bindeps 0.0.1

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA1:
+  metadata.gz: 9d3bcdb20047a2dd41c765e8f0b11a7da907f64a
+  data.tar.gz: 20503629d68af6982d499746de100d8bf1872bb8
+SHA512:
+  metadata.gz: d9517fd6405d97642b1356557ff86eb96c7f60a1cd0a1c7887cbe2e4f231ab41c72ff75a04d68c87a4c83ef61d0e73085e59182708717216227573479db28f4e
+  data.tar.gz: 09224feaa1faf1ed3e32039d4be1c97f6d8bb5e70235b74b09db813320323569517114585c533df96edd3e93cdcb91db1f877c047e45dd3c2ba940efd9674f6d

data/.gitignore

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+*.gem
+*.rbc
+.bundle
+.config
+.yardoc
+Gemfile.lock
+InstalledFiles
+_yardoc
+coverage
+doc/
+lib/bundler/man
+pkg
+rdoc
+spec/reports
+test/tmp
+test/version_tmp
+tmp

data/.travis.yml

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+language: ruby
+rvm:
+  - "2.0.0"
+  - "2.1.0"

data/Gemfile

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+source 'https://rubygems.org'
+
+# Specify your gem's dependencies in bindeps.gemspec
+gemspec

data/LICENSE.txt

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+Copyright (c) 2014 Richard Smith-Unna
+
+MIT License
+
+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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+# Bindeps
+
+[![Build Status](https://travis-ci.org/Blahah/bindeps.svg)](https://travis-ci.org/Blahah/bindeps)
+[![Dependency Status](http://img.shields.io/gemnasium/Blahah/bindeps.svg)](https://gemnasium.com/Blahah/bindeps)
+[![Coverage Status](http://img.shields.io/coveralls/Blahah/bindeps.svg)](https://coveralls.io/r/Blahah/bindeps)
+[![Code Climate](http://img.shields.io/codeclimate/github/Blahah/bindeps.svg)](https://codeclimate.com/github/Blahah/bindeps)
+[![Gem Version](http://img.shields.io/gem/v/bindeps.svg)](https://rubygems.org/gems/bindeps)
+[![License](http://img.shields.io/:license-mit-blue.svg)](http://Blahah.mit-license.org)
+
+Simple binary dependency management for Ruby gems
+
+## Installation
+
+`gem install bindeps`
+
+### Using Bundler
+
+Add this line to your application's Gemfile:
+
+    gem 'bindeps'
+
+And then execute:
+
+    $ bundle
+
+Or install it yourself as:
+
+    $ gem install bindeps
+
+## Usage
+
+Create a YAML file describing your dependencies as a dictionary. Read the [bindeps YAML format specifications](wiki/bindeps_YAML_format_specifications).
+
+```yaml
+blastplus:
+  binaries:
+    - makeblastdb
+    - blastn
+    - tblastn
+    - blastp
+    - blastx
+  version:
+    number: '2.2.29'
+    command: 'blastx -version'
+  url:
+    64bit:
+      macosx: ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.29/ncbi-blast-2.2.29+-universal-macosx.tar.gz
+      linux: ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.29/ncbi-blast-2.2.29+-x64-linux.tar.gz
+bowtie2:
+  binaries:
+    - bowtie2
+    - bowtie2-align-l
+    - bowtie2-align-s
+    - bowtie2-build
+    - bowtie2-build-l
+    - bowtie2-build-s
+    - bowtie2-inspect
+    - bowtie2-inspect-l
+    - bowtie2-inspect-s
+  version:
+    number: '2.2.3'
+    command: 'bowtie2 --version'
+  url:
+    64bit:
+      linux: http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.2.3/bowtie2-2.2.3-linux-x86_64.zip
+      macosx: http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.2.3/bowtie2-2.2.3-macos-x86_64.zip
+```
+
+Then as soon as your app is executed, let `bindeps` check for and install any missing dependencies.
+
+```ruby
+require 'bindeps'
+
+Bindeps.require 'binary_dependencies.yaml'
+```
+
+`bindeps` will check run the `versioncmd` for each dependency. If the return value of the command doesn't match a regular expression test against the `version` field, `bindeps` will download the file that matches your system architecture, unpack it and place the binary in your path. If the return value does match, `bindeps` will do nothing.
+
+## Contributing
+
+1. Fork it
+2. Create your feature branch (`git checkout -b my-new-feature`)
+3. Commit your changes *with tests* (`git commit -am 'Add some feature'`)
+4. Push to the branch (`git push origin my-new-feature`)
+5. Create new Pull Request

data/Rakefile

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+require 'rake/testtask'
+
+Rake::TestTask.new do |t|
+  t.libs << 'test'
+end
+
+desc "Run tests"
+task :default => :test

data/bindeps.gemspec

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+# coding: utf-8
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'bindeps/version'
+
+Gem::Specification.new do |spec|
+  spec.name          = "bindeps"
+  spec.version       = Bindeps::VERSION
+  spec.authors       = ["Richard Smith-Unna"]
+  spec.email         = ["rds45@cam.ac.uk"]
+  spec.description   = %q{binary dependency management for ruby gems}
+  spec.summary       = %q{binary dependency management for ruby gems}
+  spec.homepage      = "https://github.com/Blahah/bindeps"
+  spec.license       = "MIT"
+
+  spec.files         = `git ls-files`.split($/)
+  spec.executables   = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
+  spec.test_files    = spec.files.grep(%r{^(test|spec|features)/})
+  spec.require_paths = ["lib"]
+
+  spec.add_dependency "which_works"
+
+  spec.add_development_dependency "bundler", "~> 1.3"
+  spec.add_development_dependency "rake"
+  spec.add_development_dependency 'turn'
+  spec.add_development_dependency 'minitest'
+  spec.add_development_dependency 'simplecov'
+  spec.add_development_dependency 'shoulda-context'
+  spec.add_development_dependency 'coveralls', '>= 0.6.7'
+end

data/lib/bindeps/version.rb

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+module Bindeps
+  VERSION = "0.0.1"
+end

data/lib/bindeps.rb

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+require "bindeps/version"
+require "unpacker"
+require "which_works"
+require "tmpdir"
+require "yaml"
+
+module Bindeps
+
+  class DownloadFailedError < StandardError; end
+  class UnsupportedSystemError < StandardError; end
+
+  def self.require dependencies
+    if dependencies.is_a? String
+      dependencies = YAML.load_file dependencies
+    end
+    tmpdir = Dir.mktmpdir
+    Dir.chdir(tmpdir) do
+      dependencies.each_pair do |name, config|
+        d = Dependency.new(name,
+                           config['binaries'],
+                           config['version'],
+                           config['url'])
+        d.install_missing
+      end
+    end
+  end
+
+  class Dependency
+
+    def initialize(name, binaries, versionconfig, urlconfig)
+      @name = name
+      unless binaries.is_a? Array
+        raise ArgumentError,
+              "binaries must be an array"
+      end
+      @binaries = binaries
+      @version = versionconfig['number']
+      @version_cmd = versionconfig['command']
+      @url = choose_url urlconfig
+    end
+
+    def install_missing
+      unless all_installed?
+        @binaries.each do |bin|
+          download
+          unpack
+          return
+        end
+      end
+    end
+
+    def choose_url urlconfig
+      arch = System.arch
+      if urlconfig.key? arch
+        sys = urlconfig[arch]
+        os = System.os.to_s
+        if sys.key? os
+          return sys[os]
+        else
+          raise UnsupportedSystemError,
+                "bindeps config for #{@name} #{arch} doesn't contain an entry for #{os}"
+        end
+      else
+        raise UnsupportedSystemError,
+              "bindeps config for #{@name} doesn't contain an entry for #{arch}"
+      end
+    end
+
+    def download
+      `curl --silent -O -J -L #{@url}`
+      unless $?.to_i == 0
+        raise DownloadFailedError,
+              "download of #{@url} for #{@name} failed"
+      end
+    end
+
+    def unpack
+      archive = File.basename(@url)
+      Unpacker.unpack(archive) do |dir|
+        Dir.chdir dir do
+          Dir['*'].each do |extracted|
+            if @binaries.include? extracted
+              install extracted
+            end
+          end
+        end
+      end
+    end
+
+    def all_installed?
+      @binaries.each do |bin|
+        return false unless installed? bin
+      end
+      true
+    end
+
+    def installed? bin
+      path = Which.which(bin)
+      if path
+        ret = `#{@version_cmd}`.strip
+        if $?.to_i == 0 && ret.equal?(@version)
+          return path
+        end
+      end
+      false
+    end
+
+    def install bin
+      bindir = File.join(ENV['GEM_HOME'], 'bin')
+      puts "installing #{bin} to #{bindir}"
+      FileUtils.cp(bin, File.join(bindir, File.basename(bin)))
+    end
+
+  end
+
+  class System
+
+    require 'rbconfig'
+
+    def self.os
+      (
+        host_os = RbConfig::CONFIG['host_os']
+        case host_os
+        when /mswin|msys|mingw|cygwin|bccwin|wince|emc/
+          :windows
+        when /darwin|mac os/
+          :macosx
+        when /linux/
+          :linux
+        when /solaris|bsd/
+          :unix
+        else
+          raise UnsupportedSystemError,
+                "can't install #{@name}, unknown os: #{host_os.inspect}"
+        end
+      )
+    end
+
+    def self.arch
+      Gem::Platform.local.cpu == 'x86_64' ? '64bit' : '32bit'
+    end
+
+  end
+
+end

data/lib/unpacker.rb

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+# Lifted from https://github.com/underlog/unpacker with the reliance on ShellShot removed
+#
+# Copyright (c) 2009 Petyo Ivanov
+#
+# 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.
+
+require 'fileutils'
+require 'tmpdir'
+
+module Unpacker
+
+  class UnrecognizedArchiveError < StandardError; end
+
+  SUPPORTED_FILEEXTS = %w[tar rar zip gz bz tgz bgz tar]
+
+  def self.unpack(file, tmpdir = "/tmp", &block)
+    Dir.mktmpdir 'unpacker' do |dir|
+      cmd = case file
+            when /rar$/
+              "unrar x -y #{file} #{dir}"
+            when /(tar|tgz|tar\.gz|tar\.bz|tbz)$/
+              "tar xvf #{file} --directory #{dir}"
+            when /zip$/
+              "unzip #{file} -d #{dir}"
+            when /gz$/
+              "gunzip -c #{file} #{File.join(dir, "gz-contents")}"
+            else
+              raise UnrecognizedArchiveError
+            end
+      puts cmd
+      puts `#{cmd}`
+      block.call Dir.new(dir)
+    end
+  end
+
+  def self.archive?(file_name)
+    SUPPORTED_FILEEXTS.include? File.extname(file_name).sub('.', '')
+  end
+
+  def self.valid?(file_path, file_name = file_path)
+    cmd = case file_name
+          when /rar$/
+            "unrar t #{file_path}"
+          when /(tar|tar\.bz|tbz)$/
+            "tar tf #{file_path}"
+          when /zip$/
+            "zip -T #{file_path}"
+          when /gz|tgz$/
+            "gunzip -t #{file_path}"
+          else
+            raise UnrecognizedArchiveError
+          end
+    `#{cmd}`
+    true
+  rescue
+    false
+  end
+
+end # module Unpacker

data/test/data/bowtie2_test.yaml

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+bowtie2:
+  binaries:
+    - bowtie2
+    - bowtie2-align-l
+    - bowtie2-align-s
+    - bowtie2-build
+    - bowtie2-build-l
+    - bowtie2-build-s
+    - bowtie2-inspect
+    - bowtie2-inspect-l
+    - bowtie2-inspect-s
+  version:
+    number: '2.2.3'
+    command: 'bowtie2 --version'
+  url:
+    64bit:
+      linux: http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.2.3/bowtie2-2.2.3-linux-x86_64.zip
+      macosx: http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.2.3/bowtie2-2.2.3-macos-x86_64.zip

data/test/data/fakebin

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+#! /bin/sh
+echo 'success'

data/test/data/fakebin.yaml

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+fakebin:
+  binaries:
+    - fakebin
+  version:
+    number: success
+    command: fakebin
+  url:
+    64bit:
+      macosx: https://github.com/Blahah/bindeps/raw/master/test/data/fakebin.tgz
+      linux: https://github.com/Blahah/bindeps/raw/master/test/data/fakebin.tgz
+      unix: https://github.com/Blahah/bindeps/raw/master/test/data/fakebin.tgz
+    32bit:
+      macosx: https://github.com/Blahah/bindeps/raw/master/test/data/fakebin.tgz
+      linux: https://github.com/Blahah/bindeps/raw/master/test/data/fakebin.tgz
+      unix: https://github.com/Blahah/bindeps/raw/master/test/data/fakebin.tgz

data/test/helper.rb

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+require 'simplecov'
+require 'coveralls'
+
+SimpleCov.formatter = SimpleCov::Formatter::MultiFormatter[
+  SimpleCov::Formatter::HTMLFormatter,
+  Coveralls::SimpleCov::Formatter
+]
+SimpleCov.start
+
+require 'minitest/autorun'
+begin; require 'turn/autorun'; rescue LoadError; end
+require 'shoulda-context'
+require 'bindeps'
+
+Turn.config.format = :pretty
+Turn.config.trace = 5
+
+require 'yaml'

data/test/test_bindeps.rb

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+require 'helper'
+
+class TestBinDeps < Test::Unit::TestCase
+
+  context "bindeps" do
+
+    setup do
+      test_dir = File.dirname(__FILE__)
+      data_dir = File.join(test_dir, 'data')
+      @test_yaml = File.join(data_dir, 'fakebin.yaml')
+    end
+
+    # teardown do
+    #
+    # end
+    #
+    # should "check if dependencies are installed" do
+    #
+    # end
+    #
+    # should "download and unpack dependencies" do
+    # end
+
+    should "identify and install missing dependencies" do
+      Bindeps.require @test_yaml
+      assert_equal 'success', `fakebin`.strip
+    end
+
+  end
+
+end

metadata

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+--- !ruby/object:Gem::Specification
+name: bindeps
+version: !ruby/object:Gem::Version
+  version: 0.0.1
+platform: ruby
+authors:
+- Richard Smith-Unna
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2014-06-26 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: which_works
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.3'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.3'
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: turn
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: minitest
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: simplecov
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: shoulda-context
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: coveralls
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 0.6.7
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 0.6.7
+description: binary dependency management for ruby gems
+email:
+- rds45@cam.ac.uk
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- ".gitignore"
+- ".travis.yml"
+- Gemfile
+- LICENSE.txt
+- README.md
+- Rakefile
+- bindeps.gemspec
+- lib/bindeps.rb
+- lib/bindeps/version.rb
+- lib/unpacker.rb
+- test/data/bowtie2_test.yaml
+- test/data/fakebin
+- test/data/fakebin.tgz
+- test/data/fakebin.yaml
+- test/helper.rb
+- test/test_bindeps.rb
+homepage: https://github.com/Blahah/bindeps
+licenses:
+- MIT
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.3.0
+signing_key: 
+specification_version: 4
+summary: binary dependency management for ruby gems
+test_files:
+- test/data/bowtie2_test.yaml
+- test/data/fakebin
+- test/data/fakebin.tgz
+- test/data/fakebin.yaml
+- test/helper.rb
+- test/test_bindeps.rb