bio-gem 0.3.2 → 1.0.0

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@@ -44,7 +44,7 @@ Some of these steps have been condensed:
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  * $ biogem mystuff
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  * pass just the simple name, it will add bioruby- for the first level directory and for the github repository
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  BUT you'll require the library with bio-mystuff (and this will be the name used on rubygems)
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- * creates a basic gem structure with a default dependencies for bioruby (bio) version 1.4.1
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+ * creates a basic gem structure with a default dependencies for bioruby (bio) version 1.4.2
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  |-- bin [optional = --with-bin]
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  | `-- biomystuff (executable)
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  |-- Gemfile
@@ -126,40 +126,40 @@ These options are for Jeweler
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  == Tasks
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- rake build # Build gem into pkg/
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- rake clobber_rcov # Remove rcov products for rcov
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- rake clobber_rdoc # Remove rdoc products
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- rake console[script] # Start IRB with all runtime dependencies loaded
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- rake db:create # Create the database from config/database.yml for the current default (use db:create:all to create all dbs in the config)
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- rake db:drop # Drops the database for the current default (use db:drop:all to drop all databases)
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- rake db:fixtures:load # Load fixtures into the current environment's database.
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- rake db:migrate # Migrate the database (options: VERSION=x, VERBOSE=false).
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- rake db:migrate:status # Display status of migrations
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- rake db:rollback # Rolls the schema back to the previous version (specify steps w/ STEP=n).
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- rake db:schema:dump # Create a db/schema.rb file that can be portably used against any DB supported by AR
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- rake db:schema:load # Load a schema.rb file into the database
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- rake db:seed # Load the seed data from db/seeds.rb
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- rake db:setup # Create the database, load the schema, and initialize with the seed data (use db:reset to also drop the db first)
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- rake db:structure:dump # Dump the database structure to an SQL file
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- rake db:version # Retrieves the current schema version number
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- rake gemcutter:release # Release gem to Gemcutter
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- rake gemspec # Generate and validate gemspec
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- rake gemspec:debug # Display the gemspec for debugging purposes, as jeweler knows it (not from the filesystem)
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- rake gemspec:generate # Regenreate the gemspec on the filesystem
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- rake gemspec:release # Regenerate and validate gemspec, and then commits and pushes to git
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- rake gemspec:validate # Validates the gemspec on the filesystem
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- rake git:release # Tag and push release to git.
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- rake install # Build and install gem using `gem install`
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- rake rcov # Analyze code coverage with tests
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- rake rdoc # Build the rdoc HTML Files
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- rake release # Release gem
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- rake rerdoc # Force a rebuild of the RDOC files
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- rake test # Run tests
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- rake version # Displays the current version
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- rake version:bump:major # Bump the major version by 1
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- rake version:bump:minor # Bump the a minor version by 1
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- rake version:bump:patch # Bump the patch version by 1
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- rake version:write # Writes out an explicit version.
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+ rake build # Build gem into pkg/
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+ rake clobber_rcov # Remove rcov products for rcov
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+ rake clobber_rdoc # Remove rdoc products
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+ rake console[script] # Start IRB with all runtime dependencies loaded
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+ rake db:create # Create the database from config/database.yml for the current default (use db:create:all to create all dbs in the config)
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+ rake db:drop # Drops the database for the current default (use db:drop:all to drop all databases)
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+ rake db:fixtures:load # Load fixtures into the current environment's database.
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+ rake db:migrate # Migrate the database (options: VERSION=x, VERBOSE=false).
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+ rake db:migrate:status # Display status of migrations
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+ rake db:rollback # Rolls the schema back to the previous version (specify steps w/ STEP=n).
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+ rake db:schema:dump # Create a db/schema.rb file that can be portably used against any DB supported by AR
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+ rake db:schema:load # Load a schema.rb file into the database
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+ rake db:seed # Load the seed data from db/seeds.rb
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+ rake db:setup # Create the database, load the schema, and initialize with the seed data (use db:reset to also drop the db first)
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+ rake db:structure:dump # Dump the database structure to an SQL file
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+ rake db:version # Retrieves the current schema version number
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+ rake gemcutter:release # Release gem to Gemcutter
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+ rake gemspec # Generate and validate gemspec
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+ rake gemspec:debug # Display the gemspec for debugging purposes, as jeweler knows it (not from the filesystem)
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+ rake gemspec:generate # Regenreate the gemspec on the filesystem
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+ rake gemspec:release # Regenerate and validate gemspec, and then commits and pushes to git
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+ rake gemspec:validate # Validates the gemspec on the filesystem
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+ rake git:release # Tag and push release to git.
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+ rake install # Build and install gem using `gem install`
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+ rake rcov # Analyze code coverage with tests
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+ rake rdoc # Build the rdoc HTML Files
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+ rake release # Release gem
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+ rake rerdoc # Force a rebuild of the RDOC files
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+ rake test # Run tests
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+ rake version # Displays the current version
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+ rake version:bump:major # Bump the major version by 1
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+ rake version:bump:minor # Bump the a minor version by 1
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+ rake version:bump:patch # Bump the patch version by 1
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+ rake version:write # Writes out an explicit version.
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  == NoTes For Developers
data/VERSION CHANGED
@@ -1 +1 @@
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- 0.3.2
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+ 1.0.0
@@ -5,11 +5,11 @@
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  Gem::Specification.new do |s|
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  s.name = %q{bio-gem}
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- s.version = "0.3.2"
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+ s.version = "1.0.0"
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  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
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  s.authors = [%q{Raoul J.P. Bonnal}]
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- s.date = %q{2011-09-23}
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+ s.date = %q{2011-09-26}
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  s.description = %q{BioGem is a scaffold generator for those Bioinformaticans who want to start coding an application or a library for using/extending BioRuby core library and sharing it through rubygems.org .
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  The basic idea is to simplify and promote a modular approach to the BioRuby package.}
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  s.email = %q{ilpuccio.febo@gmail.com}
@@ -9,7 +9,7 @@ class Jeweler
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  alias original_initialize initialize
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  def initialize(options = {})
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  original_initialize(options)
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- development_dependencies << ["bio", ">= 1.4.1"]
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+ development_dependencies << ["bio", ">= 1.4.2"]
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  if options[:biogem_db]
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  development_dependencies << ["activerecord", ">= 3.0.7"]
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  development_dependencies << ["activesupport", ">= 3.0.7"]
@@ -1,5 +1,9 @@
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- require 'rubygems'
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+ require 'jeweler/generator'
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  require 'bundler'
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+ require 'bundler/cli'
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+ require 'fileutils'
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+ require 'rake'
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+
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  begin
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  Bundler.setup(:default, :development)
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  rescue Bundler::BundlerError => e
@@ -12,7 +16,8 @@ require 'shoulda'
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  $LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
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  $LOAD_PATH.unshift(File.dirname(__FILE__))
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- require 'bioruby-gem'
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+
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+ require 'bio-gem'
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  class Test::Unit::TestCase
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  end
@@ -1,7 +1,32 @@
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  require 'helper'
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+ require 'fileutils'
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  class TestBiorubyGem < Test::Unit::TestCase
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- should "probably rename this file and start testing for real" do
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- flunk "hey buddy, you should probably rename this file and start testing for real"
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+ TEST_DIR = 'test/int_test'
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+ def setup
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+ #check and create test directory
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+ FileUtils.rm_rf(TEST_DIR) if Dir.exist?(TEST_DIR)
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+ Dir.mkdir TEST_DIR
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  end
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+
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+ def teardown
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+ #check and remove tested directory
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+ FileUtils.rm_rf TEST_DIR if Dir.exist?(TEST_DIR)
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+ end
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+
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+
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+ def test_create_basic_project
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+ project_name = "integration"
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+ Dir.chdir(TEST_DIR) do
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+ application_exit = Bio::Gem::Generator::Application.run!(project_name)
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+ files_tested = %W(Gemfile lib lib/bio-#{project_name}.rb LICENSE.txt Rakefile README.rdoc test test/helper.rb test/test_bio-#{project_name}.rb).map do |file_name_to_test|
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+ File.exist?(File.join("bioruby-#{project_name}",file_name_to_test))
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+ end
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+ assert_equal [true, true, true, true, true, true, true, true, true], files_tested
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+ end
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+
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+ end
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+ # should "probably rename this file and start testing for real" do
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+ # flunk "hey buddy, you should probably rename this file and start testing for real"
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+ # end
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  end
metadata CHANGED
@@ -1,7 +1,7 @@
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  --- !ruby/object:Gem::Specification
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  name: bio-gem
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  version: !ruby/object:Gem::Version
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- version: 0.3.2
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+ version: 1.0.0
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  prerelease:
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  platform: ruby
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  authors:
@@ -9,11 +9,11 @@ authors:
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  autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2011-09-23 00:00:00.000000000Z
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+ date: 2011-09-26 00:00:00.000000000Z
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  dependencies:
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  - !ruby/object:Gem::Dependency
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  name: bundler
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- requirement: &2169062040 !ruby/object:Gem::Requirement
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+ requirement: &2164719420 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ~>
@@ -21,10 +21,10 @@ dependencies:
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  version: 1.0.18
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  type: :runtime
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  prerelease: false
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- version_requirements: *2169062040
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+ version_requirements: *2164719420
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  - !ruby/object:Gem::Dependency
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  name: jeweler
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- requirement: &2169060060 !ruby/object:Gem::Requirement
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+ requirement: &2164717980 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ~>
@@ -32,10 +32,10 @@ dependencies:
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  version: 1.6.4
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  type: :runtime
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  prerelease: false
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- version_requirements: *2169060060
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+ version_requirements: *2164717980
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  - !ruby/object:Gem::Dependency
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  name: shoulda
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- requirement: &2169058620 !ruby/object:Gem::Requirement
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+ requirement: &2164716880 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ! '>='
@@ -43,10 +43,10 @@ dependencies:
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  version: '0'
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  type: :development
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  prerelease: false
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- version_requirements: *2169058620
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+ version_requirements: *2164716880
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  - !ruby/object:Gem::Dependency
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  name: bundler
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- requirement: &2169057460 !ruby/object:Gem::Requirement
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+ requirement: &2164716080 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ~>
@@ -54,10 +54,10 @@ dependencies:
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  version: 1.0.18
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  type: :development
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  prerelease: false
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- version_requirements: *2169057460
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+ version_requirements: *2164716080
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  - !ruby/object:Gem::Dependency
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  name: jeweler
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- requirement: &2169056280 !ruby/object:Gem::Requirement
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+ requirement: &2164714920 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ~>
@@ -65,10 +65,10 @@ dependencies:
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  version: 1.6.4
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  type: :development
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  prerelease: false
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- version_requirements: *2169056280
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+ version_requirements: *2164714920
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  - !ruby/object:Gem::Dependency
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  name: rcov
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- requirement: &2169052780 !ruby/object:Gem::Requirement
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+ requirement: &2164713220 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ! '>='
@@ -76,7 +76,7 @@ dependencies:
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  version: '0'
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  type: :development
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  prerelease: false
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- version_requirements: *2169052780
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+ version_requirements: *2164713220
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  description: ! "BioGem is a scaffold generator for those Bioinformaticans who want
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  to start coding an application or a library for using/extending BioRuby core library
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  and sharing it through rubygems.org .\n The basic idea is to simplify and promote
@@ -126,7 +126,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
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  version: '0'
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  segments:
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  - 0
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- hash: 2559316480446829434
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+ hash: -913022692014142837
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  required_rubygems_version: !ruby/object:Gem::Requirement
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  none: false
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  requirements: