bio 1.5.1 → 2.0.2

data/{gemfiles/Gemfile.travis-ruby2.2 → Gemfile}

@@ -4,6 +4,3 @@ gem "rake"
 gem "rdoc"
 gem "test-unit"
 
-gem "xmlparser"
-gem "libxml-ruby"
-

data/KNOWN_ISSUES.rdoc

@@ -1,5 +1,5 @@
 = KNOWN_ISSUES.rdoc - Known issues and bugs in BioRuby
-Copyright:: Copyright (C) 2009-2012 Naohisa Goto <ng@bioruby.org>
+Copyright:: Copyright (C) 2009-2020 Naohisa Goto <ng@bioruby.org>
 License::   The Ruby License
 
 = Known issues and bugs in BioRuby
@@ -12,10 +12,13 @@ they are not BioRuby's issues and/or it is very difficult to fix them.
 
 == 1. Ruby version specific issues
 
-=== Ruby 1.9.1 or later
+==== Ruby 3.0
 
-Some classes/modules/methods still may not work or may return incorrect
-results in Ruby 1.9.X, especially those not covered by the unit tests.
+Since Ruby 3.0, internal inplementation of String methods are changed and
+methods in a subclass of String return String instead of the subclass
+instance. Bio::Sequence::NA, AA, and Generic inherit String and are severely
+affected by this change.
+See GitHub issue https://github.com/bioruby/bioruby/issues/137 .
 
 ==== String encodings
 
@@ -28,12 +31,11 @@ Encoding::CompatibilityError or "ArgumentError: invalid byte sequence in
 ==== Ruby 1.9.0
 
 (WONT_FIX) Ruby 1.9.0 is NOT supported because it isn't a stable release.
-Use Ruby 1.9.1 or later.
 
-==== Ruby 1.8.6 or earlier
+==== Ruby 1.9.1 or earlier (including Ruby 1.8.7)
 
-(WONT_FIX) Problems observed only with Ruby 1.8.6 or earlier will not be
-fixed. Note that Ruby 1.8.6 or earlier is no longer supported, as described
+(WONT_FIX) Problems observed only with Ruby 1.9.1 or earlier will not be
+fixed. Note that Ruby 1.9.1 or earlier is no longer supported, as described
 in README.rdoc.
 
 ==== Ruby 1.8.2 or earlier
@@ -162,11 +164,6 @@ do not recommend to do so because the format is unstable.
 
 == 4. Compatibility issues with other libraries/extensions
 
-=== ActiveRecord
-
-BioSQL support uses ActiveRecord, but the author of the document does not
-know which version is suitable.
-
 === Ruby on Rails
 
 BioRuby Shell on Web uses Ruby on Rails, but the author of the document does

data/LEGAL

@@ -6,15 +6,6 @@ license (see the file COPYING) or public-domain except some files
 mentioned below.
 
 
-setup.rb:
-
- Copyright (c) 2000-2006 Minero Aoki
-
- This program is free software.
- You can distribute/modify this program under the terms of
- the GNU LGPL, Lesser General Public License version 2.1.
-
-
 sample/any2fasta.rb:
 
    Copyright (C) 2006 Pjotr Prins <p@bioruby.org>
@@ -68,7 +59,6 @@ sample/vs-genes.rb:
 
 sample/fastagrep.rb:
 sample/fastasort.rb:
-sample/na2aa.rb:
 
    Copyright (C) 2008 KATAYAMA Toshiaki <k@bioruby.org> & Pjotr Prins
 

data/README.rdoc

@@ -2,7 +2,7 @@
 = README.rdoc - README for BioRuby
 Copyright:: Copyright (C) 2001-2007 Toshiaki Katayama <k@bioruby.org>,
             Copyright (C) 2008      Jan Aerts <jandot@bioruby.org>
-            Copyright (C) 2011-2015 Naohisa Goto <ng@bioruby.org>
+            Copyright (C) 2011-2019 Naohisa Goto <ng@bioruby.org>
 License::   The Ruby License
 * The above statement is limited to this file. See below about BioRuby's
   copyright and license.
@@ -10,7 +10,7 @@ License::   The Ruby License
 
 = BioRuby
 
-Copyright (C) 2001-2012 Toshiaki Katayama <k@bioruby.org>
+Copyright (C) 2001-2019 Toshiaki Katayama <k@bioruby.org>
 
 BioRuby is an open source Ruby library for developing bioinformatics
 software.  Object oriented scripting language Ruby has many features
@@ -30,7 +30,7 @@ Blast, Fasta, Hmmer and many other software packages for biological
 analysis can be executed within the BioRuby script, and the results
 can be fully parsed to extract the portion you need.  BioRuby supports
 major biological database formats and provides many ways for accessing
-them through flatfile indexing, SQL, web services etc.  Various web
+them through flatfile indexing, web services etc.  Various web
 services can be easily utilized by BioRuby.
 
 
@@ -45,10 +45,7 @@ See RELEASE_NOTES.rdoc for news and important changes in this version.
 README.rdoc:: This file. General information and installation procedure.
 RELEASE_NOTES.rdoc:: News and important changes in this release.
 KNOWN_ISSUES.rdoc:: Known issues and bugs in BioRuby.
-doc/RELEASE_NOTES-1.4.3.rdoc:: News and incompatible changes from 1.4.2 to 1.4.3.
-doc/RELEASE_NOTES-1.4.2.rdoc:: News and incompatible changes from 1.4.1 to 1.4.2.
-doc/RELEASE_NOTES-1.4.1.rdoc:: News and incompatible changes from 1.4.0 to 1.4.1.
-doc/RELEASE_NOTES-1.4.0.rdoc:: News and incompatible changes from 1.3.1 to 1.4.0.
+doc/RELEASE_NOTES-*.rdoc:: Release notes for old versions.
 doc/Changes-1.3.rdoc:: News and incompatible changes from 1.2.1 to 1.3.0.
 doc/Changes-0.7.rd:: News and incompatible changes from 0.6.4 to 1.2.1.
 
@@ -60,7 +57,7 @@ doc/Tutorial.rd.html:: HTML version of Tutorial.rd.
 ==== BioRuby development
 
 ChangeLog:: History of changes.
-doc/ChangeLog-1.4.3:: changes from 1.4.2 to 1.4.3.
+doc/ChangeLog-*:: ChangeLog for old versions.
 doc/ChangeLog-before-1.4.2:: changes before 1.4.2.
 doc/ChangeLog-before-1.3.1:: changes before 1.3.1.
 README_DEV.rdoc:: Describes ways to contribute to the BioRuby project, including coding styles and documentation guidelines.
@@ -114,9 +111,8 @@ and can be obtained by the following procedure:
 
 == REQUIREMENTS
 
-* Ruby 1.8.7 or later (except Ruby 1.9.0) -- http://www.ruby-lang.org/
-  * Ruby 2.1.6 or later, or Ruby 2.2.2 or later is recommended.
-  * This is the final version running on Ruby 1.8, tested with Ruby1.8.7-p374.
+* Ruby 2.0.0 or later -- http://www.ruby-lang.org/
+  * Ruby 2.4.6, 2.5.5, 2.6.3 or later is recommended.
   * See KNOWN_ISSUES.rdoc for Ruby version specific problems.
 
 
@@ -126,37 +122,12 @@ Some optional libraries can be utilized to extend BioRuby's functionality.
 If your needs meets the following conditions, install them by using RubyGems,
 or download and install from the following web sites.
 
-For faster parsing of the BLAST XML output format:
-
-* {xmlparser}[https://rubygems.org/gems/xmlparser]
-  * For Ruby 1.8: {gem install xmlparser}[http://rubygems.org/gems/xmlparser]
-  * For Ruby 1.9 or later: http://www.yoshidam.net/Ruby.html#xmlparser
-  * In both cases, {The Expat XML Parser}[http://expat.sourceforge.net/]
-    and C compiler will be required.
-
 Creating faster flatfile index using Berkley DB:
 
 * {GitHub:ruby-bdb}[https://github.com/knu/ruby-bdb]
   (which took over {bdb}[https://github.com/ruby-bdb/bdb])
   (No RubyGems available)
   * {Oracle Berkeley DB}[http://www.oracle.com/technetwork/database/berkeleydb/index.html] and C compiler will be required.
-  
-Accessing BioSQL database created by other Open Bio* libraries:
-
-* {gem install activerecord}[http://rubygems.org/gems/activerecord]
-  and at least one driver (or adapter):
-  * {gem install mysql}[http://rubygems.org/gems/mysql] or
-    {gem install mysql2}[http://rubygems.org/gems/mysql2]
-  * {gem install pg}[http://rubygems.org/gems/pg]
-  * {gem install sqlite-ruby}[http://rubygems.org/gems/sqlite-ruby] or
-    {gem install sqlite3}[http://rubygems.org/gems/sqlite3]
-  * {gem install activerecord-oracle_enhanced-adapter}[http://rubygems.org/gems/activerecord-oracle_enhanced-adapter]
-
-For parsing PhyloXML format files:
-
-* {gem install libxml-ruby}[http://rubygems.org/gems/libxml-ruby]
-  * {GNOME Libxml2 XML toolkit}[http://xmlsoft.org/] and C compiler will be
-    required.
 
 
 == INSTALL
@@ -170,40 +141,6 @@ If you are using RubyGems, just type
 Alternatively, manually download bio-X.X.X.gem from 
 http://bioruby.org/archive/ and install it by using gems command.
 
-RubyGems is bundled with Ruby 1.9.1 or later. For Ruby 1.8.7 or earlier,
-download and install RubyGems from http://rubygems.org/ .
-
-=== INSTALL without RubyGems
-
-In the bioruby source directory (such as bioruby-x.x.x/), run setup.rb
-as follows:
-
-  % su
-  # ruby setup.rb
-
-These simple step installs this program under the default location of
-Ruby libraries.  You can also install files into your favorite directory
-by supplying setup.rb some options. Try "ruby setup.rb --help".
-
-If your operating system supports 'sudo' command (such as Mac OS X),
-try the following procedure instead of the above.
-
-  % sudo ruby setup.rb
-
-For older version users: "install.rb" is now renamed to "setup.rb".
-The options "config", "setup", and "install" are still available.
-
-  % ruby setup.rb config
-  % ruby setup.rb setup
-  % su
-  # ruby setup.rb install
-
-You can run
-
-  % ruby setup.rb --help
-
-for more details.
-
 
 === Running self-test
 
@@ -214,19 +151,6 @@ To run tests,
 
  % ruby test/runner.rb
 
-If you are using Ruby 1.8.x and you want to use components installed by using
-RubyGems, explicit loading of RubyGems may be needed.
-
- % ruby -rubygems test/runner.rb
-
-Alternatively, testrb, the test runner command of ruby, can be used.
-
- % testrb test/
-
-With testrb, you can select tests to run, for example,
-
- % testrb test/unit
-
 For those familiar with Rake,
 
  % rake test
@@ -270,15 +194,6 @@ You can also read other documentation in the 'doc' directory.
 
   bioruby-x.x.x/doc/
 
-=== RubyGems on Ruby 1.8.x
-
-With RubyGems on Ruby 1.8.x, you may need to load 'rubygems' library before
-using 'bio'. This may not be needed, depending on settings of Ruby.
-
-  #!/usr/bin/env ruby
-  require 'rubygems'
-  require 'bio'
-
 
 == PLUGIN (Biogem)
 
@@ -287,20 +202,49 @@ for list of plugins and related software utilizing BioRuby.
 
 * http://biogems.info/
 
+Plugins (Biogems) listed below had been included in BioRuby in former days,
+and were split to separate packages to reduce complexity and external
+dependencies.
+
+* {bio-shell}[https://rubygems.org/gems/bio-shell]
+* {bio-executables}[https://rubygems.org/gems/bio-executables]
+* {bio-blast-xmlparser}[https://rubygems.org/gems/bio-blast-xmlparser]
+* {bioruby-phyloxml}[https://rubygems.org/gems/bioruby-phyloxml]
+  * NOTE: Please uninstall bio-phyloxml, that have been created as a
+    preliminary trial of splitting a module in 2012 and have not been
+    maintained after that.
+* {bio-biosql}[https://rubygems.org/gems/bio-biosql]
+
+Plugins (Biogems) listed below may be useful for running existing codes.
+
+* {bio-old-biofetch-emulator}[https://rubygems.org/gems/bio-old-biofetch-emulator] -- Emulates deprecated BioRuby's BioFetch server by using other existing web services.
+
 To develop your own plugin, see "Plugins" pages of BioRuby Wiki.
 
 * http://bioruby.open-bio.org/wiki/Plugins
 
+=== Recommended Plugins (gems)
+
+For existing BioRuby users, it is recommended to install the following gems:
+
+bio-shell :: If you use the BioRuby Shell.
+bio-executables :: If you use br_bio* commands.
+bio-old-biofetch-emulator :: If you run existing codes using BioFetch, including sample and demo codes in sample/.
+bio-blast-xmlparser :: If you treat BLAST XML result files and Expat XML parser (with development files) is installed in your system.
+bioruby-phyloxml :: If you use Bio::PhyloXML and Libxml2 (with developemnt files) is installed in your system.
+
+Note that it is NOT recommended to install bio-biosql unless you have
+really used Bio::SQL, because it depends on older version of ActiveRecords
+and ActiveSupport that may not be run on recent Ruby versions.
+
+
 == LICENSE
 
 BioRuby can be freely distributed under the same terms as Ruby.
 See the file COPYING (or COPYING.ja written in Japanese).
 
 As written in the file COPYING, see the file LEGAL for files distributed
-under different license. For example, setup.rb which comes from "setup"
-developed by Minero Aoki (http://i.loveruby.net/en/projects/setup/) is
-licensed under LGPL 2.1.
-
+under different license.
 
 == REFERENCE
 

data/README_DEV.rdoc

@@ -2,7 +2,7 @@
 
 Copyright::  Copyright (C) 2005, 2006 Toshiaki Katayama <k@bioruby.org>
 Copyright::  Copyright (C) 2006, 2008 Jan Aerts <jandot@bioruby.org>
-Copyright::  Copyright (C) 2011       Naohisa Goto <ng@bioruby.org>
+Copyright::  Copyright (C) 2011, 2019 Naohisa Goto <ng@bioruby.org>
 
 = HOW TO CONTRIBUTE TO THE BIORUBY PROJECT?
 
@@ -360,16 +360,16 @@ We are mainly using Ruby MRI (Matz' Ruby Implementation, or Matz' Ruby
 Interpreter).  Please confirm that your code is running on current stable
 release versions of Ruby MRI.
 
-We are very happy if your code can run on both Ruby 1.8.x and 1.9.x.
-Note that Ruby 1.9.0 should be ignored because it was discontinued.
-Ruby 1.8.5 or earlier versions can also be ignored. See README.rdoc and
-RELEASE_NOTES.rdoc for recommended Ruby versions.
+See README.rdoc and RELEASE_NOTES.rdoc for recommended Ruby versions.
 
 It is welcome to support JRuby, Rubinius, etc, in addition to Ruby MRI.
 
 Of course, it is strongly encouraged to write code that is not affected by
 differences between Ruby versions and/or implementations, as far as possible.
 
+Although we no longer support Ruby 1.8, it might be useful if your code
+could also run on Ruby 1.8.7 in addition to supported Ruby versions.
+
 = OS and ARCHITECTURE
 
 We hope BioRuby can be run on both UNIX (and UNIX-like OS) and Microsoft

data/RELEASE_NOTES.rdoc

@@ -1,311 +1,195 @@
-= BioRuby 1.5.1 RELEASE NOTES
-
-Few changes have been made to the BioRuby 1.5.1 after the version 1.5.0 is
-released.
-
-== NEWS
-
-=== HTTPS is used to access NCBI web services
-
-As you may know, NCBI announced that all HTTP resources will be switched
-to HTTPS on September 30, 2016. To follow the transition, all URLs for
-accessing NCBI E-utilities in BioRuby are changed to use HTTPS.
-
-In BioRuby, the following classes/modules are affected.
-
-* Bio::NCBI::REST and descending classes
-* Bio::PubMed
-
-In some rare cases (especially when building Ruby and/or OpenSSL by yourself
-from source code), Ruby does not include SSL/TLS support, or Ruby fails to
-detect SSL root certificates. In such cases, you may need to reinstall or
-upgrade Ruby, OpenSSL (or alternatives), and/or SSL root certificates with
-appropriate configuration options. Alternatively, installing binary packages
-is generally a good idea.
-
-
-= BioRuby 1.5.0 RELEASE NOTES
-
-A lot of changes have been made to the BioRuby 1.5.0 after the version 1.4.3
-is released. This document describes important and/or incompatible changes
-since the BioRuby 1.4.3 release.
-
-For known problems, see KNOWN_ISSUES.rdoc.
-
-== NEWS
-
-=== Full support of Ruby 2.0.0, 2.1, and 2.2
-
-Ruby 2.0.0, 2.1, and 2.2 are now recommended Ruby versions for running
-BioRuby codes.
-
-=== Support of Ruby 1.8 will be stopped
-
-This release is the final BioRuby version that can be run on Ruby 1.8.
-
-=== License is updated to the new Ruby's License
-
-BioRuby is distributed under the same license as Ruby's. In October 2011,
-Ruby's License was changed from a dual license with GPLv2 to a dual license
-with 2-clause BSDL. Since BioRuby 1.5.0, we have updated to the
-new version of Ruby's License. For details about the license, see COPYING
-or COPYING.ja and BSDL. In addition, please do not forget to see LEGAL for
-exception files that are subjected to different licenses.
-
-=== Semantic Versioning will be introduced
-
-We will adopt the Semantic Versioning since the next release version, which
-will be BioRuby 1.5.1. This means that BioRuby 1.5.0 is NOT subject to the
-Semantic Versioning.
-
-
-== New features and improvements
-
-=== New method Bio::FastaFormat#first_name
-
-Bio::FastaFormat#first_name method is added to get the first word in the
-definition line. This method was proposed by Ben J. Woodcroft.
-
-=== Accuracy of Bio::SiRNA
-
-Accuracy of siRNA designing algorithms in Bio::SiRNA is improved,
-contributed by meso_cacase.
-
-=== Speed up of Bio::ClustalW::Report
-
-Running speed of Bio::ClustalW::Report is optimized, contributed by
-Andrew Grimm.
-
-=== Many warning messages are squashed
-
-Most warning messages when running ruby with "-w" option, e.g. "assigned
-but unused variable", "instance variable @xxx not initialized", are
-suppressed. Fixes are contributed by Kenichi Kamiya, Andrew Grimm, and
-BioRuby core members.
-
-=== Refactoring of codes
-
-Many existing codes are reviewed and refactored. Patches are contributed
-by Iain Barnett, Kenichi Kamiya, and BioRuby core members.
+= BioRuby 2.0.2 RELEASE NOTES
 
+Some bugs fixes have been made in BioRuby 2.0.2 after the release of 2.0.1.
 
 == Bug fixes
 
-=== Bugs due to remote server changes
+* Fix NameError in Bio::Sequence#output(:embl)
+  (https://github.com/bioruby/bioruby/issues/135 )
+* Suppress warning: Gem::Specification#has_rdoc= is deprecated
+  (https://github.com/bioruby/bioruby/issues/138 )
+* Fix misspelling URL in README.rdoc
 
-==== Bio::PubMed
+== Known issues
 
-Bio::PubMed#search, query, and pmfetch are re-implemented by using NCBI
-E-Utilities. They were broken because unofficial API was used.
-Paul Leader reported the bug and gave discussion.
+A known issue about Ruby 3.0 is added to KNOWN_ISSUES.rdoc.
+The issue will be fixed in the near future.
 
-==== Bio::Hinv
 
-Bio::Hinv did not work because of the API server URL is changed.
 
-==== Bio::TogoWS::REST
+= BioRuby 2.0.1 RELEASE NOTES
 
-* Bio::TogoWS::REST#search with offset and limit did not work due to
-  TogoWS server spec change about URI escape.
-* Bio::TogoWS::REST#convert did not work because of the spec change of
-  TogoWS REST API.
+Some bug fixes and improvements have been made to the BioRuby 2.0.1 after
+the version 2.0.0 is released.
 
-=== Bio::Fetch
+== Bug fixes
 
-Bio::Fetch with default parameters did not work because BioRuby's default
-BioFetch server had been down. We have decided not to restore the service.
-For smooth migration of codes using BioRuby's BioFetch server, we provide
-"bio-old-biofetch-emulator" gem. See below "Imcompatible changes" for details.
+* Bio::GFF::GFF2::Record.parse did not return correct object.
 
-The bug was reported and discussed by Jose Irizarry, Robert A. Heiler, and
-others.
+== Improvement of sample scripts
 
-=== BioSQL
+The following scripts in the sample/ directiry are newly added.
 
-* Only do gsub on bio_ref.reference.authors if it exists.
-* Missing require when generating genbank output for BioSQL sequence.
+* color_scheme_aa.rb: Example of Bio::ColorScheme for an amino acid sequence.
+* fastq2html.rb: Visualization of FASTQ sequences, colored by quality scores.
+* rev_comp.rb: Shows reverse-complement sequences of the given sequences.
 
-Contributed by Brynjar Smari Bjarnason.
+The floowing scripts are modified to fix bug and/or to improve features.
 
-=== Bugs found in data format parsers
+* na2aa.rb: Completely rewritten to fix bug. Shows translated sequences.
+* color_scheme_na.rb: Added support for various sequence formats.
 
-* Bio::PDB#seqres SEQRES serNum digits were extended in PDB v3.2 (2008).
-  Thanks to a researcher who sent the patch.
-* Bio::Blast::Default::Report parse error when subject sequence contains
-  spaces. Edward Rice reported the bug.
-* Bio::UniProtKB#gene_name raised NoMethodError when gene_names method
-  returns nil. It should return nil. Candidate fix sent by Jose Irizarry.
-* Bio::PhyloXML::Parser.open_uri did not return block return value when
-  giving a block.
+=== CWL (Common Workflow Language) workflow files are added
 
-=== Other bugs
+CWL (Common Workflow Language) workflow files are added for some sample
+scripts. The usage of each sample script will be clarified with the CWL
+workflow files.
 
-* lib/bio/shell/plugin/seq.rb: String#step and #skip (extended by bioruby
-  shell) did not yield the last part of the string due to a change from
-  Ruby 1.8 to 1.9.
-* Documentation and typo fixes. Contributed by many persons, including
-  Iain Barnett and ctSkennerton.
+Two type of files are prepared for CWL workflow engine. *.cwl is a workflow
+definition file for each sample script. *.testdata.yaml describes sample
+input data for each CWL workflow.
 
+In this version, cwl files for the 3 sample scripts are added.
 
-== Renamed features
+* fastq2html.rb: fastq2html.cwl with fastq2html.testdata.yaml
+* na2aa.rb: na2aa.cwl with na2aa.testdata.yaml
+* rev_comp.rb: rev_comp.cwl with rev_comp.testdata.yaml
 
-=== Bio::SPTR, Bio::UniProt, Bio::SwissProt, and Bio::TrEMBL => Bio::UniProtKB
 
-The classes for parsing UniProtKB (former SwissProt and TrEMBL) data,
-Bio::SPTR, Bio::UniProt, Bio::SwissProt, and Bio::TrEMBL, are unified into
-the new class name Bio::UniProtKB, and old names are deprecated.
 
-For keeping backward compatibility, old class names Bio::SPTR, Bio::UniProt,
-Bio::SwissProt, and Bio::TrEMBL are still available, but warning message
-will be shown when using the old class names. These old class names will be
-deleted in the future.
+= BioRuby 2.0.0 RELEASE NOTES
 
-The file contatining Bio::UniProtKB class definition is also changed to
-lib/bio/db/embl/uniprotkb.rb. For keeping backward compatibility, old
-files sptr.rb, uniprot.rb, tremble.rb are still kept, but they will be
-removed in the future.
+A lot of changes have been made to the BioRuby 2.0.0 after the version 1.5.x
+is released. This document describes important and/or incompatible changes
+since the BioRuby 1.5.0 release.
 
+For known problems, see KNOWN_ISSUES.rdoc.
 
-== Deprecated features
+== Features moved to separete gems
 
-=== Bio::RefSeq, Bio::DDBJ
+Some features are moved to separate gems because of reducing complexity
+and/or to avoid external library dependency of BioRuby core.
 
-Bio::RefSeq and Bio::DDBJ are deprecated because they are only an alias of
-Bio::GenBank. Warning message will be shown when loading the classes and
-initializing new instances. Please use Bio::GenBank instead.
+=== BioRuby Shell is moved to "bio-shell"
 
-lib/bio/db/genbank/ddbj.rb and lib/bio/db/genbank/refseq.rb which contain
-Bio::DDBJ and Bio::RefSeq, respectively, are also deprecated. For keeping
-backward compatibility, old file are still kept, but they will be removed
-in the future.
+BioRuby Shell is split to "bio-shell" gem.
 
+=== Executable files are moved to "bio-executables"
 
-== Removed features
+To avoid unexpected loading of executable files by some Rails software,
+all executable commands are moved to "bio-executables" gem
+(except the "bioruby" command that is included in the above "bio-shell" gem).
 
-=== Bio::SOAPWSDL
+=== Fast BLAST XML result parser by using Expat XML Parser is moved to "bio-blast-xmlparser"
 
-Bio::SOAPWSDL (lib/bio/io/soapwsdl.rb) is removed because SOAP4R
-(SOAP/WSDL library in Ruby) is no longer bundled with Ruby since Ruby 1.9.
-For Ruby 1.9 or later, some gems of SOAP4R are available, but we think they
-are not well-maintained. Moreover, many SOAP servers have been retired
-(see below). So, we give up maintaining Bio::SOAPWSDL and all SOAP client
-classes in BioRuby.
+Fast BLAST XML result parser by using Expat XML Parser is split to
+"bio-blast-xmlparser" gem, because of external C library dependency.
+Please install "bio-blast-xmlparser" gem if possible.
+If it is installed, BioRuby automatically use it.
 
-=== Bio::EBI::SOAP
+=== Bio::PhyloXML is moved to "bioruby-phyloxml"
 
-Bio::EBI::SOAP (lib/bio/io/ebisoap.rb) is removed because Bio::SOAPWSDL
-is removed.
+Bio::PhyloXML is split to "bioruby-phyloxml" gem.
 
-=== Bio::KEGG::API
+NOTE: Please uninstall "bio-phyloxml" gem, that have been created as a
+preliminary trial of splitting a module in 2012 and have not been
+maintained after that.
 
-Bio::KEGG::API is removed because KEGG API SOAP service was discontinued in
-December 31, 2012. See http://www.kegg.jp/kegg/rest/ for the announcement
-of service discontinuation.
+=== Bio::SQL is moved to "bio-biosql"
 
-=== Bio::DBGET
+Bio::SQL is split to "bio-biosql" gem.
 
-Bio::DBGET is removed because it only supports old original DBGET protocols
-that was discontinued in 2004. Note that the DBGET is still available via
-the web. See http://www.genome.jp/en/gn_dbget.html for details.
 
-=== Bio::Ensembl
+== New features and improvements
 
-Bio::Ensembl is removed because it does not work after the renewal of Ensembl
-web site in 2008. Instead, bio-ensembl gem which supports recent ensembl API
-is available.
+=== HTTPS is used to access NCBI web services
 
-=== Bio::DDBJ::XML, Bio::DDBJ::REST
+As you may know, NCBI announced that all HTTP resources will be switched
+to HTTPS on September 30, 2016. To follow the transition, all URLs for
+accessing NCBI E-utilities in BioRuby are changed to use HTTPS.
 
-Bio::DDBJ::XML and Bio::DDBJ::REST are removed because DDBJ Web API (WABI)
-web services were suspended in 2012 and then they were completely renewed
-with incompatible APIs in 2013.
+In BioRuby, the following classes/modules are affected.
 
-=== Bio::HGC::HiGet
+* Bio::NCBI::REST and descending classes
+* Bio::PubMed
 
-Bio::HGC::HiGet (lib/bio/io/higet.rb) is removed because the HiGet web server
-http://higet.hgc.jp/ have been down since 2011, and we think that the server
-will not be restored again.
+In some rare cases (especially when building Ruby and/or OpenSSL by yourself
+from source code), Ruby does not include SSL/TLS support, or Ruby fails to
+detect SSL root certificates. In such cases, you may need to reinstall or
+upgrade Ruby, OpenSSL (or alternatives), and/or SSL root certificates with
+appropriate configuration options. Alternatively, installing binary packages
+is generally a good idea.
 
-=== Bio::NCBI::SOAP
+=== KEGG::GENES#diseases and related methods are added
 
-Bio::NCBI::SOAP is removed because it always raises error during the parsing
-of WSDL files provided by NCBI. In addition, NCBI announced that the SOAP
-web service for the E-utilities will be terminated on July 1, 2015. Instead,
-Bio::NCBI::REST, REST client for the NCBI E-utility web service, is available.
+The following methods are added to KEGG::GENES, contributed by @kojix2.
 
-=== Bio::KEGG::Taxonomy
+* networks_as_strings
+* diseases_as_strings
+* diseases_as_hash
+* diseases
+* drug_targets_as_strings
 
-Bio::KEGG::Taxonomy is removed because it does not work correctly. It raises
-error, it falls into infinite loop, or it returns apparently broken data.
-Moreover, KEGG closed public FTP site and the file "taxonomy" could only be
-obtained by paid subscribers.
+=== Pre-calculated ambiguity codon tables in Bio::CodonTable
 
-=== Bio.method_missing
+Pre-calculated ambiguity codon tables are added, contributed by
+Tomoaki NISHIYAMA.
 
-Bio.method_missing, that aims to provide shortcuts of Bio::Shell methods
-with shorter name without typing "Shell", is removed because most of the
-methods raises error mainly due to bypassing of initialization procedure.
-In addition, we now think that the use of method_missing should generally
-be avoid unless it is really necessary.
 
-=== extconf.rb
+== Bug fixes
 
-extconf.rb, an alternative way to install BioRuby to the system, is removed
-because of avoiding potential confusions. Nowadays, extconf.rb is usually
-only used for building native extensions, but no native extensions are
-included in this release. Use gem or setup.rb to install BioRuby.
+* Fixed a parser bug in Bio::Fasta::Report, FASTA output (-m 10) parser,
+  contributed by William Van Etten and Mark Wilkinson via GitHub.
+* HTTPS is used to access GenomeNet BLAST web service, contributed
+  by @ramadis via GitHub.
+* Bio::AAindex documentation fix, suggested by @kojix2 via GitHub.
+* Suppress warning messages in Ruby 2.4 and later.
 
 
 == Incompatible changes
 
-Also see the above "Renamed features", "Deprecated features", and
-"Removed features" sections.
-
-=== Bio::Fetch
+=== Bio::Taxonomy is removed and merged to Bio::PhyloXML::Taxonomy
 
-The BioRuby default BioFetch server http://bioruby.org/cgi-bin/biofetch.rb,
-that was the default server for Bio::Fetch before BioRuby 1.4, is deprecated.
-Due to the service stop, default server URL in Bio::Fetch is removed, and
-we decide not to give any server URL by default for Bio::Fetch.
+Bio::Taxonomy in lib/bio/db/phyloxml/phyloxml_elements.rb was written for
+PhyloXML in 2009. It was intended to become general taxonomy data class in
+BioRuby in these days. However, no efforts have been made to improve the
+Bio::Taxonomy class, and it still remains to be a PhyloXML specific class.
+Because Bio::PhyloXML is split as a different Gem (Biogem) package, we now
+decide to remove Bio::Taxonomy and merge it to Bio::PhyloXML::Taxonomy.
 
-As an alternative, new class Bio::Fetch::EBI which uses the EBI Dbfetch
-server is added. When changing codes form Bio::Fetch to Bio::Fetch::EBI,
-be careful of the differences of database names, default and available
-data formats between the former BioRuby BioFetch server and the EBI Dbfetch
-server.
+In the codes using Bio::Taxonomy directly, changing Bio::Taxonomy to
+Bio::PhyloXML::Taxonomy or adding the following monkey patch may be needed.
 
-Methods directly affected are:
+   module Bio
+      unless defined? Taxonomy
+         Taxonomy = Bio::PhyloXML::Taxonomy
+      end
+   end
 
-* Bio::Fetch.new (Bio::Fetch#initialize) does not have default server URL,
-  and URL of a server must always be explicitly given as the first argument.
-* Bio::Fetch.query is removed.
+In the future, Bio::Taxonomy might be added as general taxonomy data class.
+The new Bio::Taxonomy might be incompatible with the current Bio::Taxonmy.
 
-For the purpose running old codes, it is recommended to install
-bio-old-biofetch-emulator gem. The bio-old-biofetch-emulator gem emulates
-old BioRuby's default BioFetch server by using other existing web services.
-See https://rubygems.org/gems/bio-old-biofetch-emulator for details.
-We think many codes can run with no changes by simply installing the gem and
-adding "-r bio-old-biofetch-emulator" into the command-line when executing
-ruby.
+=== Some features are moved to separete gems
 
+Some features are split to separete gems and removed from this "bio" gem.
+See the above "Features moved to separete gems" topics for details.
 
 == Known issues
 
 The following issues are added or updated. See KNOWN_ISSUES.rdoc for other
 already known issues.
 
-=== Bio::PDB
 
-Bio::PDB should be updated to follow PDB format version 3.3.
+== Other important news
 
-=== Bio::Blast::Report
+=== Ruby 1.8 is no longer supported
 
-NCBI announces that that they are makeing a new version of BLAST XML data
-format. BioRuby should support it.
+Ruby 1.8.x is no longer supported. Though unsupported, some components
+may still run on Ruby 1.8.7. Please use Ruby 1.8.7 at your own risk
+with this version of BioRuby.
 
-=== Bio::Blast::Default::Report
+=== Installation without RubyGems is no longer supported
 
-Bio::Blast::Default::Report currently supports legacy BLAST only.
-It may be better to support BLAST+ text output format, although NCBI
-do not recommend to do so because the format is unstable.
+Installation by using setup.rb without RubyGems is no longer supported,
+and setup.rb is no longer included in BioRuby distribution.