* Add tests for Bio::PubMed#search, query, pmfetch, although they will be deprecated in the future. * This commit and commit bfe4292 are inspired by #76 (though the pull request have not been merged), and the commits fix the issue #75. Thanks to Paul Leader who reported the issue and the pull request.
* Bio::PubMed#search, query, pmfetch: remove old code using deprecated and/or unofficial web API, and change use esearch or efetch methods which use NCBI E-utilities. These methods will be deprecated in the future. To indicate this, show warning message if $VERBOSE is true. * Update RDoc documentation
…server * Change default server to EBI Dbfetch server. * The BioRuby BioFetch server is removed. When "-r" option (force to use BioRuby server) is specified, warning message is shown, and the program exits with code 1 (abnormal exit). * Usage message is also changed.
* Issue about Bio::Fetch is resolved by recent commits. * The BioRuby BioFetch server is deprecated. There is no hope to restart the service again. EBI Dbfetch server is an alternative.
* Incompatible change: remove a class method Bio::Fetch.query because default server URL in Bio::Fetch is deprecated. * New class method: Bio::Fetch::EBI.query. This can be used as an alternative method of deprecated Bio::Fetch.query method.
* Incompatible change: Default server URL in Bio::Fetch.new is deprecated. Users must explicitly specify the URL. Alternatively, users must change their code to use Bio::Fetch::EBI. * New class Bio::Fetch::EBI, EBI Dbfetch client. This acts the same as Bio::Fetch.new(Bio::Fetch::EBI::URL) with default database name "ena_sequence".
* Bio::Sequence::NA#gc_content, at_content, gc_skew, at_skew: Return value is Rational or Float in recent versions of Ruby. Documentation added for the treatment of "u" and to return 0.0 if there are no bases. Reported by ctSkennerton (#73 ).
* Bug fix: SEQRES serNum digits were extended in PDB v3.2 (2008). Thanks to a researcher who reports the patch via email.
* gemfiles/Gemfile.travis-rbx: Gemfile for rbx (Rubinius) on Travis-ci * .travis.yml is modified to use gemfile/Gemfile.travis-rbx for rbx.
* workaround to avoid error in Ruby 1.8.7 and jruby-18mode (reference: rubygems/rubygems#763 )
* In tar and gem integration tests, Ruby versions are changed to MRI 2.0.0 and jruby-19mode. * Add jruby-18mode * Add rbx-2.1.1
* Add 2.1.0 and 2.0.0 * Remove rbx-18mode and rbx-19mode * 1.9.2 is moved from "include" to "rvm". * 1.8.7 is moved from "rvm" to "include", and remove "gemfiles/Gemfile.travis-ruby1.8" line from "gemfile". * Remove "exclude" and simplify build matrix. * Suggested by agrimm in #91
* Bug fix: Only do gsub on bio_ref.reference.authors if it exists. Fix #89