github.com/mooreryan/shaq)
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+ assembler.
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+
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+ ## Installation ##
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+
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+ Add this line to your application's Gemfile:
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+
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+ ```ruby
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+ gem 'shaq_lib'
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+ ```
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+
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+ And then execute:
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+
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+ $ bundle
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+
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+ Or install it yourself as:
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+
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+ $ gem install shaq_lib
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+
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+
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+ ## Development ##
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+
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+ After checking out the repo, run `bin/setup` to install
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+ dependencies. Then, run `rake spec` to run the tests. You can also run
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+ `bin/console` for an interactive prompt that will allow you to
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+ experiment.
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+
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+ To install this gem onto your local machine, run `bundle exec rake
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+ install`. To release a new version, update the version number in
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+ `version.rb`, and then run `bundle exec rake release`, which will
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+ create a git tag for the version, push git commits and tags, and push
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+ the `.gem` file to [rubygems.org](https://rubygems.org).
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+
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+ ## Contributing ##
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+
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+ Bug reports and pull requests are welcome on GitHub at
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+ https://github.com/[mooreryan]/shaq_lib. This project is intended to be
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+ a safe, welcoming space for collaboration, and contributors are
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+ expected to adhere to the
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+ [Contributor Covenant](http://contributor-covenant.org) code of
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+ conduct.
data/Rakefile ADDED
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+ require "bundler/gem_tasks"
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+ require "rspec/core/rake_task"
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+ require "rake/extensiontask"
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+
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+ RSpec::Core::RakeTask.new(:spec)
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+
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+ task :default => :spec
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+
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+ Rake::ExtensionTask.new do |ext|
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+ ext.name = "shaq_lib"
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+ ext.ext_dir = "ext/shaq_lib"
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+ ext.lib_dir = "lib/shaq_lib"
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+ end
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+
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+ Rake::Task[:spec].prerequisites << :compile
data/bin/console ADDED
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+ #!/usr/bin/env ruby
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+
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+ require "bundler/setup"
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+ require "shaq_lib"
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+
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+ # You can add fixtures and/or initialization code here to make experimenting
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+ # with your gem easier. You can also use a different console, if you like.
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+
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+ # (If you use this, don't forget to add pry to your Gemfile!)
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+ # require "pry"
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+ # Pry.start
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+
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+ require "irb"
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+ IRB.start
data/bin/setup ADDED
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+ #!/usr/bin/env bash
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+ set -euo pipefail
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+ IFS=$'\n\t'
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+ set -vx
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+
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+ bundle install
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+
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+ # Do any other automated setup that you need to do here
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+ require "mkmf"
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+
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+ create_makefile "shaq_lib/shaq_lib"
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+ #include <ruby.h>
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+
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+ static VALUE kmers(VALUE klass, VALUE str, VALUE ksize)
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+ {
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+ long i = 0;
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+ long j = 0;
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+ long k = NUM2LONG(ksize);
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+ long num_kmers = RSTRING_LEN(str) - k + 1;
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+
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+ char *c_str = RSTRING_PTR(str);
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+
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+ for (i = 0; i < num_kmers; ++i) {
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+ char substr[k+1];
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+
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+ for (j = 0; j < k; ++j) {
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+ substr[j] = c_str[i+j];
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+ }
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+ substr[j] = '\0';
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+
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+ /* for this, put the length without the null char */
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+ rb_yield(rb_str_new(substr, k));
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+ }
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+
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+ return str;
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+ }
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+
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+ void Init_shaq_lib(void)
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+ {
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+ VALUE ModuleShaqLib = rb_define_module("ShaqLib");
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+ rb_define_singleton_method(ModuleShaqLib, "kmers", kmers, 2);
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+ }
Binary file
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+ module ShaqLib
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+ VERSION = "0.0.1"
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+ end
Binary file
data/lib/shaq_lib.rb ADDED
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+ require "shaq_lib/shaq_lib"
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+ require "shaq_lib/version"
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+
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+ module ShaqLib
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+ end
data/shaq_lib.gemspec ADDED
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+ # coding: utf-8
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+ lib = File.expand_path('../lib', __FILE__)
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+ $LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
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+ require 'shaq_lib/version'
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+
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+ Gem::Specification.new do |spec|
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+ spec.name = "shaq_lib"
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+ spec.version = ShaqLib::VERSION
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+ spec.authors = ["Ryan Moore"]
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+ spec.email = ["moorer@udel.edu"]
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+ spec.license = "GPLv3"
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+
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+ spec.summary = %q{Library code for Shaq assembler}
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+ spec.description = %q{Library code for Shaq assembler}
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+ spec.homepage = "https://github.com/mooreryan/shaq_lib"
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+
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+ spec.files = `git ls-files -z`.split("\x0").reject { |f| f.match(%r{^(test|spec|features)/}) }
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+ spec.bindir = "exe"
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+ spec.executables = spec.files.grep(%r{^exe/}) { |f| File.basename(f) }
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+ spec.require_paths = ["lib", "ext"]
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+
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+ spec.platform = Gem::Platform::RUBY
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+ spec.extensions = ["ext/shaq_lib/extconf.rb"]
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+
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+ spec.add_development_dependency "bundler", "~> 1.11"
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+ spec.add_development_dependency "rake", "~> 10.0"
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+ spec.add_development_dependency "rspec", "~> 3.0"
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+ spec.add_development_dependency "rake-compiler", "~> 0.9.7"
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+ end
metadata ADDED
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+ --- !ruby/object:Gem::Specification
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+ name: shaq_lib
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+ version: !ruby/object:Gem::Version
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+ version: 0.0.1
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+ platform: ruby
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+ authors:
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+ - Ryan Moore
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+ autorequire:
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+ bindir: exe
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+ cert_chain: []
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+ date: 2016-04-23 00:00:00.000000000 Z
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+ dependencies:
13
+ - !ruby/object:Gem::Dependency
14
+ name: bundler
15
+ requirement: !ruby/object:Gem::Requirement
16
+ requirements:
17
+ - - "~>"
18
+ - !ruby/object:Gem::Version
19
+ version: '1.11'
20
+ type: :development
21
+ prerelease: false
22
+ version_requirements: !ruby/object:Gem::Requirement
23
+ requirements:
24
+ - - "~>"
25
+ - !ruby/object:Gem::Version
26
+ version: '1.11'
27
+ - !ruby/object:Gem::Dependency
28
+ name: rake
29
+ requirement: !ruby/object:Gem::Requirement
30
+ requirements:
31
+ - - "~>"
32
+ - !ruby/object:Gem::Version
33
+ version: '10.0'
34
+ type: :development
35
+ prerelease: false
36
+ version_requirements: !ruby/object:Gem::Requirement
37
+ requirements:
38
+ - - "~>"
39
+ - !ruby/object:Gem::Version
40
+ version: '10.0'
41
+ - !ruby/object:Gem::Dependency
42
+ name: rspec
43
+ requirement: !ruby/object:Gem::Requirement
44
+ requirements:
45
+ - - "~>"
46
+ - !ruby/object:Gem::Version
47
+ version: '3.0'
48
+ type: :development
49
+ prerelease: false
50
+ version_requirements: !ruby/object:Gem::Requirement
51
+ requirements:
52
+ - - "~>"
53
+ - !ruby/object:Gem::Version
54
+ version: '3.0'
55
+ - !ruby/object:Gem::Dependency
56
+ name: rake-compiler
57
+ requirement: !ruby/object:Gem::Requirement
58
+ requirements:
59
+ - - "~>"
60
+ - !ruby/object:Gem::Version
61
+ version: 0.9.7
62
+ type: :development
63
+ prerelease: false
64
+ version_requirements: !ruby/object:Gem::Requirement
65
+ requirements:
66
+ - - "~>"
67
+ - !ruby/object:Gem::Version
68
+ version: 0.9.7
69
+ description: Library code for Shaq assembler
70
+ email:
71
+ - moorer@udel.edu
72
+ executables: []
73
+ extensions:
74
+ - ext/shaq_lib/extconf.rb
75
+ extra_rdoc_files: []
76
+ files:
77
+ - ".gitignore"
78
+ - ".rspec"
79
+ - ".ruby-gemset"
80
+ - ".ruby-version"
81
+ - ".travis.yml"
82
+ - CODE_OF_CONDUCT.md
83
+ - Gemfile
84
+ - README.md
85
+ - Rakefile
86
+ - bin/console
87
+ - bin/setup
88
+ - ext/shaq_lib/extconf.rb
89
+ - ext/shaq_lib/shaq_lib.c
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+ - lib/shaq_lib.bundle
91
+ - lib/shaq_lib.rb
92
+ - lib/shaq_lib/shaq_lib.bundle
93
+ - lib/shaq_lib/version.rb
94
+ - shaq_lib.gemspec
95
+ homepage: https://github.com/mooreryan/shaq_lib
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+ licenses:
97
+ - GPLv3
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+ metadata: {}
99
+ post_install_message:
100
+ rdoc_options: []
101
+ require_paths:
102
+ - lib
103
+ - ext
104
+ required_ruby_version: !ruby/object:Gem::Requirement
105
+ requirements:
106
+ - - ">="
107
+ - !ruby/object:Gem::Version
108
+ version: '0'
109
+ required_rubygems_version: !ruby/object:Gem::Requirement
110
+ requirements:
111
+ - - ">="
112
+ - !ruby/object:Gem::Version
113
+ version: '0'
114
+ requirements: []
115
+ rubyforge_project:
116
+ rubygems_version: 2.5.1
117
+ signing_key:
118
+ specification_version: 4
119
+ summary: Library code for Shaq assembler
120
+ test_files: []