bio-gem 1.2.1 → 1.2.2

data/lib/bio-gem.rb

@@ -1,3 +1,4 @@
 #load Jeweler's mod for adapting it to our BioGem Project
+require 'bio-gem/generator/render'
 require 'bio-gem/mod/jeweler'
-require 'bio-gem/application'
+require 'bio-gem/application'

data/lib/bio-gem/application.rb

@@ -46,7 +46,7 @@ module Bio
               $stderr.puts %Q{No github.token found in ~/.gitconfig. Please tell git about your GitHub account (see http://github.com/blog/180-local-github-config for details). For example: git config --global github.token 6ef8395fecf207165f1a82178ae1b984}
               return {:exit=>1}
             rescue Jeweler::FileInTheWay
-              $stderr.puts "The directory #{options[:project_name]} already exists. Maybe move it out of the way before continuing?"
+              $stderr.puts "The directory for #{options[:project_name]} already exists. Maybe move it out of the way before continuing?"
               return {:exit=>1}
             end
           end #run!

data/lib/bio-gem/generator/render.rb

@@ -0,0 +1,144 @@
+module Biogem
+  module Render
+    # new hook for removing stuff
+    def after_render_template(source,buf)
+      if source == 'other_tasks.erb'
+        $stdout.puts "\tremove jeweler rcov lines"
+        # remove rcov related lines from jeweler Rakefile
+        remove = "require 'rcov/rcovtask'"
+        if buf =~ /#{remove}/
+          # $stdout.puts buf,'---'
+          buf1 = buf.split(/\n/)
+          i = buf1.index(remove)
+          buf = (buf1[0..i-1] + buf1[i+7..-1]).join("\n")
+        end
+      end
+      buf
+    end
+
+    def render_template_generic(source, template_dir = template_dir_biogem)
+      template_contents = File.read(path(template_dir, source))
+      template          = ERB.new(template_contents, nil, '<>')
+
+      # squish extraneous whitespace from some of the conditionals
+      template.result(binding).gsub(/\n\n\n+/, "\n\n")
+    end
+
+    def output_template_in_target_generic(source, destination = source, template_dir = template_dir_biogem)
+      final_destination = path(target_dir, destination)
+      template_result   = render_template_generic(source, template_dir)
+
+      File.open(final_destination, 'w') {|file| file.write(template_result)}
+      $stdout.puts "\tcreate\t#{destination}"
+    end
+
+    def output_template_in_target_generic_append(source, destination = source, template_dir = template_dir_biogem)
+      final_destination = path(target_dir, destination)
+      template_result   = render_template_generic(source, template_dir)
+
+      File.open(final_destination, 'a') {|file| file.write(template_result)}
+
+      $stdout.puts "\tappend\t#{destination}"
+    end    
+
+    def template_dir_biogem
+      path(File.dirname(__FILE__),'..', 'templates')
+    end
+
+    def create_plugin_files
+      if options[:biogem_meta]
+        create_meta 
+      else
+        original_create_files
+        create_lib
+        create_bin if options[:biogem_bin]
+        create_test_data if options[:biogem_test_data]
+        create_ffi_structure if options[:biogem_ffi]
+        create_db_structure if options[:biogem_db]
+        create_rails_engine if options[:biogem_engine]
+      end 
+      # Always do these
+      output_template_in_target_generic 'README.rdoc'
+      output_template_in_target_generic_append 'gitignore', '.gitignore'
+    end
+
+    def create_meta
+      # this section is for Biogem META packages only!
+      unless File.exists?(target_dir) || File.directory?(target_dir)
+        FileUtils.mkdir target_dir
+      else
+        raise FileInTheWay, "The directory #{target_dir} already exists, aborting. Maybe move it out of the way before continuing?"
+      end
+      output_template_in_target '.gitignore'
+      output_template_in_target 'Rakefile'
+      output_template_in_target 'Gemfile'  if should_use_bundler
+      output_template_in_target 'LICENSE.txt'
+      output_template_in_target '.document'
+    end
+
+    def create_lib
+      output_template_in_target_generic path('lib/bioruby-plugin.rb'), path(lib_dir, lib_filename)
+      mkdir_in_target(lib_plugin_dir)
+      output_template_in_target_generic path('lib/plugin.rb'), path(lib_dir, project_name, lib_plugin_filename)
+    end
+
+    def create_bin
+      # create the 'binary' in ./bin
+      mkdir_in_target bin_dir
+      output_template_in_target_generic path('bin/bio-plugin'), path(bin_dir, bin_name)
+      # TODO: set the file as executable (Windows?)
+      File.chmod 0655, path(target_dir, bin_dir, bin_name)
+    end
+
+    def create_test_data
+      mkdir_in_target("test") unless File.exists? "#{target_dir}/test"
+      mkdir_in_target test_data_dir  
+    end
+
+    def create_ffi_structure
+      # create ./ext/src and ./ext/include for the .c and .h files
+      mkdir_in_target(ext_dir)
+      src_dir = path(ext_dir,'src')
+      mkdir_in_target(src_dir)
+      # create ./lib/ffi for the Ruby ffi
+      mkdir_in_target(path(lib_dir,"ffi"))
+      # copy C files
+      output_template_in_target_generic path('ffi/ext.c'), path(src_dir, "ext.c" )
+      output_template_in_target_generic path('ffi/ext.h'), path(src_dir, "ext.h" )
+    end
+
+    def create_db_structure
+      migrate_dir = path(db_dir, "migrate")
+      mkdir_in_target(db_dir)
+      mkdir_in_target(migrate_dir)
+      mkdir_in_target("config") unless exists_dir?("config")
+      mkdir_in_target(path("lib/bio"))
+      mkdir_in_target(lib_sub_module)
+      output_template_in_target_generic 'database', path("config/database.yml")
+      output_template_in_target_generic 'migration', path(migrate_dir,"001_create_example.rb" )
+      output_template_in_target_generic 'seeds', path(db_dir, "seeds.rb")
+      output_template_in_target_generic_append 'rakefile', 'Rakefile', template_dir_biogem
+      #TODO I'd like to have a parameter from command like with defines the Namespace of the created bio-gem to automatically costruct directory structure
+      output_template_in_target_generic 'db_connection', path(lib_sub_module,"connect.rb")
+      output_template_in_target_generic 'db_model', path(lib_sub_module,"example.rb")
+    end
+
+    def create_rails_engine
+      # create the structures and files needed to have a ready to go Rails' engine
+      namespace = options[:biogem_engine] # are we using this?
+      engine_dirs.each do |dir|
+        mkdir_in_target(dir) unless exists_dir?(dir)
+      end
+      output_template_in_target_generic 'engine', path('lib', engine_filename )
+      output_template_in_target_generic_append 'library', path('lib', lib_filename)
+      output_template_in_target_generic 'routes', path('config', "routes.rb" )
+      output_template_in_target_generic 'foos_controller', path('app',"controllers", "foos_controller.rb" )
+      output_template_in_target_generic 'foos_view_index', path('app',"views","foos", "index.html.erb" )
+      output_template_in_target_generic 'foos_view_show', path('app',"views","foos", "show.html.erb" )
+      output_template_in_target_generic 'foos_view_example', path('app',"views","foos", "example.html.erb" )
+      output_template_in_target_generic 'foos_view_new', path('app',"views","foos", "new.html.erb" )
+    end
+  end
+
+
+end

data/lib/bio-gem/mod/biogem-rails.rb

@@ -0,0 +1,14 @@
+# Using Biogem with Rails
+
+class String
+  # Handle underscore in routing template
+  def underscore
+    self.gsub(/::/, '/').
+    gsub(/([A-Z]+)([A-Z][a-z])/,'\1_\2').
+    gsub(/([a-z\d])([A-Z])/,'\1_\2').
+    tr("-", "_").
+    downcase
+  end
+end
+
+

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

@@ -0,0 +1,107 @@
+# Biogem helpers for templates
+
+module Biogem
+  module Path
+
+    def path(*items)
+      File.join(*items).gsub(File::SEPARATOR, File::ALT_SEPARATOR || File::SEPARATOR)
+    end
+
+    def exists_dir?(dir)
+      Dir.exists?(path(target_dir,dir))
+    end
+
+    def short_name
+      original_project_name.sub(/^bio-/,'')
+    end
+
+
+    def lib_dir
+      'lib'
+    end
+
+    def lib_filename
+      "#{project_name}.rb"
+    end
+
+    def lib_plugin_dir
+      path(lib_dir, project_name)
+    end
+
+    def lib_plugin_filename
+      short_name + ".rb"
+    end
+
+    def require_name
+      project_name
+    end
+
+    def test_data_dir
+      'test/data'
+    end
+
+    def db_dir
+      'db'
+    end
+
+    def bin_dir
+      'bin'
+    end
+
+    def ext_dir
+      'ext'
+    end
+
+    def bin_name
+      "#{original_project_name}"
+    end
+  end
+
+  module Naming
+    def engine_dirs
+      %w{app app/controllers app/views app/helpers config app/views/foos}
+    end
+
+    def engine_name
+      "#{project_name}-engine"
+    end
+
+    def engine_filename
+      "#{engine_name}.rb"
+    end
+
+    def engine_module_name
+      module_name = project_name.split('-').map{|module_sub_name| module_sub_name.capitalize}.join
+      module_name.instance_eval do
+        # Handle underscore in routing template
+        def underscore
+          self.gsub(/::/, '/').
+          gsub(/([A-Z]+)([A-Z][a-z])/,'\1_\2').
+          gsub(/([a-z\d])([A-Z])/,'\1_\2').
+          tr("-", "_").
+          downcase
+        end
+      end
+      module_name
+    end
+
+    def engine_name_prefix
+      project_name.split('-').gsub(/-/,'_')<<'_'
+    end
+
+    def engine_namespace
+      "/#{options[:biogem_engine]}"
+    end
+    
+    def sub_module
+      project_name.split('-')[1..-1].map{|x| x.capitalize}.join
+    end
+    
+    def lib_sub_module
+      path(lib_dir,"bio",sub_module.downcase)
+    end
+  end
+
+  module Github
+  end
+end

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

@@ -1,25 +1,25 @@
-#Overdrive Jeweler's classes for properly configure a BioRuby Development Environment/Layout.
+#Override Jeweler's classes for properly configure a BioRuby Development Environment/Layout.
+# This module should only include methods that are overridden in Jeweler (by
+# breaking open the Jeweler::Generator class
 
 require 'bio-gem/mod/jeweler/options'
 require 'bio-gem/mod/jeweler/github_mixin'
-
-class String
-  def underscore
-    self.gsub(/::/, '/').
-    gsub(/([A-Z]+)([A-Z][a-z])/,'\1_\2').
-    gsub(/([a-z\d])([A-Z])/,'\1_\2').
-    tr("-", "_").
-    downcase
-  end
-end
+require 'bio-gem/mod/biogem'
 
 class Jeweler
   class Generator 
 
+    include Biogem::Naming
+    include Biogem::Path
+    include Biogem::Render
+    include Biogem::Github
+
     alias original_initialize initialize
     def initialize(options = {})
       original_initialize(options)
       development_dependencies << ["bio", ">= 1.4.2"]
+      # RCov is not properly supported for Ruby 1.9.2, so we remove it
+      development_dependencies.delete_if { |k,v| k == "rcov" }
       if options[:biogem_db]
         development_dependencies << ["activerecord", ">= 3.0.7"]
         development_dependencies << ["activesupport", ">= 3.0.7"]
@@ -29,184 +29,44 @@ class Jeweler
 
     alias original_project_name project_name  
     def project_name
-      prj_name = original_project_name=~/^bio-/ ? original_project_name : "bio-#{original_project_name}" 
-      prj_name
+      name = original_project_name
+      return 'bio-'+name if name !~ /^bio-/
+      name
     end
 
-    def lib_dir
-      'lib'
-    end
-
-    def lib_filename
-      "#{project_name}.rb"
+    alias original_render_template render_template
+    def render_template(source)
+      buf = original_render_template(source)
+      # call hook (returns edited buf)
+      after_render_template(source,buf)
     end
 
     def target_dir
-      project_name.gsub('bio','bioruby')
+      project_name.sub('bio','bioruby')
     end      
     alias github_repo_name target_dir
 
-    def require_name
-      project_name
-    end
-
-    def test_data_dir
-      'test/data'
-    end
-
-    def db_dir
-      'db'
-    end
-
-    def bin_dir
-      'bin'
-    end
-
-    def bin_name
-      "bio#{original_project_name}"
-    end
-
-    def engine_dirs
-      %w{app app/controllers app/views app/helpers config app/views/foos}
-    end
-
-    def engine_name
-      "#{project_name}-engine"
-    end
-
-    def engine_filename
-      "#{engine_name}.rb"
-    end
-
-    def engine_module_name
-      project_name.split('-').map{|module_sub_name| module_sub_name.capitalize}.join      
-    end
-
-    def engine_name_prefix
-      project_name.split('-').gsub(/-/,'_')<<'_'
-    end
-
-    def engine_namespace
-      "/#{options[:biogem_engine]}"
-    end
-    
-    def sub_module
-      project_name.split('-')[1..-1].map{|x| x.capitalize}.join
-    end
-    
-    def lib_sub_module
-      File.join(lib_dir,"bio",sub_module.downcase)
-    end
-    
-    def exists_dir?(dir)
-      Dir.exists?(File.join(target_dir,dir))
-    end
-
-    def render_template_generic(source, template_dir = template_dir_biogem)
-      template_contents = File.read(File.join(template_dir, source))
-      template          = ERB.new(template_contents, nil, '<>')
-
-      # squish extraneous whitespace from some of the conditionals
-      template.result(binding).gsub(/\n\n\n+/, "\n\n")
-    end
-
-    def output_template_in_target_generic(source, destination = source, template_dir = template_dir_biogem, write_type='w')
-      final_destination = File.join(target_dir, destination)
-      template_result   = render_template_generic(source, template_dir)
-
-      File.open(final_destination, write_type) {|file| file.write(template_result)}
-      status = case write_type
-      when 'w' then 'create'
-      when 'a' then 'update'
-      end
-      $stdout.puts "\t#{status}\t#{destination}"
-    end
-
-    def output_template_in_target_generic_update(source, destination = source, template_dir = template_dir_biogem)
-      final_destination = File.join(target_dir, destination)
-      template_result   = render_template_generic(source, template_dir)
-
-      File.open(final_destination, 'a') {|file| file.write(template_result)}
-
-      $stdout.puts "\tcreate\t#{destination}"
-    end    
-
-    def template_dir_biogem
-      File.join(File.dirname(__FILE__),'..', 'templates')
-    end
-
-
-    def create_db_structure
-      migrate_dir = File.join(db_dir, "migrate")
-      mkdir_in_target(db_dir)
-      mkdir_in_target(migrate_dir)
-      mkdir_in_target("config") unless exists_dir?("config")
-      mkdir_in_target("lib/bio")
-      mkdir_in_target(lib_sub_module)
-      output_template_in_target_generic 'database', File.join("config", "database.yml")
-      output_template_in_target_generic 'migration', File.join(migrate_dir, "001_create_example.rb" )
-      output_template_in_target_generic 'seeds', File.join(db_dir, "seeds.rb")
-      output_template_in_target_generic 'rakefile', 'Rakefile', template_dir_biogem, 'a' #need to spec all the option to enable the append option
-      #TODO I'd like to have a parameter from command like with defines the Namespace of the created bio-gem to automatically costruct directory structure
-      output_template_in_target_generic 'db_connection', File.join(lib_sub_module,"connect.rb")
-      output_template_in_target_generic 'db_model', File.join(lib_sub_module,"example.rb")
-    end
-
     alias original_create_files create_files
     # this is the default directory for storing library datasets
     # creates a data directory for every needs.
     #the options are defined in mod/jeweler/options.rb
     def create_files
-      if options[:biogem_meta]
-
-        unless File.exists?(target_dir) || File.directory?(target_dir)
-          FileUtils.mkdir target_dir
-        else
-          raise FileInTheWay, "The directory #{target_dir} already exists, aborting. Maybe move it out of the way before continuing?"
-        end
-
-        output_template_in_target '.gitignore'
-        output_template_in_target 'Rakefile'
-        output_template_in_target 'Gemfile'  if should_use_bundler
-        output_template_in_target 'LICENSE.txt'
-        output_template_in_target 'README.rdoc'
-        output_template_in_target '.document'
-      else
-        original_create_files
-
-        if options[:biogem_test_data]
-          mkdir_in_target("test") unless File.exists? "#{target_dir}/test"
-          mkdir_in_target test_data_dir  
-        end
-        create_db_structure if options[:biogem_db]
-        if options[:biogem_bin] 
-          mkdir_in_target bin_dir
-          output_template_in_target_generic 'bin', File.join(bin_dir, bin_name)
-          # TODO: set the file as executable
-          File.chmod 0655, File.join(target_dir, bin_dir, bin_name)
-        end
-
-        # Fill lib/bio-plugin.rb with some default comments
-        output_template_in_target_generic 'lib', File.join(lib_dir, lib_filename)
+      create_plugin_files
+    end
 
-        #creates the strutures and files needed to have a ready to go Rails' engine
-        if namespace=options[:biogem_engine]
-          engine_dirs.each do |dir|
-            mkdir_in_target(dir) unless exists_dir?(dir)
-          end
-          output_template_in_target_generic 'engine', File.join('lib', engine_filename )
-          output_template_in_target_generic_update 'library', File.join('lib', lib_filename)
-          output_template_in_target_generic 'routes', File.join('config', "routes.rb" )
-          output_template_in_target_generic 'foos_controller', File.join('app',"controllers", "foos_controller.rb" )
-          output_template_in_target_generic 'foos_view_index', File.join('app',"views","foos", "index.html.erb" )
-          output_template_in_target_generic 'foos_view_show', File.join('app',"views","foos", "show.html.erb" )
-          output_template_in_target_generic 'foos_view_example', File.join('app',"views","foos", "example.html.erb" )
-          output_template_in_target_generic 'foos_view_new', File.join('app',"views","foos", "new.html.erb" )
-        end
-      end #not_bio_gem_meta
+    def puts_template_message(message, length=70, padding=4)
+      puts "*"*(length+padding*2+2)
+      puts "*"+" "*(length+padding*2)+"*"
+      message=message.join("\n") if message.kind_of? Array
+      message.scan(/.{1,70}/).map do |sub_message|
+        puts "*"+" "*padding+sub_message+" "*(length-sub_message.size+padding)+"*"
+      end
+      puts "*"+" "*(length+padding*2)+"*"
+      puts "*"*(length+padding*2+2)
     end
 
     def create_and_push_repo
+      return if $UNITTEST  # skip github create when testing
       begin 
         Net::HTTP.post_form URI.parse('http://github.com/api/v2/yaml/repos/create'),
         'login' => github_username,
@@ -221,17 +81,5 @@ class Jeweler
         puts_template_message("Seems you are not connected to Internet, can't create a remote repository. Do not forget to create it by hand, from GitHub, and sync it with this project.")
       end
     end
-
-
-    def puts_template_message(message, length=70, padding=4)
-      puts "*"*(length+padding*2+2)
-      puts "*"+" "*(length+padding*2)+"*"
-      message=message.join("\n") if message.kind_of? Array
-      message.scan(/.{1,70}/).map do |sub_message|
-        puts "*"+" "*padding+sub_message+" "*(length-sub_message.size+padding)+"*"
-      end
-      puts "*"+" "*(length+padding*2)+"*"
-      puts "*"*(length+padding*2+2)
-    end
   end #Generator
-end #Jeweler
+end #Jeweler