RubyGems - search_biomodel - Versions diffs - 1.0.0 → 1.0.1 - Mend

search_biomodel 1.0.0 → 1.0.1

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data/search_biomodel/ruby/1.8/gems/rake-0.9.2/README.rdoc DELETED Viewed

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-= RAKE -- Ruby Make
-Supporting Rake version: 0.8.7.
-This package contains Rake, a simple ruby build program with
-capabilities similar to make.
-Rake has the following features:
-* Rakefiles (rake's version of Makefiles) are completely defined in
-  standard Ruby syntax.  No XML files to edit.  No quirky Makefile
-  syntax to worry about (is that a tab or a space?)
-* Users can specify tasks with prerequisites.
-* Rake supports rule patterns to synthesize implicit tasks.
-* Flexible FileLists that act like arrays but know about manipulating
-  file names and paths.
-* A library of prepackaged tasks to make building rakefiles easier. For example,
-  tasks for building tarballs, gems and RDoc output are provided.
-* Supports parallel execution of tasks.
-== Installation
-=== Gem Installation
-Download and install  rake with the following.
-   gem install rake
-=== Normal Installation
-You can download the source tarball of the latest version of Rake from
-* http://rubyforge.org/project/showfiles.php?group_id=50
-Extract the tarball and run
-  % ruby install.rb
-from its distribution directory.
-== Usage
-=== Simple Example
-First, you must write a "Rakefile" file which contains the build rules. Here's
-a simple example:
-  task :default => [:test]
-  task :test do
-    ruby "test/unittest.rb"
-  end
-This Rakefile has two tasks:
-* A task named "test", which - upon invocation - will run a unit test file in
-  Ruby.
-* A task named "default". This task does nothing by itself, but it has exactly
-  one dependency, namely the "test" task. Invoking the "default" task will
-  cause Rake to invoke the "test" task as well.
-Running the "rake" command without any options will cause it to run the
-"default" task in the Rakefile:
-  % ls
-  Rakefile     test/
-  % rake
-  (in /home/some_user/Projects/rake)
-  ruby test/unittest.rb
-  ....unit test output here...
-Type "rake --help" for all available options.
-=== More Information
-* For details on Rake's command-line invocation, read
-  doc/command_line_usage.rdoc[http://rake.rubyforge.org/files/doc/command_line_usage_rdoc.html]
-* For details on writing Rakefiles, see
-  doc/rakefile.rdoc[http://rake.rubyforge.org/files/doc/rakefile_rdoc.html].
-* For the original announcement of Rake, see
-  doc/rational.rdoc[http://rake.rubyforge.org/files/doc/rational_rdoc.html].
-* For a glossary of terms, see
-  doc/glossary.rdoc[http://rake.rubyforge.org/files/doc/glossary_rdoc.html].
-== Development
-=== Source Repository
-Rake is currently hosted at github. The github web page is
-http://github.com/jimweirich/rake. The public git clone URL is
-* git://github.com/jimweirich/rake.git
-=== Running the Rake Test Suite
-If you wish to run the unit and functional tests that come with Rake:
-* Install the 'flexmock' gem
-* Install the 'session' gem in order to run the functional tests.
-* CD into the top project directory of rake.
-* Type one of the following:
-     rake                  # If you have a version of rake installed
-     ruby -Ilib bin/rake   # If you do not have a version of rake installed.
-=== Issues and Bug Reports
-Feature requests and bug reports can be made here
-* http://onestepback.org/cgi-bin/bugs.cgi?project=rake
-No account is needed for posting requests.  Or you can send me an
-email (at jim dot weirich at gmail dot com)
-Issues and bug reports can be tracked here:
-* http://www.pivotaltracker.com/projects/28469
-== Online Resources
-=== Rake References
-* Rake Documentation Home: http://docs.rubyrake.org
-* Rake Project Page: http://rubyforge.org/projects/rake
-* Rake API Documents: http://rake.rubyforge.org
-* Rake Source Code Repo:  http://github.com/jimweirich/rake
-* Rake Git Repo Clone URL: git://github.com/jimweirich/rake.git
-* Rake Issue Tracking: http://www.pivotaltracker.com/projects/28469
-* Rake Bug Reports: http://onestepback.org/cgi-bin/bugs.cgi?project=rake
-=== Presentations and Articles about Rake
-* Jim Weirich's 2003 RubyConf presentation: http://onestepback.org/articles/buildingwithrake/
-* Martin Fowler's article on Rake: http://martinfowler.com/articles/rake.html
-== Other Make Reinvisionings ...
-Rake is a late entry in the make replacement field.  Here are links to
-other projects with similar (and not so similar) goals.
-* http://directory.fsf.org/bras.html -- Bras, one of earliest
-  implementations of "make in a scripting language".
-* http://www.a-a-p.org -- Make in Python
-* http://www.aromatic.com/tools/jam.txt -- JAM, Java Automated Make
-* http://ant.apache.org -- The Ant project
-* http://ppt.perl.org/commands/make/index.html -- Make from the Perl
-  Power Tools implementation.
-* http://search.cpan.org/search?query=PerlBuildSystem -- The Perl Build System
-* http://make.rubyforge.org -- Rant, another Ruby make tool.
-== Credits
-[<b>Ryan Dlugosz</b>] For the initial conversation that sparked Rake.
-[<b>nobu.nokada@softhome.net</b>] For the initial patch for rule support.
-[<b>Tilman Sauerbeck <tilman@code-monkey.de></b>] For the recursive rule patch.
-== License
-Rake is available under an MIT-style license.
-:include: MIT-LICENSE
-== Support
-The Rake homepage is http://rake.rubyforge.org.  You can find the Rake
-RubyForge page at http://rubyforge.org/projects/rake.
-Feel free to submit commits or feature requests.  If you send a patch,
-remember to update the corresponding unit tests.  In fact, I prefer
-new feature to be submitted in the form of new unit tests.
-For other information, feel free to ask on the ruby-talk mailing list
-(which is mirrored to comp.lang.ruby) or contact
-jim dot weirich at gmail.com.
----
-= Other stuff
-Author::   Jim Weirich <jim.weirich@gmail.com>
-Requires:: Ruby 1.8.0 or later
-License::  Copyright 2003-2008 by Jim Weirich.
-           Released under an MIT-style license.  See the LICENSE file
-           included in the distribution.
-== Warranty
-This software is provided "as is" and without any express or
-implied warranties, including, without limitation, the implied
-warranties of merchantibility and fitness for a particular
-purpose.

data/search_biomodel/ruby/1.8/gems/rake-0.9.2/RRR DELETED Viewed

@@ -1,9 +0,0 @@
-class Zippy
-  def initialize
-    task :a
-    task :b
-    file "x"
-  end
-end
-Zippy.new

data/search_biomodel/ruby/1.8/gems/rake-0.9.2/Rakefile DELETED Viewed

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-# Rakefile for rake        -*- ruby -*-
-# Copyright 2003, 2004, 2005 by Jim Weirich (jim@weirichhouse.org)
-# All rights reserved.
-# This file may be distributed under an MIT style license.  See
-# MIT-LICENSE for details.
-require 'rbconfig'
-require 'rubygems'
-system_rake = File.join RbConfig::CONFIG['rubylibdir'], 'rake.rb'
-# Use our rake, not the installed rake from system
-if $".include? system_rake then
-  exec Gem.ruby, '-Ilib', 'bin/rake', *ARGV
-end
-require 'rubygems/package_task'
-require 'rake/clean'
-require 'rake/testtask'
-begin
-  gem 'rdoc'
-  require 'rdoc/task'
-rescue Gem::LoadError
-end
-CLEAN.include('**/*.o', '*.dot', '**/*.rbc')
-CLOBBER.include('doc/example/main', 'testdata')
-CLOBBER.include('test/data/**/temp_*')
-CLOBBER.include('test/data/chains/play.*')
-CLOBBER.include('test/data/file_creation_task/build')
-CLOBBER.include('test/data/file_creation_task/src')
-CLOBBER.include('TAGS')
-CLOBBER.include('coverage', 'rcov_aggregate')
-# Prevent OS X from including extended attribute junk in the tar output
-ENV['COPY_EXTENDED_ATTRIBUTES_DISABLE'] = 'true'
-def announce(msg='')
-  STDERR.puts msg
-end
-# Determine the current version of the software
-if `ruby -Ilib ./bin/rake --version` =~ /rake, version ([0-9a-z.]+)$/
-  CURRENT_VERSION = $1
-else
-  CURRENT_VERSION = "0.0.0"
-end
-$package_version = CURRENT_VERSION
-SRC_RB = FileList['lib/**/*.rb']
-# The default task is run if rake is given no explicit arguments.
-desc "Default Task"
-task :default => :test
-# Test Tasks ---------------------------------------------------------
-Rake::TestTask.new do |t|
-  files = FileList['test/helper.rb', 'test/test_*.rb']
-  t.test_files = files
-  t.libs << "."
-  t.warning = true
-end
-begin
-  require 'rcov/rcovtask'
-  IGNORE_COVERAGE_IN = FileList[
-    'lib/rake/rdoctask.rb',
-    'lib/rake/testtask.rb',
-    'lib/rake/packagetask.rb',
-    'lib/rake/clean.rb',
-  ]
-  unless File::ALT_SEPARATOR
-    IGNORE_COVERAGE_IN.include(
-      'lib/rake/alt_system.rb',
-      'lib/rake/win32.rb')
-  end
-  Rcov::RcovTask.new do |t|
-    t.libs << "test"
-    t.rcov_opts = [
-      '-xRakefile', '-xrakefile', '-xpublish.rf',
-      '-xlib/rake/contrib', '-x/Library', '-x.rvm',
-      '--text-report',
-      '--sort coverage'
-    ] + FileList['rakelib/*.rake'].pathmap("-x%p") +
-      IGNORE_COVERAGE_IN.map { |fn| "-x#{fn}" }
-    t.test_files = FileList[
-      'test/lib/*_test.rb',
-      'test/contrib/*_test.rb',
-      'test/functional/*_test.rb'
-    ]
-    t.output_dir = 'coverage'
-    t.verbose = true
-  end
-rescue LoadError
-  task :rcov do
-    puts "RCov is not available"
-  end
-end
-directory 'testdata'
-task :test => ['testdata']
-# CVS Tasks ----------------------------------------------------------
-# Install rake using the standard install.rb script.
-desc "Install the application"
-task :install do
-  ruby "install.rb"
-end
-# Create a task to build the RDOC documentation tree.
-BASE_RDOC_OPTIONS = [
-  '--line-numbers', '--show-hash',
-  '--main', 'README.rdoc',
-  '--title', 'Rake -- Ruby Make'
-]
-if defined?(RDoc::Task) then
-  RDoc::Task.new do |rdoc|
-    rdoc.rdoc_dir = 'html'
-    rdoc.title    = "Rake -- Ruby Make"
-    rdoc.options = BASE_RDOC_OPTIONS.dup
-    rdoc.rdoc_files.include('README.rdoc', 'MIT-LICENSE', 'TODO', 'CHANGES')
-    rdoc.rdoc_files.include('lib/**/*.rb', 'doc/**/*.rdoc')
-    rdoc.rdoc_files.exclude(/\bcontrib\b/)
-  end
-else
-  warn "RDoc 2.4.2+ is required to build documentation"
-end
-# ====================================================================
-# Create a task that will package the Rake software into distributable
-# tar, zip and gem files.
-PKG_FILES = FileList[
-  '.gemtest',
-  'install.rb',
-  '[A-Z]*',
-  'bin/**/*',
-  'lib/**/*.rb',
-  'test/**/*.rb',
-  'test/**/*.rf',
-  'test/**/*.mf',
-  'test/**/Rakefile',
-  'test/**/subdir',
-  'doc/**/*'
-]
-PKG_FILES.exclude('doc/example/*.o')
-PKG_FILES.exclude('TAGS')
-PKG_FILES.exclude(%r{doc/example/main$})
-if ! defined?(Gem)
-  puts "Package Target requires RubyGEMs"
-else
-  SPEC = Gem::Specification.new do |s|
-    #### Basic information.
-    s.name = 'rake'
-    s.version = $package_version
-    s.summary = "Ruby based make-like utility."
-    s.description = <<-EOF
-      Rake is a Make-like program implemented in Ruby. Tasks
-      and dependencies are specified in standard Ruby syntax.
-    EOF
-    #### Dependencies and requirements.
-    s.required_rubygems_version = '>= 1.3.2'
-    s.add_development_dependency 'minitest', '~> 2.1'
-    s.add_development_dependency 'session', '~> 2.4'
-    s.add_development_dependency 'flexmock', '~> 0.8.11'
-    #### Which files are to be included in this gem?  Everything!  (Except CVS directories.)
-    s.files = PKG_FILES.to_a
-    #### C code extensions.
-    #s.extensions << "ext/rmagic/extconf.rb"
-    #### Load-time details: library and application (you will need one or both).
-    s.require_path = 'lib'                         # Use these for libraries.
-    s.bindir = "bin"                               # Use these for applications.
-    s.executables = ["rake"]
-    #### Documentation and testing.
-    s.extra_rdoc_files = FileList[
-      'README.rdoc',
-      'MIT-LICENSE',
-      'TODO',
-      'CHANGES',
-      'doc/**/*.rdoc'
-    ]
-    s.rdoc_options = BASE_RDOC_OPTIONS
-    #### Author and project details.
-    s.author = "Jim Weirich"
-    s.email = "jim@weirichhouse.org"
-    s.homepage = "http://rake.rubyforge.org"
-    s.rubyforge_project = "rake"
-#     if ENV['CERT_DIR']
-#       s.signing_key = File.join(ENV['CERT_DIR'], 'gem-private_key.pem')
-#       s.cert_chain  = [File.join(ENV['CERT_DIR'], 'gem-public_cert.pem')]
-#     end
-  end
-  Gem::PackageTask.new(SPEC) do |pkg|
-    pkg.need_zip = true
-    pkg.need_tar = true
-  end
-  file "rake.gemspec" => ["Rakefile", "lib/rake.rb"] do |t|
-    require 'yaml'
-    open(t.name, "w") { |f| f.puts SPEC.to_yaml }
-  end
-  desc "Create a stand-alone gemspec"
-  task :gemspec => "rake.gemspec"
-end
-# Misc tasks =========================================================
-def count_lines(filename)
-  lines = 0
-  codelines = 0
-  open(filename) { |f|
-    f.each do |line|
-      lines += 1
-      next if line =~ /^\s*$/
-      next if line =~ /^\s*#/
-      codelines += 1
-    end
-  }
-  [lines, codelines]
-end
-def show_line(msg, lines, loc)
-  printf "%6s %6s   %s\n", lines.to_s, loc.to_s, msg
-end
-desc "Count lines in the main rake file"
-task :lines do
-  total_lines = 0
-  total_code = 0
-  show_line("File Name", "LINES", "LOC")
-  SRC_RB.each do |fn|
-    lines, codelines = count_lines(fn)
-    show_line(fn, lines, codelines)
-    total_lines += lines
-    total_code  += codelines
-  end
-  show_line("TOTAL", total_lines, total_code)
-end
-# Define an optional publish target in an external file.  If the
-# publish.rf file is not found, the publish targets won't be defined.
-load "publish.rf" if File.exist? "publish.rf"
-# Support Tasks ------------------------------------------------------
-RUBY_FILES = FileList['**/*.rb'].exclude('pkg')
-desc "Look for TODO and FIXME tags in the code"
-task :todo do
-  RUBY_FILES.egrep(/#.*(FIXME|TODO|TBD)/)
-end
-desc "List all ruby files"
-task :rubyfiles do
-  puts RUBY_FILES
-  puts FileList['bin/*'].exclude('bin/*.rb')
-end
-task :rf => :rubyfiles
-# --------------------------------------------------------------------
-# Creating a release
-def plugin(plugin_name)
-  require "rake/plugins/#{plugin_name}"
-end
-task :noop
-#plugin "release_manager"
-desc "Make a new release"
-task :release, [:rel, :reuse, :reltest] => [
-    :prerelease,
-    :clobber,
-    :test,
-    :update_version,
-    :package,
-    :tag
-  ] do
-  announce
-  announce "**************************************************************"
-  announce "* Release #{$package_version} Complete."
-  announce "* Packages ready to upload."
-  announce "**************************************************************"
-  announce
-end
-# Validate that everything is ready to go for a release.
-task :prerelease, :rel, :reuse, :reltest do |t, args|
-  $package_version = args.rel
-  announce
-  announce "**************************************************************"
-  announce "* Making RubyGem Release #{$package_version}"
-  announce "* (current version #{CURRENT_VERSION})"
-  announce "**************************************************************"
-  announce
-  # Is a release number supplied?
-  unless args.rel
-    fail "Usage: rake release[X.Y.Z] [REUSE=tag_suffix]"
-  end
-  # Is the release different than the current release.
-  # (or is REUSE set?)
-  if $package_version == CURRENT_VERSION && ! args.reuse
-    fail "Current version is #{$package_version}, must specify REUSE=tag_suffix to reuse version"
-  end
-  # Are all source files checked in?
-  if args.reltest
-    announce "Release Task Testing, skipping checked-in file test"
-  else
-    announce "Checking for unchecked-in files..."
-    data = `svn st`
-    unless data =~ /^$/
-      abort "svn status is not clean ... do you have unchecked-in files?"
-    end
-    announce "No outstanding checkins found ... OK"
-  end
-end
-task :update_version, [:rel, :reuse, :reltest] => [:prerelease] do |t, args|
-  if args.rel == CURRENT_VERSION
-    announce "No version change ... skipping version update"
-  else
-    announce "Updating Rake version to #{args.rel}"
-    open("lib/rake.rb") do |rakein|
-      open("lib/rake.rb.new", "w") do |rakeout|
-        rakein.each do |line|
-          if line =~ /^RAKEVERSION\s*=\s*/
-            rakeout.puts "RAKEVERSION = '#{args.rel}'"
-          else
-            rakeout.puts line
-          end
-        end
-      end
-    end
-    mv "lib/rake.rb.new", "lib/rake.rb"
-    if args.reltest
-      announce "Release Task Testing, skipping commiting of new version"
-    else
-      sh %{svn commit -m "Updated to version #{args.rel}" lib/rake.rb} # "
-    end
-  end
-end
-desc "Tag all the CVS files with the latest release number (REL=x.y.z)"
-task :tag, [:rel, :reuse, :reltest] => [:prerelease] do |t, args|
-  reltag = "REL_#{args.rel.gsub(/\./, '_')}"
-  reltag << args.reuse.gsub(/\./, '_') if args.reuse
-  announce "Tagging Repository with [#{reltag}]"
-  if args.reltest
-    announce "Release Task Testing, skipping CVS tagging"
-  else
-    sh %{svn copy svn+ssh://rubyforge.org/var/svn/rake/trunk svn+ssh://rubyforge.org/var/svn/rake/tags/#{reltag} -m 'Commiting release #{reltag}'} ###'
-  end
-end
-# Require experimental XForge/Metaproject support.
-load 'xforge.rf' if File.exist?('xforge.rf')
-desc "Where is the current directory.  This task displays\nthe current rake directory"
-task :where_am_i do
-  puts Rake.original_dir
-end
-task :failure => :really_fail
-task :really_fail do
-  fail "oops"
-end

data/search_biomodel/ruby/1.8/gems/rake-0.9.2/TODO DELETED Viewed

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-= Rake Project -- To Do List
-Send suggestions for this list to mailto:jim@weirichhouse.org or on
-the rake-devel@rubyforge.org mailing list.
-=== To Do
-* Need a nice API for accessing tasks in namespaces, namespaces in an app, etc.
-* Provide a way to disable -w warning mode.
-* Define a set of default rules that work in the absence of any Rakefile
-* What about cyclic dependencies?
-* Java support utilities
-* Installation support utilities
-  * Check out installpkg.rb
-* Autogenerate Dependencies
-* Rules should apply to existing tasks if no actions are defined.
-* How to create multiple package tasks without task name collision?
-* Trap "ln -s" commands that fail and use "cp" instead (SMB mounted
-  drives have problems with "ln -s".
-(moved DONE list to CHANGES file)

data/search_biomodel/ruby/1.8/gems/rake-0.9.2/bin/rake DELETED Viewed

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-#!/usr/bin/env ruby
-#--
-# Copyright (c) 2003, 2004, 2005, 2006, 2007  Jim Weirich
-#
-# Permission is hereby granted, free of charge, to any person obtaining a copy
-# of this software and associated documentation files (the "Software"), to
-# deal in the Software without restriction, including without limitation the
-# rights to use, copy, modify, merge, publish, distribute, sublicense, and/or
-# sell copies of the Software, and to permit persons to whom the Software is
-# furnished to do so, subject to the following conditions:
-#
-# The above copyright notice and this permission notice shall be included in
-# all copies or substantial portions of the Software.
-#
-# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
-# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS
-# IN THE SOFTWARE.
-#++
-begin
-  require 'rubygems'
-rescue LoadError
-end
-require 'rake'
-Rake.application.run