bio 1.6.0.pre.20181210 → 2.0.0

data/Gemfile

@@ -4,5 +4,3 @@ gem "rake"
 gem "rdoc"
 gem "test-unit"
 
-gem "xmlparser"
-

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) 2009-2019 Naohisa Goto <ng@bioruby.org>
 License::   The Ruby License
 
 = Known issues and bugs in BioRuby
@@ -12,11 +12,6 @@ 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
-
-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.
-
 ==== String encodings
 
 Currently, BioRuby do not care string encodings. In some cases,
@@ -28,12 +23,11 @@ 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

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>

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
@@ -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.
 
 
@@ -126,14 +122,6 @@ 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]
@@ -153,40 +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
 
@@ -197,19 +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
@@ -253,15 +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)
 
@@ -274,26 +206,45 @@ Plugins (Biogems) listed below had been included in BioRuby in former days,
 and were split to separate packages to reduce complexity and external
 dependencies.
 
-* {bioruby-phyloxml}[http://rubygems.org/gems/bioruby-phyloxml]
+* {bio-shell}[https://rubygems.org/gems/bioruby-shell]
+* {bio-executables}[https://rubygems.org/gems/bioruby-executables]
+* {bio-blast-xmlparser}[https://rubygems.org/gems/bioruby-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}[http://rubygems.org/gems/bio-biosql]
+* {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

@@ -1,32 +1,91 @@
-= BioRuby 1.5.1 RELEASE NOTES
+= BioRuby 2.0.0 RELEASE NOTES
 
-A lot of changes have been made to the BioRuby 1.5.1 after the version 1.5.0
+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.
 
-== New features
+== Features moved to separete gems
 
-=== (tbd)
+Some features are moved to separate gems because of reducing complexity
+and/or to avoid external library dependency of BioRuby core.
 
-(paragraph)
+=== BioRuby Shell is moved to "bio-shell"
 
-=== Other new features
+BioRuby Shell is split to "bio-shell" gem.
 
-* (tbd)
-* (tbd)
+=== Executable files are moved to "bio-executables"
 
-== Bug fixes
+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).
+
+=== Fast BLAST XML result parser by using Expat XML Parser is moved to "bio-blast-xmlparser"
+
+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::PhyloXML is moved to "bioruby-phyloxml"
+
+Bio::PhyloXML is split to "bioruby-phyloxml" gem.
+
+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::SQL is moved to "bio-biosql"
+
+Bio::SQL is split to "bio-biosql" gem.
+
+
+== New features and improvements
+
+=== 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.
 
-=== (tbd)
+In BioRuby, the following classes/modules are affected.
 
-(paragraph)
+* Bio::NCBI::REST and descending classes
+* Bio::PubMed
 
-=== Other bug fixes
+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.
+
+=== KEGG::GENES#diseases and related methods are added
+
+The following methods are added to KEGG::GENES, contributed by @kojix2.
+
+* networks_as_strings
+* diseases_as_strings
+* diseases_as_hash
+* diseases
+* drug_targets_as_strings
+
+=== Pre-calculated ambiguity codon tables in Bio::CodonTable
+
+Pre-calculated ambiguity codon tables are added, contributed by
+Tomoaki NISHIYAMA.
+
+
+== Bug fixes
+
+* 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.
 
-* Fixed: (...)
-* Fixed: (...)
 
 == Incompatible changes
 
@@ -51,18 +110,27 @@ Bio::PhyloXML::Taxonomy or adding the following monkey patch may be needed.
 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.
 
-=== (tbd)
+=== Some features are moved to separete gems
 
-(paragraph)
+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.
 
-* (tbd)
 
 == Other important news
 
-(tbd)
+=== Ruby 1.8 is no longer supported
+
+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.
+
+=== Installation without RubyGems is no longer supported
+
+Installation by using setup.rb without RubyGems is no longer supported,
+and setup.rb is no longer included in BioRuby distribution.
 

data/Rakefile

@@ -272,36 +272,6 @@ task :"see-env" do
   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")
@@ -318,10 +288,6 @@ task :"installed-test" do
   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")