bio-gem 0.3.2 → 1.0.0

data/README.rdoc

@@ -44,7 +44,7 @@ Some of these steps have been condensed:
 * $ biogem mystuff
   * pass just the simple name, it will add bioruby- for the first level directory and for the github repository
     BUT you'll require the library with bio-mystuff (and this will be the name used on rubygems)
-  * creates a basic gem structure with a default dependencies for bioruby (bio) version 1.4.1
+  * creates a basic gem structure with a default dependencies for bioruby (bio) version 1.4.2
 	    |-- bin [optional = --with-bin]
 	    |   `-- biomystuff (executable)        
 	    |-- Gemfile
@@ -126,40 +126,40 @@ These options are for Jeweler
 
 == Tasks
 
-	rake build               # Build gem into pkg/
-	rake clobber_rcov        # Remove rcov products for rcov
-	rake clobber_rdoc        # Remove rdoc products
-	rake console[script]     # Start IRB with all runtime dependencies loaded
-	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)
-	rake db:drop             # Drops the database for the current default (use db:drop:all to drop all databases)
-	rake db:fixtures:load    # Load fixtures into the current environment's database.
-	rake db:migrate          # Migrate the database (options: VERSION=x, VERBOSE=false).
-	rake db:migrate:status   # Display status of migrations
-	rake db:rollback         # Rolls the schema back to the previous version (specify steps w/ STEP=n).
-	rake db:schema:dump      # Create a db/schema.rb file that can be portably used against any DB supported by AR
-	rake db:schema:load      # Load a schema.rb file into the database
-	rake db:seed             # Load the seed data from db/seeds.rb
-	rake db:setup            # Create the database, load the schema, and initialize with the seed data (use db:reset to also drop the db first)
-	rake db:structure:dump   # Dump the database structure to an SQL file
-	rake db:version          # Retrieves the current schema version number
-	rake gemcutter:release   # Release gem to Gemcutter
-	rake gemspec             # Generate and validate gemspec
-	rake gemspec:debug       # Display the gemspec for debugging purposes, as jeweler knows it (not from the filesystem)
-	rake gemspec:generate    # Regenreate the gemspec on the filesystem
-	rake gemspec:release     # Regenerate and validate gemspec, and then commits and pushes to git
-	rake gemspec:validate    # Validates the gemspec on the filesystem
-	rake git:release         # Tag and push release to git.
-	rake install             # Build and install gem using `gem install`
-	rake rcov                # Analyze code coverage with tests
-	rake rdoc                # Build the rdoc HTML Files
-	rake release             # Release gem
-	rake rerdoc              # Force a rebuild of the RDOC files
-	rake test                # Run tests
-	rake version             # Displays the current version
-	rake version:bump:major  # Bump the major version by 1
-	rake version:bump:minor  # Bump the a minor version by 1
-	rake version:bump:patch  # Bump the patch version by 1
-	rake version:write       # Writes out an explicit version.
+    rake build               # Build gem into pkg/
+    rake clobber_rcov        # Remove rcov products for rcov
+    rake clobber_rdoc        # Remove rdoc products
+    rake console[script]     # Start IRB with all runtime dependencies loaded
+    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)
+    rake db:drop             # Drops the database for the current default (use db:drop:all to drop all databases)
+    rake db:fixtures:load    # Load fixtures into the current environment's database.
+    rake db:migrate          # Migrate the database (options: VERSION=x, VERBOSE=false).
+    rake db:migrate:status   # Display status of migrations
+    rake db:rollback         # Rolls the schema back to the previous version (specify steps w/ STEP=n).
+    rake db:schema:dump      # Create a db/schema.rb file that can be portably used against any DB supported by AR
+    rake db:schema:load      # Load a schema.rb file into the database
+    rake db:seed             # Load the seed data from db/seeds.rb
+    rake db:setup            # Create the database, load the schema, and initialize with the seed data (use db:reset to also drop the db first)
+    rake db:structure:dump   # Dump the database structure to an SQL file
+    rake db:version          # Retrieves the current schema version number
+    rake gemcutter:release   # Release gem to Gemcutter
+    rake gemspec             # Generate and validate gemspec
+    rake gemspec:debug       # Display the gemspec for debugging purposes, as jeweler knows it (not from the filesystem)
+    rake gemspec:generate    # Regenreate the gemspec on the filesystem
+    rake gemspec:release     # Regenerate and validate gemspec, and then commits and pushes to git
+    rake gemspec:validate    # Validates the gemspec on the filesystem
+    rake git:release         # Tag and push release to git.
+    rake install             # Build and install gem using `gem install`
+    rake rcov                # Analyze code coverage with tests
+    rake rdoc                # Build the rdoc HTML Files
+    rake release             # Release gem
+    rake rerdoc              # Force a rebuild of the RDOC files
+    rake test                # Run tests
+    rake version             # Displays the current version
+    rake version:bump:major  # Bump the major version by 1
+    rake version:bump:minor  # Bump the a minor version by 1
+    rake version:bump:patch  # Bump the patch version by 1
+    rake version:write       # Writes out an explicit version.
 
 
 == NoTes For Developers

data/VERSION

@@ -1 +1 @@
-0.3.2
+1.0.0

data/bio-gem.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = %q{bio-gem}
-  s.version = "0.3.2"
+  s.version = "1.0.0"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = [%q{Raoul J.P. Bonnal}]
-  s.date = %q{2011-09-23}
+  s.date = %q{2011-09-26}
   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 .
   The basic idea is to simplify and promote a modular approach to the BioRuby package.}
   s.email = %q{ilpuccio.febo@gmail.com}

data/lib/bio-gem/mod/jeweler.rb

@@ -9,7 +9,7 @@ class Jeweler
     alias original_initialize initialize
     def initialize(options = {})
       original_initialize(options)
-      development_dependencies << ["bio", ">= 1.4.1"]
+      development_dependencies << ["bio", ">= 1.4.2"]
       if options[:biogem_db]
         development_dependencies << ["activerecord", ">= 3.0.7"]
         development_dependencies << ["activesupport", ">= 3.0.7"]

data/test/helper.rb

@@ -1,5 +1,9 @@
-require 'rubygems'
+require 'jeweler/generator'
 require 'bundler'
+require 'bundler/cli'
+require 'fileutils'
+require 'rake'
+
 begin
   Bundler.setup(:default, :development)
 rescue Bundler::BundlerError => e
@@ -12,7 +16,8 @@ require 'shoulda'
 
 $LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
 $LOAD_PATH.unshift(File.dirname(__FILE__))
-require 'bioruby-gem'
+
+require 'bio-gem'
 
 class Test::Unit::TestCase
 end

data/test/test_bio-gem.rb

@@ -1,7 +1,32 @@
 require 'helper'
+require 'fileutils'
 
 class TestBiorubyGem < Test::Unit::TestCase
-  should "probably rename this file and start testing for real" do
-    flunk "hey buddy, you should probably rename this file and start testing for real"
+  TEST_DIR = 'test/int_test'
+  def setup
+    #check and create test directory
+     FileUtils.rm_rf(TEST_DIR) if Dir.exist?(TEST_DIR)
+     Dir.mkdir TEST_DIR
   end
+  
+  def teardown
+    #check and remove tested directory
+    FileUtils.rm_rf TEST_DIR if Dir.exist?(TEST_DIR)
+  end
+  
+
+  def test_create_basic_project
+    project_name = "integration"
+    Dir.chdir(TEST_DIR) do
+      application_exit = Bio::Gem::Generator::Application.run!(project_name)
+      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|
+        File.exist?(File.join("bioruby-#{project_name}",file_name_to_test))
+      end
+      assert_equal [true, true, true, true, true, true, true, true, true], files_tested
+    end
+
+  end
+  # should "probably rename this file and start testing for real" do
+  #   flunk "hey buddy, you should probably rename this file and start testing for real"
+  # end
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-gem
 version: !ruby/object:Gem::Version
-  version: 0.3.2
+  version: 1.0.0
   prerelease: 
 platform: ruby
 authors:
@@ -9,11 +9,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2011-09-23 00:00:00.000000000Z
+date: 2011-09-26 00:00:00.000000000Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &2169062040 !ruby/object:Gem::Requirement
+  requirement: &2164719420 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -21,10 +21,10 @@ dependencies:
         version: 1.0.18
   type: :runtime
   prerelease: false
-  version_requirements: *2169062040
+  version_requirements: *2164719420
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &2169060060 !ruby/object:Gem::Requirement
+  requirement: &2164717980 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -32,10 +32,10 @@ dependencies:
         version: 1.6.4
   type: :runtime
   prerelease: false
-  version_requirements: *2169060060
+  version_requirements: *2164717980
 - !ruby/object:Gem::Dependency
   name: shoulda
-  requirement: &2169058620 !ruby/object:Gem::Requirement
+  requirement: &2164716880 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -43,10 +43,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2169058620
+  version_requirements: *2164716880
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &2169057460 !ruby/object:Gem::Requirement
+  requirement: &2164716080 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -54,10 +54,10 @@ dependencies:
         version: 1.0.18
   type: :development
   prerelease: false
-  version_requirements: *2169057460
+  version_requirements: *2164716080
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &2169056280 !ruby/object:Gem::Requirement
+  requirement: &2164714920 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -65,10 +65,10 @@ dependencies:
         version: 1.6.4
   type: :development
   prerelease: false
-  version_requirements: *2169056280
+  version_requirements: *2164714920
 - !ruby/object:Gem::Dependency
   name: rcov
-  requirement: &2169052780 !ruby/object:Gem::Requirement
+  requirement: &2164713220 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -76,7 +76,7 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2169052780
+  version_requirements: *2164713220
 description: ! "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 .\n  The basic idea is to simplify and promote
@@ -126,7 +126,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: 2559316480446829434
+      hash: -913022692014142837
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements: