bio-gem 1.2.1 → 1.2.2

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

@@ -45,6 +45,10 @@ class Jeweler
             self[:biogem_bin] = true
           end
 
+          o.on('--with-ffi', 'generate a C extension with foreign function interface (FFI)') do
+            self[:biogem_ffi] = true
+          end
+
           o.on('--with-db', 'create the database directory for a db application-library.') do
             self[:biogem_db] = true
           end
@@ -190,4 +194,4 @@ class Jeweler
 
     end #Options
   end #Generator
-end #Jeweler
+end #Jeweler

data/lib/bio-gem/templates/README.rdoc

@@ -0,0 +1,40 @@
+= <%= project_name %>
+
+Full description goes here
+
+Note: this software is under active development!
+
+== Installation
+
+        gem install <%= project_name %>
+
+== Usage
+
+== Developers
+
+To use the library 
+
+        require '<%= project_name %>
+
+The API doc is online. For more code examples see also the test files in
+the source tree.
+        
+== Project home page
+
+Information on the source tree, documentation, issues and how to contribute, see
+
+  <%= homepage %>
+
+== Cite
+
+  If you use this software, please cite http://dx.doi.org/10.1093/bioinformatics/btq475
+
+== Biogems.info
+
+This Biogem is published at http://biogems.info/index.html#<%= project_name %>
+
+== Copyright
+
+Copyright (c) <%= Time.now.year %> <%= user_name %>. See LICENSE.txt for further details.
+
+

data/lib/bio-gem/templates/{bin → bin/bio-plugin}

@@ -1,10 +1,8 @@
 #!/usr/bin/env ruby
 #
-# BioRuby <%= project_name %> Plugin
-# Version 0.0.0 
+# BioRuby <%= project_name %> Plugin <%= constant_name %>
 # Author:: <%= user_name %>
 # Copyright:: <%= Time.now.year %>
-# License:: The Ruby License
 
  USAGE = "Describe <%= bin_name %>"
 

data/lib/bio-gem/templates/ffi/ext.c

@@ -0,0 +1,8 @@
+/* Example of a C extension */
+
+/**
+ * Test function adds 1 to input
+ */
+int add_one(int number) {
+  return number + 1;
+}

data/lib/bio-gem/templates/ffi/ext.h

@@ -0,0 +1,10 @@
+#ifdef __cplusplus
+  extern "C" {
+#endif
+
+int add_one(int number);
+
+#ifdef __cplusplus
+}
+#endif
+

data/lib/bio-gem/templates/gitignore

@@ -0,0 +1,3 @@
+# Ignore Gemfile.lock for gems. See http://yehudakatz.com/2010/12/16/clarifying-the-roles-of-the-gemspec-and-gemfile/
+Gemfile.lock
+*.gemspec

data/lib/bio-gem/templates/lib/bioruby-plugin.rb

@@ -0,0 +1,18 @@
+# Please require your code below, respecting the naming conventions in the
+# bioruby directory tree.
+#
+# For example, say you have a plugin named bio-plugin, the only uncommented
+# line in this file would be 
+#
+#   require 'bio/bio-plugin/plugin'
+#
+# In this file only require other files. Avoid other source code.
+
+require '<%= path(project_name,lib_plugin_filename) %>'
+
+<% if options[:biogem_db] %>
+require '<%= File.join("bio",sub_module.downcase,"connect") %>'
+  <% unless options[:biogem_engine] %>
+require '<%= File.join("bio",sub_module.downcase,"example") %>'
+  <% end %>
+<% end %>

data/lib/bio-gem/templates/lib/plugin.rb

@@ -0,0 +1,3 @@
+module <%= constant_name %>
+
+end

data/test/test_bio-gem.rb

@@ -1,22 +1,24 @@
 require 'helper'
 require 'fileutils'
 
+$UNITTEST=true   # prevents github push
+
 class TestBiorubyGem < Test::Unit::TestCase
-  TEST_DIR = 'test/int_test'
+  TEST_DIR = 'test/bioruby-biogem-test'
   def setup
-    #check and create test directory
+    # 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
+    # check and remove test directory
     FileUtils.rm_rf TEST_DIR if Dir.exist?(TEST_DIR)
   end
-  
 
+  # This test creates a project named 'bioruby-biogem-test'.
   def test_create_basic_project
-    project_name = "integration"
+    project_name = "biogem-test"
     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|
@@ -26,7 +28,4 @@ class TestBiorubyGem < Test::Unit::TestCase
     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

@@ -1,19 +1,20 @@
 --- !ruby/object:Gem::Specification
 name: bio-gem
 version: !ruby/object:Gem::Version
-  version: 1.2.1
+  version: 1.2.2
   prerelease: 
 platform: ruby
 authors:
 - Raoul J.P. Bonnal
+- Pjotr Prins
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-01-05 00:00:00.000000000 Z
+date: 2012-02-16 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &2164563920 !ruby/object:Gem::Requirement
+  requirement: &2164358520 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -21,21 +22,21 @@ dependencies:
         version: 1.0.18
   type: :runtime
   prerelease: false
-  version_requirements: *2164563920
+  version_requirements: *2164358520
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &2164579040 !ruby/object:Gem::Requirement
+  requirement: &2164357900 !ruby/object:Gem::Requirement
     none: false
     requirements:
-    - - ~>
+    - - ! '>='
       - !ruby/object:Gem::Version
-        version: 1.6.4
+        version: 1.7.0
   type: :runtime
   prerelease: false
-  version_requirements: *2164579040
+  version_requirements: *2164357900
 - !ruby/object:Gem::Dependency
   name: rdoc
-  requirement: &2164578060 !ruby/object:Gem::Requirement
+  requirement: &2164357060 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -43,10 +44,10 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *2164578060
+  version_requirements: *2164357060
 - !ruby/object:Gem::Dependency
   name: shoulda
-  requirement: &2164576000 !ruby/object:Gem::Requirement
+  requirement: &2164355560 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -54,10 +55,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2164576000
+  version_requirements: *2164355560
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &2164574520 !ruby/object:Gem::Requirement
+  requirement: &2164355000 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -65,32 +66,21 @@ dependencies:
         version: 1.0.18
   type: :development
   prerelease: false
-  version_requirements: *2164574520
+  version_requirements: *2164355000
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &2164573360 !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - ~>
-      - !ruby/object:Gem::Version
-        version: 1.6.4
-  type: :development
-  prerelease: false
-  version_requirements: *2164573360
-- !ruby/object:Gem::Dependency
-  name: rcov
-  requirement: &2164572440 !ruby/object:Gem::Requirement
+  requirement: &2164354440 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
       - !ruby/object:Gem::Version
-        version: '0'
+        version: 1.7.0
   type: :development
   prerelease: false
-  version_requirements: *2164572440
+  version_requirements: *2164354440
 - !ruby/object:Gem::Dependency
   name: rdoc
-  requirement: &2164571480 !ruby/object:Gem::Requirement
+  requirement: &2164353960 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -98,11 +88,11 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2164571480
-description: ! "BioGem is a scaffold generator for those Bioinformaticans who want
+  version_requirements: *2164353960
+description: ! "Biogem is a software 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
-  a modular approach to the BioRuby package."
+  a modular approach to bioinformatics software development"
 email: ilpuccio.febo@gmail.com
 executables:
 - biogem
@@ -122,22 +112,31 @@ files:
 - VERSION
 - bin/biogem
 - bio-gem.gemspec
+- doc/biogem-hacking.md
 - lib/bio-gem.rb
 - lib/bio-gem/application.rb
+- lib/bio-gem/generator/render.rb
+- lib/bio-gem/mod/biogem-rails.rb
+- lib/bio-gem/mod/biogem.rb
 - lib/bio-gem/mod/jeweler.rb
 - lib/bio-gem/mod/jeweler/github_mixin.rb
 - lib/bio-gem/mod/jeweler/options.rb
-- lib/bio-gem/templates/bin
+- lib/bio-gem/templates/README.rdoc
+- lib/bio-gem/templates/bin/bio-plugin
 - lib/bio-gem/templates/database
 - lib/bio-gem/templates/db_connection
 - lib/bio-gem/templates/db_model
 - lib/bio-gem/templates/engine
+- lib/bio-gem/templates/ffi/ext.c
+- lib/bio-gem/templates/ffi/ext.h
 - lib/bio-gem/templates/foos_controller
 - lib/bio-gem/templates/foos_view_example
 - lib/bio-gem/templates/foos_view_index
 - lib/bio-gem/templates/foos_view_new
 - lib/bio-gem/templates/foos_view_show
-- lib/bio-gem/templates/lib
+- lib/bio-gem/templates/gitignore
+- lib/bio-gem/templates/lib/bioruby-plugin.rb
+- lib/bio-gem/templates/lib/plugin.rb
 - lib/bio-gem/templates/library
 - lib/bio-gem/templates/migration
 - lib/bio-gem/templates/rakefile
@@ -172,6 +171,5 @@ rubyforge_project:
 rubygems_version: 1.8.10
 signing_key: 
 specification_version: 3
-summary: BioGem helps Bioinformaticians start developing plugins/modules for BioRuby
-  creating a scaffold and a gem package
+summary: Biogem is a software generator for Ruby in bioinformatics
 test_files: []

data/lib/bio-gem/templates/lib

@@ -1,17 +0,0 @@
-# Please require your code below, respecting the bioruby directory tree. 
-# For instance, perhaps the only uncommented line in this file might 
-# be something like this:
-#
-#   require 'bio/sequence/awesome_sequence_plugin_thingy'
-#
-# and then create the ruby file 'lib/bio/sequence/awesome_sequence_thingy.rb'
-# and put your plugin's code there. It is bad practice to write other code 
-# directly into this file, because doing so causes confusion if this biogem 
-# was ever to get merged into the main bioruby tree.
-
-<% if options[:biogem_db] %>
-require '<%= File.join("bio",sub_module.downcase,"connect") %>'
-  <% unless options[:biogem_engine] %>
-require '<%= File.join("bio",sub_module.downcase,"example") %>'
-  <% end %>
-<% end %>