genomer 0.0.5
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- data/.document +5 -0
- data/.gitignore +45 -0
- data/Gemfile +2 -0
- data/LICENSE.txt +20 -0
- data/README.rdoc +23 -0
- data/Rakefile +23 -0
- data/bin/genomer +18 -0
- data/cucumber.yml +2 -0
- data/features/api/annotation_ids.feature +152 -0
- data/features/api/annotation_location.feature +269 -0
- data/features/api/scaffold.feature +38 -0
- data/features/cli/create.feature +19 -0
- data/features/cli/error.feature +17 -0
- data/features/cli/help.feature +48 -0
- data/features/cli/man.feature +71 -0
- data/features/cli/plugins.feature +34 -0
- data/features/step_definitions/genomer_steps.rb +10 -0
- data/features/support/env.rb +13 -0
- data/genomer-plugin-simple/genomer-plugin-simple.gemspec +18 -0
- data/genomer-plugin-simple/lib/genomer-plugin-simple.rb +19 -0
- data/genomer-plugin-simple/man/genomer-simple-subcommand.ronn +6 -0
- data/genomer-plugin-simple/man/genomer-simple.ronn +6 -0
- data/genomer.gemspec +39 -0
- data/lib/genomer.rb +6 -0
- data/lib/genomer/error.rb +4 -0
- data/lib/genomer/plugin.rb +126 -0
- data/lib/genomer/runtime.rb +101 -0
- data/lib/genomer/version.rb +3 -0
- data/man/genomer-init.1.ronn +20 -0
- data/spec/genomer/plugin_spec.rb +341 -0
- data/spec/genomer/runtime_spec.rb +262 -0
- data/spec/spec_helper.rb +45 -0
- metadata +290 -0
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require 'spec_helper'
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describe Genomer::Runtime do
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include FakeFS::SpecHelpers
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subject do
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Genomer::Runtime.new MockSettings.new arguments, flags
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end
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let(:flags){ {} }
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let(:arguments){ [] }
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describe "with the command" do
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describe "none" do
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it "should print the short help description" do
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msg = <<-EOF
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genomer COMMAND [options]
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run `genomer help` for a list of available commands
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EOF
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subject.execute!.should == msg.unindent
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end
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end
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describe "unknown" do
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let(:arguments){ %w|unknown| }
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it "should print an error message" do
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error = <<-EOF
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Unknown command or plugin 'unknown.'
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run `genomer help` for a list of available commands
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EOF
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lambda{ subject.execute! }.should raise_error(Genomer::Error,error.unindent)
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end
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end
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describe "init" do
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let(:arguments){ %w|init project_name| }
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after do
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FileUtils.rm_rf('project_name') if File.exists?('project_name')
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end
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describe "with project name argument" do
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before do
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subject.execute!
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end
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it "should create a directory from the named argument" do
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File.exists?('project_name').should be_true
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end
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it "should create an 'assembly' directory" do
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File.exists?(File.join('project_name','assembly')).should be_true
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end
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end
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describe "when project already exists" do
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before do
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Dir.mkdir('project_name')
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end
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it "should raise an error" do
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lambda{ subject.execute! }.should raise_error(Genomer::Error,
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"Directory 'project_name' already exists.")
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end
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end
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end
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describe "help" do
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let(:arguments){ %w|help| }
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before do
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mock(Genomer::Plugin).plugins{ gems }
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end
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describe "with no available plugins" do
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let(:gems) do
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[]
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end
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it "should print the header description" do
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msg = <<-EOF
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genomer COMMAND [options]
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Available commands:
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EOF
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subject.execute!.should include msg.unindent.strip
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end
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it "should show the init command" do
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subject.execute!.should include "init Create a new genomer project"
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end
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it "should show the man command" do
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subject.execute!.should include "man View man page for the specified plugin"
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end
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end
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describe "with available genomer plugins" do
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let(:gems) do
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[Gem::Specification.new do |s|
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s.name = 'genomer-plugin-simple'
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s.summary = 'A simple scaffolder command'
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end]
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end
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it "should print the plugin command description" do
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subject.execute!.should include "simple A simple scaffolder command"
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end
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end
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end
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describe "man" do
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before do
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stub(Genomer::Plugin).plugins{ gems }
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end
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describe "with no command specified" do
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let(:arguments){ %w|man| }
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it "should print the man help description" do
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msg = <<-EOF
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genomer man COMMAND
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run `genomer help` for a list of available commands
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EOF
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subject.execute!.should include msg.unindent.strip
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end
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end
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describe "with a command specified" do
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let(:arguments){ %w|man simple| }
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let(:man_file){ 'a' }
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let(:groffed_man_file){ mock!.path{ 'b' } }
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before do
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mock(subject).man_file(['simple']){ man_file }
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mock(subject).groffed_man_file(man_file){ groffed_man_file }
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mock(File).exists?(man_file){true}
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end
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it "should call man for the groffed path" do
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mock(Kernel).exec("man b")
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subject.execute!
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end
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end
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describe "with a subcommand specified" do
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let(:arguments){ %w|man simple subcommand| }
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let(:man_file){ 'a' }
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let(:groffed_man_file){ mock!.path{ 'b' } }
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before do
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mock(subject).man_file(['simple','subcommand']){ man_file }
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mock(subject).groffed_man_file(man_file){ groffed_man_file }
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mock(File).exists?(man_file){true}
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end
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it "should call man for the groffed path" do
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mock(Kernel).exec("man b")
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subject.execute!
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end
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end
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describe "with an unknown subcommand specified" do
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let(:arguments){ %w|man simple subcommand| }
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let(:man_file){ 'a' }
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before do
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mock(subject).man_file(['simple','subcommand']){ man_file }
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mock(File).exists?(man_file){false}
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end
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it "should call man for the groffed path" do
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lambda{ subject.execute! }.
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should raise_error(Genomer::Error,"No manual entry for command 'simple subcommand'")
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end
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end
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end
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end
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describe "#initialize" do
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describe "with arguments and flags" do
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let(:arguments){ %w|init project_name| }
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let(:flags){ {:flag => 'something'} }
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it "should set the runtime variables" do
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subject.command.should == 'init'
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subject.arguments.should == ['project_name']
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subject.flags[:flag] == flags[:flag]
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end
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end
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end
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describe "#man_file" do
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before do
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mock(Genomer::Plugin).fetch('simple') do
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mock!.full_gem_path{ '/tmp' }
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end
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end
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it "should return the path to the man page for a command" do
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subject.man_file(['simple']).should == '/tmp/man/genomer-simple.ronn'
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end
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it "should return the path to the man page for a subcommand" do
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subject.man_file(['simple','subcommand']).should == '/tmp/man/genomer-simple-subcommand.ronn'
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end
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end
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describe "#run_plugin" do
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before do
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mock(Genomer::Plugin).[]('plugin') do
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mock!.new(anything,anything) do
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mock!.run
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end
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end
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end
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let(:arguments){ %w|plugin arg1 arg2| }
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let(:flags){ {:flag => 'arg3'} }
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it "should fetch, initialize and run the required plugin" do
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subject.run_plugin
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end
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end
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end
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data/spec/spec_helper.rb
ADDED
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$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
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require 'rspec'
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require 'fakefs/spec_helpers'
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require 'scaffolder/test/helpers'
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require 'genomer'
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# Requires supporting files with custom matchers and macros, etc,
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# in ./support/ and its subdirectories.
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Dir["#{File.dirname(__FILE__)}/support/**/*.rb"].each do |f|
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require File.expand_path(f)
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end
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RSpec.configure do |config|
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config.mock_with :rr
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include Scaffolder::Test
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include Scaffolder::Test::Helpers
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class MockSettings
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attr :rest
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def initialize(rest = [], command_args = {})
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@rest = rest
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@args = command_args
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end
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def [](arg)
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@args[arg]
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end
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def flags
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@args
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end
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end
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config.after(:each) do
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instance_variables.each do |ivar|
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instance_variable_set(ivar, nil)
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end
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end
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end
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metadata
ADDED
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--- !ruby/object:Gem::Specification
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name: genomer
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version: !ruby/object:Gem::Version
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version: 0.0.5
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prerelease:
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platform: ruby
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authors:
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- Michael Barton
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autorequire:
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bindir: bin
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cert_chain: []
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date: 2012-05-28 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: rake
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requirement: !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ~>
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- !ruby/object:Gem::Version
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version: 0.9.0
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type: :runtime
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ~>
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- !ruby/object:Gem::Version
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version: 0.9.0
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- !ruby/object:Gem::Dependency
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name: bundler
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requirement: !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ~>
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- !ruby/object:Gem::Version
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version: 1.1.0
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type: :runtime
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ~>
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- !ruby/object:Gem::Version
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version: 1.1.0
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- !ruby/object:Gem::Dependency
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name: configliere
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requirement: !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ~>
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- !ruby/object:Gem::Version
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version: 0.4.8
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type: :runtime
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ~>
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- !ruby/object:Gem::Version
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version: 0.4.8
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- !ruby/object:Gem::Dependency
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name: scaffolder
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requirement: !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ~>
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- !ruby/object:Gem::Version
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version: 0.4.0
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type: :runtime
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ~>
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- !ruby/object:Gem::Version
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version: 0.4.0
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- !ruby/object:Gem::Dependency
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name: scaffolder-annotation-locator
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requirement: !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ! '>='
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- !ruby/object:Gem::Version
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version: 0.1.2
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type: :runtime
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
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none: false
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requirements:
|
91
|
+
- - ! '>='
|
92
|
+
- !ruby/object:Gem::Version
|
93
|
+
version: 0.1.2
|
94
|
+
- !ruby/object:Gem::Dependency
|
95
|
+
name: unindent
|
96
|
+
requirement: !ruby/object:Gem::Requirement
|
97
|
+
none: false
|
98
|
+
requirements:
|
99
|
+
- - ~>
|
100
|
+
- !ruby/object:Gem::Version
|
101
|
+
version: 1.0.0
|
102
|
+
type: :runtime
|
103
|
+
prerelease: false
|
104
|
+
version_requirements: !ruby/object:Gem::Requirement
|
105
|
+
none: false
|
106
|
+
requirements:
|
107
|
+
- - ~>
|
108
|
+
- !ruby/object:Gem::Version
|
109
|
+
version: 1.0.0
|
110
|
+
- !ruby/object:Gem::Dependency
|
111
|
+
name: ronn
|
112
|
+
requirement: !ruby/object:Gem::Requirement
|
113
|
+
none: false
|
114
|
+
requirements:
|
115
|
+
- - ~>
|
116
|
+
- !ruby/object:Gem::Version
|
117
|
+
version: 0.7.3
|
118
|
+
type: :runtime
|
119
|
+
prerelease: false
|
120
|
+
version_requirements: !ruby/object:Gem::Requirement
|
121
|
+
none: false
|
122
|
+
requirements:
|
123
|
+
- - ~>
|
124
|
+
- !ruby/object:Gem::Version
|
125
|
+
version: 0.7.3
|
126
|
+
- !ruby/object:Gem::Dependency
|
127
|
+
name: rspec
|
128
|
+
requirement: !ruby/object:Gem::Requirement
|
129
|
+
none: false
|
130
|
+
requirements:
|
131
|
+
- - ~>
|
132
|
+
- !ruby/object:Gem::Version
|
133
|
+
version: 2.7.0
|
134
|
+
type: :development
|
135
|
+
prerelease: false
|
136
|
+
version_requirements: !ruby/object:Gem::Requirement
|
137
|
+
none: false
|
138
|
+
requirements:
|
139
|
+
- - ~>
|
140
|
+
- !ruby/object:Gem::Version
|
141
|
+
version: 2.7.0
|
142
|
+
- !ruby/object:Gem::Dependency
|
143
|
+
name: fakefs
|
144
|
+
requirement: !ruby/object:Gem::Requirement
|
145
|
+
none: false
|
146
|
+
requirements:
|
147
|
+
- - ~>
|
148
|
+
- !ruby/object:Gem::Version
|
149
|
+
version: 0.4.0
|
150
|
+
type: :development
|
151
|
+
prerelease: false
|
152
|
+
version_requirements: !ruby/object:Gem::Requirement
|
153
|
+
none: false
|
154
|
+
requirements:
|
155
|
+
- - ~>
|
156
|
+
- !ruby/object:Gem::Version
|
157
|
+
version: 0.4.0
|
158
|
+
- !ruby/object:Gem::Dependency
|
159
|
+
name: rr
|
160
|
+
requirement: !ruby/object:Gem::Requirement
|
161
|
+
none: false
|
162
|
+
requirements:
|
163
|
+
- - ~>
|
164
|
+
- !ruby/object:Gem::Version
|
165
|
+
version: 1.0.4
|
166
|
+
type: :development
|
167
|
+
prerelease: false
|
168
|
+
version_requirements: !ruby/object:Gem::Requirement
|
169
|
+
none: false
|
170
|
+
requirements:
|
171
|
+
- - ~>
|
172
|
+
- !ruby/object:Gem::Version
|
173
|
+
version: 1.0.4
|
174
|
+
- !ruby/object:Gem::Dependency
|
175
|
+
name: scaffolder-test-helpers
|
176
|
+
requirement: !ruby/object:Gem::Requirement
|
177
|
+
none: false
|
178
|
+
requirements:
|
179
|
+
- - ~>
|
180
|
+
- !ruby/object:Gem::Version
|
181
|
+
version: 0.4.0
|
182
|
+
type: :development
|
183
|
+
prerelease: false
|
184
|
+
version_requirements: !ruby/object:Gem::Requirement
|
185
|
+
none: false
|
186
|
+
requirements:
|
187
|
+
- - ~>
|
188
|
+
- !ruby/object:Gem::Version
|
189
|
+
version: 0.4.0
|
190
|
+
- !ruby/object:Gem::Dependency
|
191
|
+
name: cucumber
|
192
|
+
requirement: !ruby/object:Gem::Requirement
|
193
|
+
none: false
|
194
|
+
requirements:
|
195
|
+
- - ~>
|
196
|
+
- !ruby/object:Gem::Version
|
197
|
+
version: 1.1.4
|
198
|
+
type: :development
|
199
|
+
prerelease: false
|
200
|
+
version_requirements: !ruby/object:Gem::Requirement
|
201
|
+
none: false
|
202
|
+
requirements:
|
203
|
+
- - ~>
|
204
|
+
- !ruby/object:Gem::Version
|
205
|
+
version: 1.1.4
|
206
|
+
- !ruby/object:Gem::Dependency
|
207
|
+
name: aruba
|
208
|
+
requirement: !ruby/object:Gem::Requirement
|
209
|
+
none: false
|
210
|
+
requirements:
|
211
|
+
- - ~>
|
212
|
+
- !ruby/object:Gem::Version
|
213
|
+
version: 0.4.11
|
214
|
+
type: :development
|
215
|
+
prerelease: false
|
216
|
+
version_requirements: !ruby/object:Gem::Requirement
|
217
|
+
none: false
|
218
|
+
requirements:
|
219
|
+
- - ~>
|
220
|
+
- !ruby/object:Gem::Version
|
221
|
+
version: 0.4.11
|
222
|
+
description: Turns scaffolded contigs and annotations into a genome.
|
223
|
+
email:
|
224
|
+
- mail@michaelbarton.me.uk
|
225
|
+
executables:
|
226
|
+
- genomer
|
227
|
+
extensions: []
|
228
|
+
extra_rdoc_files: []
|
229
|
+
files:
|
230
|
+
- .document
|
231
|
+
- .gitignore
|
232
|
+
- Gemfile
|
233
|
+
- LICENSE.txt
|
234
|
+
- README.rdoc
|
235
|
+
- Rakefile
|
236
|
+
- bin/genomer
|
237
|
+
- cucumber.yml
|
238
|
+
- features/api/annotation_ids.feature
|
239
|
+
- features/api/annotation_location.feature
|
240
|
+
- features/api/scaffold.feature
|
241
|
+
- features/cli/create.feature
|
242
|
+
- features/cli/error.feature
|
243
|
+
- features/cli/help.feature
|
244
|
+
- features/cli/man.feature
|
245
|
+
- features/cli/plugins.feature
|
246
|
+
- features/step_definitions/genomer_steps.rb
|
247
|
+
- features/support/env.rb
|
248
|
+
- genomer-plugin-simple/genomer-plugin-simple.gemspec
|
249
|
+
- genomer-plugin-simple/lib/genomer-plugin-simple.rb
|
250
|
+
- genomer-plugin-simple/man/genomer-simple-subcommand.ronn
|
251
|
+
- genomer-plugin-simple/man/genomer-simple.ronn
|
252
|
+
- genomer.gemspec
|
253
|
+
- lib/genomer.rb
|
254
|
+
- lib/genomer/error.rb
|
255
|
+
- lib/genomer/plugin.rb
|
256
|
+
- lib/genomer/runtime.rb
|
257
|
+
- lib/genomer/version.rb
|
258
|
+
- man/genomer-init.1.ronn
|
259
|
+
- spec/genomer/plugin_spec.rb
|
260
|
+
- spec/genomer/runtime_spec.rb
|
261
|
+
- spec/spec_helper.rb
|
262
|
+
homepage: http://github.com/michaelbarton/genomer
|
263
|
+
licenses:
|
264
|
+
- MIT
|
265
|
+
post_install_message:
|
266
|
+
rdoc_options: []
|
267
|
+
require_paths:
|
268
|
+
- lib
|
269
|
+
required_ruby_version: !ruby/object:Gem::Requirement
|
270
|
+
none: false
|
271
|
+
requirements:
|
272
|
+
- - ! '>='
|
273
|
+
- !ruby/object:Gem::Version
|
274
|
+
version: '0'
|
275
|
+
segments:
|
276
|
+
- 0
|
277
|
+
hash: 4331820328226072819
|
278
|
+
required_rubygems_version: !ruby/object:Gem::Requirement
|
279
|
+
none: false
|
280
|
+
requirements:
|
281
|
+
- - ! '>='
|
282
|
+
- !ruby/object:Gem::Version
|
283
|
+
version: 1.8.0
|
284
|
+
requirements: []
|
285
|
+
rubyforge_project: genomer
|
286
|
+
rubygems_version: 1.8.23
|
287
|
+
signing_key:
|
288
|
+
specification_version: 3
|
289
|
+
summary: Build genome output files
|
290
|
+
test_files: []
|