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#
# = Rakefile - helper of developement and packaging
#
# Copyright:: Copyright (C) 2009, 2012 Naohisa Goto <ng@bioruby.org>
# License:: The Ruby License
#
require 'rubygems'
require 'erb'
require 'pathname'
require 'fileutils'
require 'tmpdir'
require 'rake/testtask'
require 'rake/packagetask'
begin
require 'rubygems/package_task'
rescue LoadError
# old RubyGems/Rake version
require 'rake/gempackagetask'
end
begin
require 'rdoc/task'
rescue LoadError
# old RDoc/Rake version
require 'rake/rdoctask'
end
# workaround for new module name
unless defined? Rake::GemPackageTask then
Rake::GemPackageTask = Gem::PackageTask
end
load "./lib/bio/version.rb"
BIO_VERSION_RB_LOADED = true
# Version string for tar.gz, tar.bz2, or zip archive.
# If nil, use the value in lib/bio.rb
# Note that gem version is always determined from bioruby.gemspec.erb.
version = ENV['BIORUBY_VERSION'] || Bio::BIORUBY_VERSION.join(".")
version = nil if version.to_s.empty?
extraversion = ENV['BIORUBY_EXTRA_VERSION'] || Bio::BIORUBY_EXTRA_VERSION
extraversion = nil if extraversion.to_s.empty?
BIORUBY_VERSION = version
BIORUBY_EXTRA_VERSION = extraversion
task :default => "see-env"
Rake::TestTask.new do |t|
t.test_files = FileList["test/{unit,functional}/**/test_*.rb"]
end
Rake::TestTask.new do |t|
t.name = :"test-all"
t.test_files = FileList["test/{unit,functional,network}/**/test_*.rb"]
end
Rake::TestTask.new do |t|
t.name = :"test-network"
t.test_files = FileList["test/network/**/test_*.rb"]
end
# files not included in gem but included in tar archive
tar_additional_files = []
GEM_SPEC_FILE = "bioruby.gemspec"
GEM_SPEC_TEMPLATE_FILE = "bioruby.gemspec.erb"
# gets gem spec string
gem_spec_string = File.open(GEM_SPEC_TEMPLATE_FILE, "rb") do |f|
ERB.new(f.read).result
end
# gets gem spec object
spec = eval(gem_spec_string)
# adds notice of automatically generated file
gem_spec_string = "# This file is automatically generated from #{GEM_SPEC_TEMPLATE_FILE} and\n# should NOT be edited by hand.\n# \n" + gem_spec_string
# compares current gemspec file and newly generated gemspec string
current_string = File.read(GEM_SPEC_FILE) rescue nil
if current_string and current_string != gem_spec_string then
#Rake::Task[GEM_SPEC_FILE].invoke
flag_update_gemspec = true
else
flag_update_gemspec = false
end
desc "Update gem spec file"
task :gemspec => GEM_SPEC_FILE
desc "Force update gem spec file"
task :regemspec do
#rm GEM_SPEC_FILE, :force => true
Rake::Task[GEM_SPEC_FILE].execute(nil)
end
desc "Update #{GEM_SPEC_FILE}"
file GEM_SPEC_FILE => [ GEM_SPEC_TEMPLATE_FILE, 'Rakefile',
'lib/bio/version.rb' ] do |t|
puts "creates #{GEM_SPEC_FILE}"
File.open(t.name, 'wb') do |w|
w.print gem_spec_string
end
end
task :package => [ GEM_SPEC_FILE ] do
Rake::Task[:regemspec].invoke if flag_update_gemspec
end
pkg_dir = "pkg"
tar_version = (BIORUBY_VERSION || spec.version) + BIORUBY_EXTRA_VERSION.to_s
tar_basename = "bioruby-#{tar_version}"
tar_filename = "#{tar_basename}.tar.gz"
tar_pkg_filepath = File.join(pkg_dir, tar_filename)
gem_filename = spec.full_name + ".gem"
gem_pkg_filepath = File.join(pkg_dir, gem_filename)
Rake::PackageTask.new("bioruby") do |pkg|
#pkg.package_dir = "./pkg"
pkg.need_tar_gz = true
pkg.package_files.import(spec.files)
pkg.package_files.include(*tar_additional_files)
pkg.version = tar_version
end
Rake::GemPackageTask.new(spec) do |pkg|
#pkg.package_dir = "./pkg"
end
Rake::RDocTask.new do |r|
r.rdoc_dir = "rdoc"
r.rdoc_files.include(*spec.extra_rdoc_files)
r.rdoc_files.import(spec.files.find_all {|x| /\Alib\/.+\.rb\z/ =~ x})
#r.rdoc_files.exclude /\.yaml\z"
opts = spec.rdoc_options.to_a.dup
if i = opts.index('--main') then
main = opts[i + 1]
opts.delete_at(i)
opts.delete_at(i)
else
main = 'README.rdoc'
end
r.main = main
r.options = opts
end
# Tutorial files
TUTORIAL_RD = 'doc/Tutorial.rd'
TUTORIAL_RD_JA = 'doc/Tutorial.rd.ja'
TUTORIAL_RD_HTML = TUTORIAL_RD + '.html'
TUTORIAL_RD_JA_HTML = TUTORIAL_RD_JA + '.html'
HTMLFILES_TUTORIAL = [ TUTORIAL_RD_HTML, TUTORIAL_RD_JA_HTML ]
# Formatting RD to html.
def rd2html(src, dst)
title = File.basename(src)
sh "rd2 -r rd/rd2html-lib.rb --with-css=bioruby.css --html-title=#{title} #{src} > #{dst}"
end
# Tutorial.rd to Tutorial.rd.html
file TUTORIAL_RD_HTML => TUTORIAL_RD do |t|
rd2html(t.prerequisites[0], t.name)
end
# Tutorial.rd.ja to Tutorial.html.ja
file TUTORIAL_RD_JA_HTML => TUTORIAL_RD_JA do |t|
rd2html(t.prerequisites[0], t.name)
end
desc "Update doc/Tutorial*.html"
task :tutorial2html => HTMLFILES_TUTORIAL
desc "Force update doc/Tutorial*.html"
task :retutorial2html do
# safe_unlink HTMLFILES_TUTORIAL
HTMLFILES_TUTORIAL.each do |x|
Rake::Task[x].execute(nil)
end
end
# ChangeLog
desc "Force update ChangeLog using git log"
task :rechangelog do
# The tag name in the command line should be changed
# after releasing new version, updating ChangeLog,
# and doing "git mv ChangeLog doc/ChangeLog-X.X.X".
sh "git log --stat --summary 1.4.3..HEAD > ChangeLog"
end
# define mktmpdir
if true then
# Note: arg is a subset of Dir.mktmpdir
def mktmpdir(prefix)
## prepare temporary directory for testing
top = Pathname.new(File.join(Dir.pwd, "tmp")).cleanpath.to_s
begin
Dir.mkdir(top)
rescue Errno::EEXIST
end
## prepare working directory
flag = false
dirname = nil
ret = nil
begin
10.times do |n|
# following 3 lines are copied from Ruby 1.9.3's tmpdir.rb and modified
t = Time.now.strftime("%Y%m%d")
path = "#{prefix}#{t}-#{$$}-#{rand(0x100000000).to_s(36)}"
path << "-#{n}" if n > 0
begin
dirname = File.join(top, path)
flag = Dir.mkdir(dirname)
break if flag
rescue SystemCallError
end
end
raise "Couldn't create a directory under #{tmp}." unless flag
ret = yield(dirname)
ensure
FileUtils.remove_entry_secure(dirname, true) if flag and dirname
end
ret
end #def mktmpdir
## Currently, Dir.mktmpdir isn't used Because of JRuby's behavior.
elsif Dir.respond_to?(:mktmpdir) then
def self.mktmpdir(*arg, &block)
Dir.mktmpdir(*arg, &block)
end
else
load "lib/bio/command.rb"
def mktmpdir(*arg, &block)
Bio::Command.mktmpdir(*arg, &block)
end
end
def chdir_with_message(dir)
$stderr.puts("chdir #{dir}")
Dir.chdir(dir)
end
# run in different directory
def work_in_another_directory
pwd = Dir.pwd
ret = false
mktmpdir("bioruby") do |dirname|
begin
chdir_with_message(dirname)
ret = yield(dirname)
ensure
chdir_with_message(pwd)
end
end
ret
end
desc "task specified with BIORUBY_RAKE_DEFAULT_TASK (default \"test\")"
task :"see-env" do
t = ENV["BIORUBY_RAKE_DEFAULT_TASK"]
if t then
Rake::Task[t].invoke
else
Rake::Task[:test].invoke
end
end
desc "DANGER: build tar and install (GNU tar needed)"
task :"tar-install" => [ :package ] do
pwd = Dir.pwd
work_in_another_directory do |dirname|
begin
# remove tar file in direname
FileUtils.remove_entry_secure(tar_filename, true)
# chdir to old pwd
chdir_with_message(pwd)
# copy (or link) tar file
safe_ln(tar_pkg_filepath, dirname)
# chdir to dirname again
chdir_with_message(dirname)
# remove a directory the tar file will contain
FileUtils.remove_entry_secure(tar_basename, true)
# extract tar
sh("tar zxvf #{tar_filename}")
# chdir to the directory
chdir_with_message(tar_basename)
# run tests
ruby("setup.rb")
ensure
# cleanup
chdir_with_message(dirname)
FileUtils.remove_entry_secure(tar_basename, true)
FileUtils.remove_entry_secure(tar_filename, true)
end
end
end
desc "test installed bioruby on system"
task :"installed-test" do
data_path = File.join(Dir.pwd, "test/data")
test_runner = File.join(Dir.pwd, "test/runner.rb")
data_path = Pathname.new(data_path).cleanpath.to_s
test_runner = Pathname.new(test_runner).cleanpath.to_s
ENV["BIORUBY_TEST_DATA"] = data_path
ENV["BIORUBY_TEST_LIB"] = ""
ENV["BIORUBY_TEST_GEM"] = nil
work_in_another_directory do |dirname|
ruby("-rbio", test_runner)
end
end
desc "DANGER: build tar, install and run test"
task :"tar-integration-test" => [ :"tar-install",
:"installed-test" ]
desc "test installed bioruby gem version #{spec.version.to_s}"
task :"gem-test" do
data_path = File.join(Dir.pwd, "test/data")
test_runner = File.join(Dir.pwd, "test/runner.rb")
data_path = Pathname.new(data_path).cleanpath.to_s
test_runner = Pathname.new(test_runner).cleanpath.to_s
ENV["BIORUBY_TEST_DATA"] = data_path
ENV["BIORUBY_TEST_LIB"] = nil
ENV["BIORUBY_TEST_GEM"] = spec.version.to_s
work_in_another_directory do |dirname|
ruby(test_runner)
end
end
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