config files for Travis CI continuous integration service
travis-ci: comment out soap4r-ruby1.9 in Gemfile because of error

 * travis-ci: soap4r-ruby1.9 gem in Gemfile.travis-ruby1.9 and
   Gemfile.travis-jruby1.9 is commented out because of an error
   "uninitialized constant XML::SaxParser".
.travis.yml: comment out apt-get lines

 * .travis.yml: comment out apt-get lines because libxml2-dev
   and libexpat1-dev are already installed.
removed potential circular require about Bio::Sequence::Format
Test bug fix: order of hash keys are not guaranteed

 * Test bug fix: Bio::TestSOFT#test_dataset: order of hash keys are
   not guaranteed.
Fixed spurious JRuby failures in test_tree.rb due to floating point differences.
test_tree.rb: to use %f instead of %g to prevent odd behavior.
Use libxml-ruby instead of libxml-jruby to fix JRuby test failures.

The travis-ci Gemfiles currently call for libxml-jruby; this appears
not to support the same API as libxml-ruby, resulting in several tests
in test/unit/bio/db/test_phyloxml.rb failing with "NameError:
uninitialized constant LibXMLJRuby::XML::Parser::Options". Switching
to the C libxml-ruby library allows these tests to pass under JRuby in
1.8 mode.

JRuby in 1.9 mode still fails a few PhyloXML tests due to
https://jira.codehaus.org/browse/JRUBY-6662.
libxml-ruby is disabled because of build error on Travis-ci
Retry sequence randomize test up to 10 times when fails

 * To suppress rare failure of chi-square equiprobability tests for
   Bio::Sequence::Common#randomize, test code changed to retry
   up to 10 times if the chi-square test fails.  The assertion fails
   if the chi-square test fails 10 consecutive times, and this
   strongly suggests bugs in codes or in the random number generator.
 * The chi-square equiprobability tests are separated into a new
   test class.
broader FASTQ file recognition

 * Because PacBio RS sequencer may produce kilobases long reads and
   read buffer size (default 31 lines) for file format detection
   may not be sufficient to find the second id line starting with "+",
   the regular expression for FASTQ is truncated only to check the
   first id line starting with "@".
 * Test code is added.
New env BIORUBY_TEST_GEM and BIORUBY_TEST_LIB behavior changed

 * New environment variable BIORUBY_TEST_GEM for testing installed
   bio-X.X.X gem. Version number can be specified.
   Example with version number:
    % env BIORUBY_TEST_GEM=1.4.2.5000 ruby test/runner.rb
   Example without version number:
    % env BIORUBY_TEST_GEM="" ruby test/runner.rb
 * When BIORUBY_TEST_LIB is empty, it no longer add an empty string to
   $LOAD_PATH. Moreover, when BIORUBY_TEST_GEM is set, the variable is
   ignored.
BIORUBY_TEST_LIB is always added on the top of $LOAD_PATH

 * When BIORUBY_TEST_LIB is specified, the specified directory name
   is always added on the top of $LOAD_PATH even if it is already
   included in the middle of $LOAD_PATH.
rake tasks added and default task is changed

 * New tasks:
   * gem-install: build gem and install it
   * gem-install-nodoc: build gem and install it with --no-ri --no-rdoc.
   * gem-test: test installed bioruby gem installed with gem-install
     (or gem-install-nodoc)
   * gem-integration-test: build gem, install and run test (with --no-ri
     --no-rdoc)
   * tar-install: DANGER: build tar and install by using setup.rb
   * installed-test: test installed bioruby
   * tar-integration-test: DANGER: build tar, install and run test
   * see-env: see BIORUBY_RAKE_DEFAULT_TASK environment variable and
     invoke the specified task. If the variable did not exist, it
     invokes "test" which is previously the default task. It is added
     for selecting task on Travis-ci. It is not recommended to invoke
     the task explicitly by hand.
 * Default task is changed from "test" to "see-env".
regenerate bioruby.gemspec with rake regemspec
descriptions are modified for danger operations
remove 1.9.2; add tar/gem integration tests

 * Remove ruby version 1.9.2 from matrix for reducing builds
 * Add tar/gem integration tests
 * Add a new helper script gemfiles/modify-Gemfile.rb,
   modifying gemfile when running gem integration test.
 * Remove jruby version comments
.travis.yml: .gemspec is needed to install local gem
gem-integration-test, gem-install and gem-install-nodoc are removed

 * gem-integration-test, gem-install and gem-install-nodoc are removed
   because they are useless with Bundler
Rakefile: give up using Dir.mktmpdir because of JRuby's behavior

 * Rakefile: give up using Dir.mktmpdir because of JRuby's behavior
   that may be related with http://jira.codehaus.org/browse/JRUBY-5678