search_biomodel 0.1.2 → 1.0.0

data/search_biomodel/ruby/1.8/gems/rake-0.9.2/test/test_rake_top_level_functions.rb

@@ -0,0 +1,76 @@
+require File.expand_path('../helper', __FILE__)
+
+class TestRakeTopLevelFunctions < Rake::TestCase
+
+  def setup
+    super
+
+    @app = Rake.application
+    Rake.application = flexmock("app")
+    Rake.application.should_receive(:deprecate).
+      and_return { |old, new, call| @app.deprecate(old, new, call) }
+  end
+
+  def teardown
+    Rake.application = @app
+
+    super
+  end
+
+  def test_namespace
+    Rake.application.should_receive(:in_namespace).with("xyz", any).once
+    namespace "xyz" do end
+  end
+
+  def test_import
+    Rake.application.should_receive(:add_import).with("x").once.ordered
+    Rake.application.should_receive(:add_import).with("y").once.ordered
+    Rake.application.should_receive(:add_import).with("z").once.ordered
+    import('x', 'y', 'z')
+  end
+
+  def test_when_writing
+    out, = capture_io do
+      when_writing("NOTWRITING") do
+        puts "WRITING"
+      end
+    end
+    assert_equal "WRITING\n", out
+  end
+
+  def test_when_not_writing
+    Rake::FileUtilsExt.nowrite_flag = true
+    _, err = capture_io do
+      when_writing("NOTWRITING") do
+        puts "WRITING"
+      end
+    end
+    assert_equal "DRYRUN: NOTWRITING\n", err
+  ensure
+    Rake::FileUtilsExt.nowrite_flag = false
+  end
+
+  def test_missing_constants_task
+    Rake.application.should_receive(:const_warning).with(:Task).once
+    Object.const_missing(:Task)
+  end
+
+  def test_missing_constants_file_task
+    Rake.application.should_receive(:const_warning).with(:FileTask).once
+    Object.const_missing(:FileTask)
+  end
+
+  def test_missing_constants_file_creation_task
+    Rake.application.should_receive(:const_warning).with(:FileCreationTask).once
+    Object.const_missing(:FileCreationTask)
+  end
+
+  def test_missing_constants_rake_app
+    Rake.application.should_receive(:const_warning).with(:RakeApp).once
+    Object.const_missing(:RakeApp)
+  end
+
+  def test_missing_other_constant
+    assert_raises(NameError) do Object.const_missing(:Xyz) end
+  end
+end

data/search_biomodel/ruby/1.8/gems/rake-0.9.2/test/test_rake_win32.rb

@@ -0,0 +1,83 @@
+require File.expand_path('../helper', __FILE__)
+
+class TestRakeWin32 < Rake::TestCase
+  include InEnvironment
+
+  Win32 = Rake::Win32
+
+  def test_win32_system_dir_uses_home_if_defined
+    in_environment('RAKE_SYSTEM' => nil, 'HOME' => 'C:\\HP') do
+      assert_equal "C:/HP/Rake", Win32.win32_system_dir
+    end
+  end
+
+  def test_win32_system_dir_uses_homedrive_homepath_when_no_home_defined
+    in_environment(
+      'RAKE_SYSTEM' => nil,
+      'HOME' => nil,
+      'HOMEDRIVE' => "C:",
+      'HOMEPATH' => "\\HP"
+      ) do
+      assert_equal "C:/HP/Rake", Win32.win32_system_dir
+    end
+  end
+
+  def test_win32_system_dir_uses_appdata_when_no_home_or_home_combo
+    in_environment(
+      'RAKE_SYSTEM' => nil,
+      'HOME' => nil,
+      'HOMEDRIVE' => nil,
+      'HOMEPATH' => nil,
+      'APPDATA' => "C:\\Documents and Settings\\HP\\Application Data"
+      ) do
+      assert_equal "C:/Documents and Settings/HP/Application Data/Rake", Win32.win32_system_dir
+    end
+  end
+
+  def test_win32_system_dir_fallback_to_userprofile_otherwise
+    in_environment(
+      'RAKE_SYSTEM' => nil,
+      'HOME' => nil,
+      'HOMEDRIVE' => nil,
+      'HOMEPATH' => nil,
+      'APPDATA' => nil,
+      'USERPROFILE' => "C:\\Documents and Settings\\HP"
+      ) do
+      assert_equal "C:/Documents and Settings/HP/Rake", Win32.win32_system_dir
+    end
+  end
+
+  def test_win32_system_dir_nil_of_no_env_vars
+    in_environment(
+      'RAKE_SYSTEM' => nil,
+      'HOME' => nil,
+      'HOMEDRIVE' => nil,
+      "HOMEPATH" => nil,
+      'APPDATA' => nil,
+      "USERPROFILE" => nil
+      ) do
+      assert_raises(Rake::Win32::Win32HomeError) do
+        Win32.win32_system_dir
+      end
+    end
+  end
+
+  def test_win32_backtrace_with_different_case
+    ex = nil
+    begin
+     raise 'test exception'
+    rescue => ex
+    end
+
+    ex.set_backtrace ['abc', 'rakefile']
+
+    rake = Rake::Application.new
+    rake.options.trace = true
+    rake.instance_variable_set(:@rakefile, 'Rakefile')
+
+    _, err = capture_io { rake.display_error_message(ex) }
+
+    assert_match(/rakefile/, err)
+  end
+
+end

data/search_biomodel/ruby/1.8/gems/rake-0.9.2/test/test_sys.rb

@@ -0,0 +1,20 @@
+require File.expand_path('../helper', __FILE__)
+begin
+  old_verbose = $VERBOSE
+  $VERBOSE = nil
+  require 'rake/contrib/sys'
+ensure
+  $VERBOSE = old_verbose
+end
+
+class TestSys < Rake::TestCase
+
+  def test_split_all
+    assert_equal ['a'], Sys.split_all('a')
+    assert_equal ['..'], Sys.split_all('..')
+    assert_equal ['/'], Sys.split_all('/')
+    assert_equal ['a', 'b'], Sys.split_all('a/b')
+    assert_equal ['/', 'a', 'b'], Sys.split_all('/a/b')
+    assert_equal ['..', 'a', 'b'], Sys.split_all('../a/b')
+  end
+end

data/search_biomodel/ruby/1.8/gems/rcov-0.9.9/BLURB

@@ -0,0 +1,111 @@
+Overview
+========
+rcov is a code coverage tool for Ruby. It is commonly used for viewing overall
+test coverage of target code. It features:
+* fast execution: 20-300 times faster than previous tools
+* multiple analysis modes: standard, bogo-profile, "intentional testing",
+  dependency analysis...
+* detection of uncovered code introduced since the last run ("differential
+  code coverage")
+* fairly accurate coverage information through code linkage inference using 
+  simple heuristics
+* cross-referenced XHTML and several kinds of text reports
+* support for easy automation with Rake
+* colorblind-friendliness
+
+How do I use it?
+================
+
+In the common scenario, your tests are under test/ and the target code
+(whose coverage you want) is in lib/. In that case, all you have to do is
+use rcov to run the tests (instead of testrb), and a number of XHTML files
+with the code coverage information will be generated, e.g.
+
+    rcov -Ilib test/*.rb
+
+will execute all the .rb files under test/ and generate the code coverage
+report for the target code (i.e. for the files in lib/) under coverage/. The
+target code needs not be under lib/; rcov will detect is as long as it is
+require()d by the tests. rcov is smart enough to ignore "uninteresting"
+files: the tests themselves, files installed in Ruby's standard locations,
+etc.  See  rcov --help  for the list of regexps rcov matches filenames
+against.
+
+rcov can also be used from Rake; see readme_for_rake or the RDoc documentation
+for more information.
+
+rcov can output information in several formats, and perform different kinds
+of analyses in addition to plain code coverage.  See  rcov --help  for a
+description of the available options.
+
+Sample output
+=============
+
+The text report (also used by default in RcovTasks) resembles
+
+
++-----------------------------------------------------+-------+-------+--------+
+|                  File                               | Lines |  LOC  |  COV   |
++-----------------------------------------------------+-------+-------+--------+
+|lib/rcov.rb                                          |   572 |   358 |  91.3% |
++-----------------------------------------------------+-------+-------+--------+
+|Total                                                |   572 |   358 |  91.3% |
++-----------------------------------------------------+-------+-------+--------+
+91.3%   1 file(s)   572 Lines   358 LOC
+
+
+
+The (undecorated) textual output with execution count information looks like this:
+
+ $ rcov --no-html --text-counts b.rb 
+ ================================================================================
+ ./b.rb
+ ================================================================================
+                                                                       |      2
+ a, b, c = (1..3).to_a                                                 |      2
+ 10.times do                                                           |      1
+   a += 1                                                              |     10
+   20.times do |i|                                                     |     10
+     b += i                                                            |    200
+     b.times do                                                        |    200
+       c += (j = (b-a).abs) > 0 ? j : 0                                | 738800
+     end                                                               |      0
+   end                                                                 |      0
+ end                                                                   |      0
+
+
+rcov can detect when you've added code that was not covered by your unit
+tests:
+
+    $ rcov --text-coverage-diff --no-color test/*.rb
+    Started
+    .......................................
+    Finished in 1.163085 seconds.
+    
+    39 tests, 415 assertions, 0 failures, 0 errors
+    
+    ================================================================================
+    !!!!! Uncovered code introduced in lib/rcov.rb
+    
+    ### lib/rcov.rb:207
+       
+	 def precompute_coverage(comments_run_by_default = true)
+	   changed = false
+	   lastidx = lines.size - 1
+	   if (!is_code?(lastidx) || /^__END__$/ =~ @lines[-1]) && !@coverage[lastidx]
+    !!       # mark the last block of comments
+    !!       @coverage[lastidx] ||= :inferred
+    !!       (lastidx-1).downto(0) do |i|
+    !!         break if is_code?(i)
+    !!         @coverage[i] ||= :inferred
+    !!       end
+    !!     end
+	   (0...lines.size).each do |i|
+	     next if @coverage[i]
+	     line = @lines[i]
+
+
+
+License
+-------
+rcov is released under the terms of Ruby's license.

data/search_biomodel/ruby/1.8/gems/rcov-0.9.9/LICENSE

@@ -0,0 +1,53 @@
+rcov is copyrighted free software by Mauricio Fernandez <mfp@acm.org>.
+You can redistribute it and/or modify it under either the terms of the GPL,
+or the conditions below:
+
+  1. You may make and give away verbatim copies of the source form of the
+     software without restriction, provided that you duplicate all of the
+     original copyright notices and associated disclaimers.
+
+  2. You may modify your copy of the software in any way, provided that
+     you do at least ONE of the following:
+
+       a) place your modifications in the Public Domain or otherwise
+          make them Freely Available, such as by posting said
+	  modifications to Usenet or an equivalent medium, or by allowing
+	  the author to include your modifications in the software.
+
+       b) use the modified software only within your corporation or
+          organization.
+
+       c) give non-standard binaries non-standard names, with
+          instructions on where to get the original software distribution.
+
+       d) make other distribution arrangements with the author.
+
+  3. You may distribute the software in object code or binary form,
+     provided that you do at least ONE of the following:
+
+       a) distribute the binaries and library files of the software,
+	  together with instructions (in the manual page or equivalent)
+	  on where to get the original distribution.
+
+       b) accompany the distribution with the machine-readable source of
+	  the software.
+
+       c) give non-standard binaries non-standard names, with
+          instructions on where to get the original software distribution.
+
+       d) make other distribution arrangements with the author.
+
+  4. You may modify and include the part of the software into any other
+     software (possibly commercial).  But some files in the distribution
+     are not written by the author, so that they are not under these terms.
+
+  5. The scripts and library files supplied as input to or produced as 
+     output from the software do not automatically fall under the
+     copyright of the software, but belong to whomever generated them, 
+     and may be sold commercially, and may be aggregated with this
+     software.
+
+  6. THIS SOFTWARE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR
+     IMPLIED WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED
+     WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+     PURPOSE.

data/search_biomodel/ruby/1.8/gems/rcov-0.9.9/Rakefile

@@ -0,0 +1,103 @@
+$:.unshift "lib" if File.directory? "lib"
+require 'rcov/rcovtask'
+require 'rcov/version'
+require 'rake/testtask'
+require 'rake/rdoctask'
+require 'rake/gempackagetask'
+require 'rake/clean'
+
+# Use the specified rcov executable instead of the one in $PATH
+# (this way we get a sort of informal functional test).
+# This could also be specified from the command like, e.g.
+#   rake rcov RCOVPATH=/path/to/myrcov
+ENV["RCOVPATH"] = "bin/rcov"
+
+# The following task is largely equivalent to:
+# Rcov::RcovTask.new
+desc "Create a cross-referenced code coverage report."
+Rcov::RcovTask.new do |t|
+  t.test_files = FileList['test/*_test.rb']
+  t.ruby_opts << "-Ilib:ext/rcovrt" # in order to use this rcov
+  t.rcov_opts << "--xrefs"  # comment to disable cross-references
+  t.verbose = true
+end
+
+desc "Analyze code coverage for the FileStatistics class."
+Rcov::RcovTask.new(:rcov_sourcefile) do |t|
+  t.test_files = FileList['test/file_statistics_test.rb']
+  t.verbose = true
+  t.rcov_opts << "--test-unit-only"
+  t.ruby_opts << "-Ilib:ext/rcovrt" # in order to use this rcov
+  t.output_dir = "coverage.sourcefile"
+end
+
+Rcov::RcovTask.new(:rcov_ccanalyzer) do |t|
+  t.test_files = FileList['test/code_coverage_analyzer_test.rb']
+  t.verbose = true
+  t.rcov_opts << "--test-unit-only"
+  t.ruby_opts << "-Ilib:ext/rcovrt" # in order to use this rcov
+  t.output_dir = "coverage.ccanalyzer"
+end
+
+desc "Run the unit tests with rcovrt."
+if RUBY_PLATFORM == 'java'
+  Rake::TestTask.new(:test_rcovrt => ["lib/rcovrt.jar"]) do |t|
+    t.libs << "lib"
+    t.ruby_opts << "--debug"
+    t.test_files = FileList['test/*_test.rb']
+    t.verbose = true
+  end
+
+  file "lib/rcovrt.jar" => FileList["ext/java/**/*.java"] do |t|
+    rm_f "lib/rcovrt.jar"
+    mkdir_p "pkg/classes"
+    sh "javac -classpath #{Java::JavaLang::System.getProperty('java.class.path')} -d pkg/classes #{t.prerequisites.join(' ')}"
+    sh "jar cf #{t.name} -C pkg/classes ."
+  end
+else
+  Rake::TestTask.new(:test_rcovrt => ["ext/rcovrt/rcovrt.so"]) do |t|
+    system("cd ext/rcovrt && make clean && rm Makefile")
+    t.libs << "ext/rcovrt"
+    t.test_files = FileList['test/*_test.rb']
+    t.verbose = true
+  end
+end
+
+file "ext/rcovrt/rcovrt.so" => FileList["ext/rcovrt/*.c"] do
+  ruby "setup.rb config"
+  ruby "setup.rb setup"
+end
+
+desc "Run the unit tests in pure-Ruby mode ."
+Rake::TestTask.new(:test_pure_ruby) do |t|
+  t.libs << "ext/rcovrt"
+  t.test_files = FileList['test/turn_off_rcovrt.rb', 'test/*_test.rb']
+  t.verbose = true
+end
+
+desc "Run the unit tests"
+task :test => [:test_rcovrt]
+
+desc "install by setup.rb"
+task :install do
+  sh "sudo ruby setup.rb install"
+end
+
+task :default => :test
+
+begin
+  %w{sdoc sdoc-helpers rdiscount}.each { |name| gem name }
+  require 'sdoc_helpers'
+rescue LoadError => ex
+  puts "sdoc support not enabled:"
+  puts ex.inspect
+end
+
+require 'rake/rdoctask'
+Rake::RDocTask.new do |rdoc|
+  version = File.exist?('VERSION') ? File.read('VERSION') : ''
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "rcov #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end