ngoto-bio 1.2.9.9501 → 1.3.0

data/ChangeLog

@@ -1,3 +1,196 @@
+2009-02-20  Naohisa Goto <ng@bioruby.org>
+
+	* BioRuby 1.3.0 is released.
+
+2009-02-19  Naohisa Goto <ng@bioruby.org>
+
+	* lib/bio/version.rb
+
+	  Preparation for bioruby-1.3.0 release.
+	  (commit fd7fc9f78bc5f4d9a10b3c0d457d9781c9ec2e49)
+
+	* bioruby.gemspec.erb
+
+	  Fixed a logic to determine whether in git repository, and file
+	  lists are changed to be sorted.
+	  (commit ede0c0d7aeab078b6183c4e0e7c74faec32739f7)
+
+2009-02-18  Naohisa Goto <ng@bioruby.org>
+
+	* README.rdoc
+
+	  Added list of document files bundled in the BioRuby distribution.
+	  (commit 92748f848e4708766e44c22b2f02ac662491971f)
+
+2009-02-10  Naohisa Goto <ng@bioruby.org>
+
+	* KNOWN_ISSUES.rdoc
+
+	  Added details about the text mode issue on mswin32/mingw32/bccwin32
+	  and about non-UNIX/Windows systems.
+	  (commit 342a167a23d3b078bd77b3f16f0ceb1aa071df66)
+
+2009-02-09  Naohisa Goto <ng@bioruby.org>
+
+	* test/unit/bio/db/test_gff.rb
+
+	  Test bug fix: test_gff.rb failed in some environment (e.g. Windows)
+	  because the default formatting rule of Float#to_s depends on the
+	  libc implementation.
+	  (commit f39bf88ed6a41bd328372ee7de7a23902235f833)
+
+
+2009-02-06  Naohisa Goto <ng@bioruby.org>
+
+	* lib/bio/db/gff.rb, test/unit/bio/db/test_gff.rb
+
+	  * Bug fix: Bio::GFF::GFF3::Record#id and #id= should be changed
+	    to follow the previous incompatible change of @attributes.
+	    Thanks to Tomoaki NISHIYAMA who reports the bug ([BioRuby]
+	    GFF3 status (possible bug?)).
+	  * Unit tests are added.
+	  (commit 5258d88ef98a12fd7829eb86aa8664a18a672a43)
+	  (commit c0c7708b3e91b0d2f2d0d50a4a0ba36928057cc8)
+
+2009-02-05  Naohisa Goto <ng@bioruby.org>
+
+	* Rakefile
+
+	  New task "tutorial2html" to generate html from doc/Tutorial.rd
+	  and doc/Tutorial.rd.ja.
+	  (commit 8d66fae59477f01f12b2fa3509ea34c371102725)
+
+	* doc/Tutorial.rd.html, doc/Tutorial.rd.ja.html
+
+	  Automatically generated tutorial html from RD formatted documents.
+	  (commit 90c4a23eea08b06dd758aaa0a53bea789602d252)
+
+	* doc/bioruby.css
+
+	  Newly added stylesheet for the tutorial html files. The bioruby.css
+	  have been used in http://bioruby.org/ and have been maintained by
+	  Toshiaki Katayama.
+	  (commit b69dc243787525de065bdf2e6b7da68d6079ab91)
+
+	* test/runner.rb
+
+	  Added workaroud for test-unit-2.0.x.
+	  (commit 475ac6a6b38e8df30de3d9bf4c7e810759ab023d)
+
+2009-02-04  Naohisa Goto <ng@bioruby.org>
+
+	* lib/bio/appl/blast/format0.rb
+
+	  Bug fix: a null line can be inserted after query name lines.
+	  (commit bea9ce35b4177f407575ed0752c36bba8a50f502)
+
+2009-02-03  Naohisa Goto <ng@bioruby.org>
+
+	* Tutorial.rd.ja
+
+	  * Document bug: BioRuby shell commands seq, ent, obj were renamed to
+	    getseq, getent, getobj, respectively. Thanks to Hiroyuki Mishima
+	    who reports the issue ([BioRuby-ja]).
+	  * Changes of returned value of getseq are also reflected to the
+	    document.
+	  * Recommended Ruby version and installation procedure are also
+	    changed.
+	  (commit 916e96ca549db71a550e7a5d3bd49a3149614313)
+
+	* doc/Changes-0.7.rd
+
+	  Documentation forgotten in 1.1.0: rename of BioRuby shell commands.
+	  (commit 64113314caac3453b4cc3b80ece9b5fb5841e069)
+
+2009-01-30  Naohisa Goto <ng@bioruby.org>
+
+	* lib/bio/appl/blast/format0.rb
+
+	  Bug fix: incorrect parsing of hit sequence's whole length.
+	  (commit 98e6f57630b2c3394a9403f58e76b102346c56ef)
+
+	  Bug fix: Whole length of a hit sequence is mistakenly parsed when
+	  it contains ",". WU-BLAST parser is also affected in addition to
+	  NCBI BLAST parser.
+
+	* lib/bio/db/lasergene.rb, lib/bio/db/soft.rb,
+	  lib/bio/util/color_scheme.rb, lib/bio/util/contingency_table.rb,
+	  lib/bio/util/restriction_enzyme.rb
+
+	  Removed ":nodoc:" in in "module Bio" which prevents RDoc of the
+	  Bio module.
+	  (commit 458db79b467d40ed02db0d085218f611e7dd5e04)
+
+2009-01-29  Naohisa Goto <ng@bioruby.org>
+
+	* doc/Changes-1.3.rdoc
+
+	  Added documents about Bio::TogoWS and Bio::BIORUBY_VERSION.
+
+	* lib/bio/shell/plugin/entry.rb
+
+	  getent (BioRuby shell command) is changed to use EBI Dbfetch or
+	  TogoWS in addition to NCBI or KEGG API.
+	  (commit 0e172590f60dd5a5f27a24ecd230037a7909224c)
+
+	* lib/bio/shell/plugin/togows.rb, lib/bio/shell.rb
+
+	  Added new shell plugin providing accesses to TogoWS REST services.
+	  (commit 03f6720b90e90703c23536a11b3f12c8155550ff)
+
+	* lib/bio.rb
+
+	  Added autoload of Bio::TogoWS.
+	  (commit f8605e1234164a7aa7f236b4e96a4299229753d7)
+
+	* test/functional/bio/io/test_togows.rb,
+	  test/unit/bio/io/test_togows.rb
+
+	  Newly added functional and unit tests for Bio::TogoWS::REST.
+	  (commit f04152b80d07f44f146fa3fa0729facede865aac)
+	
+	* lib/bio/io/togows.rb
+
+	  New class Bio::TogoWS::REST, a REST client for the TogoWS web
+	  service (http://togows.dbcls.jp/site/en/rest.html).
+	  (commit 652d2534163675182b9ce30cbb1dd5efff45cd60)
+
+	* bin/br_pmfetch.rb
+
+	  Changed to use Bio::BIORUBY_VERSION_ID instead of CVS version ID.
+	  (commit f69d538ffa9ded00eb68dd306e65505d03b6c656)
+
+	* lib/bio/shell/core.rb
+
+	  Changed to use BIORUBY_VERSION_ID.
+	  (commit 4ce11656a205e85cae64eca27cef7cd94eb80930)
+
+	* bioruby.gemspec.erb
+
+	  Gem version is now determined from lib/bio/version.rb or
+	  BIORUBY_GEM_VERSION environment variable.
+	  (commit 1811e845e60bc2847ea5717ef936bad93f9f2c87)
+
+	* Rakefile
+
+	  * Changed to use lib/bio/version.rb.
+	  * Environment variable BIORUBY_EXTRAVERSION is renamed to
+	    BIORUBY_EXTRA_VERSION.
+	  * Added dependency on lib/bio/version.rb to bioruby.gemspec.
+	    (commit fb27eaa584cda1bb4cb75e10085996503361c98a)
+	
+	* lib/bio.rb, lib/bio/version.rb
+
+	  Bio::BIORUBY_VERSION is split into lib/bio/version.rb.
+	  (commit 9779398c3fa0e9405a875b754a5243e0d6922c32)
+
+	  * New file lib/bio/version.rb contains BioRuby version information.
+	  * New constants: Bio::BIORUBY_EXTRA_VERSION stores extra version
+	    string (e.g. "-pre1") and Bio::BIORUBY_VERSION_ID stores BioRuby
+	    version string (e.g. "1.3.0-pre1").
+	  * Bio::BIORUBY_VERSION is changed to be frozen. Above two constants
+	    also store frozen values.
+
 2009-01-26  Naohisa Goto <ng@bioruby.org>
 
 	* KNOWN_ISSUES.rdoc
@@ -5,21 +198,25 @@
 	  Newly added KNOWN_ISSUES.rdoc that describes known issues and
 	  bugs in current BioRuby.
 	  (commit 06b10262be0bf797a3b133e4697e9b0955408944)
+	  (commit a65ad8b42613e46b0b4bb0650d6301da0dcc88c9)
 
 	* lib/bio/shell/plugin/ncbirest.rb, lib/bio/shell.rb
 
           New shell plugin lib/bio/shell/plugin/ncbirest.rb, providing
           "efetch", "einfo", "esearch", and "esearch_count" methods.
           They act the same as those defined in Bio::NCBI::REST, except
-          that efetch automatically selects databases if no options
-          are given and only 1 id is given.
+          that "efetch" fetches entries with pre-defined databases
+	  depending on arguments.
 	  (commit c482e1864aa0dbca3727b1059d4fe3d0aefb3917)
+	  (commit 3360b8905fdbcd4ca050470fdb2f02a7387e8bb9)
 
 	* lib/bio/shell/plugin/entry.rb
 
-          A shell command "getobj" is changed to use "efetch" method
-          when "gb" or some variant is specified as the database.
+          Shell commands "getent" and "getseq" are changed to use
+	  "efetch" method when "gb" or some variant is specified as
+	  the database.
 	  (commit c482e1864aa0dbca3727b1059d4fe3d0aefb3917)
+	  (commit 3360b8905fdbcd4ca050470fdb2f02a7387e8bb9)
 
 	* bioruby.gemspec.erb, bioruby.gemspec
 

data/KNOWN_ISSUES.rdoc

@@ -38,20 +38,42 @@ SOAP4R (SOAP and WSDL implementation) is no longer bundled with Ruby 1.9.
 In addition, because of the API changes in recent SOAP4R, some
 classes/modules using SOAP4R may not work.
 
+=== Problem with REXML DoS vulnerability patch before 09-Nov-2008
+
+(WONT_FIX) If you have applied a patch taken from
+http://www.ruby-lang.org/en/news/2008/08/23/dos-vulnerability-in-rexml/
+before 09 Nov 2008 12:40 +0900, because of the bug in the patch,
+parsing of Blast XML results with REXML parser may fail. The bug is already
+fixed and new patch is available on the above URL. Note that some Linux
+distributions would have incorporated the patch in their manners, and may
+have the same problem.
+
 == 2. OS and/or architecture-dependent issues
 
 === Microsoft Windows
 
-Following 4 tests failed because of the processing of file contents in the
-text mode.
+==== Text mode issues
+
+Following 4 tests failed on mswin32 (and maybe on mingw32 and bccwin32)
+because of the conversion of line feed codes in the text mode.
 
 * test_ended_pos and test_start_pos in test/unit/bio/io/test_flatfile.rb
 * test_pos in test/unit/bio/io/flatfile/test_buffer.rb
 * test_entry_pos in test/unit/bio/appl/blast/test_rpsblast.rb
 
+This indicates that br_bioflat.rb and Bio::FlatFileIndex may create
+incorrect indexes on mswin32, mingw32, and bccwin32. In addition,
+Bio::FlatFile may return incorrect data.
+
+==== Windows 95/98/98SE/ME
+
 (WONT_FIX) Some methods that call external programs may not work in
 Windows 95/98/98SE/ME because of the limitation of COMMAND.COM.
 
+=== OpenVMS, BeOS, OS/2, djgpp, Windows CE
+
+(WONT_FIX) BioRuby may not work on these platforms.
+
 == 3. Known issues and bugs in BioRuby
 
 === Bio::Ensembl

data/README.rdoc

@@ -35,6 +35,35 @@ services including KEGG API can be easily utilized by BioRuby.
 
 == FOR MORE INFORMATION
 
+=== Documents in this distribution
+
+==== General information
+
+README.rdoc:: This file. General information and installation procedure.
+KNOWN_ISSUES.rdoc:: Known issues and bugs in BioRuby.
+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.
+
+==== Tutorials and other useful information
+
+doc/Tutorial.rd:: BioRuby Tutorial.
+doc/Tutorial.rd.html:: HTML version of Tutorial.rd.
+doc/KEGG_API.rd:: Documents about KEGG API, including usage of Bio::KEGG::API.
+
+==== BioRuby development
+
+ChangeLog:: History of changes.
+README_DEV.rdoc:: Describes ways to contribute to the BioRuby project, including coding styles and documentation guidelines.
+
+==== Documents written in Japanese
+
+doc/Tutorial.rd.ja:: BioRuby Tutorial written in Japanese.
+doc/Tutorial.rd.ja.html:: HTML version of Tutorial.rd.ja.
+doc/KEGG_API.rd.ja:: Japanese translation of KEGG_API.rd.
+
+
+=== WWW
+
 BioRuby's official website is at http://bioruby.org/.
 You will find links to related resources including downloads,
 mailing lists, Wiki documentation etc. in the top page.

data/Rakefile

@@ -11,17 +11,19 @@ require 'rake/testtask'
 require 'rake/packagetask'
 require 'rake/gempackagetask'
 require 'rake/rdoctask'
-load "./lib/bio.rb"
+
+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_EXTRAVERSION']
+extraversion = ENV['BIORUBY_EXTRA_VERSION'] || Bio::BIORUBY_EXTRA_VERSION
 extraversion = nil if extraversion.to_s.empty?
-version += extraversion.to_s if version and extraversion
 BIORUBY_VERSION = version
+BIORUBY_EXTRA_VERSION = extraversion
 
 task :default => "test"
 
@@ -63,7 +65,8 @@ task :regemspec do
 end
 
 desc "Update #{GEM_SPEC_FILE}"
-file GEM_SPEC_FILE => [ GEM_SPEC_TEMPLATE_FILE, 'Rakefile' ] do |t|
+file GEM_SPEC_FILE => [ GEM_SPEC_TEMPLATE_FILE, 'Rakefile',
+                        'lib/bio/version.rb' ] do |t|
   puts "creates #{GEM_SPEC_FILE}"
   File.open(t.name, 'w') do |w|
     w.print gem_spec_string
@@ -79,7 +82,7 @@ Rake::PackageTask.new("bioruby") do |pkg|
   pkg.need_tar_gz = true
   pkg.package_files.import(spec.files)
   pkg.package_files.include(*tar_additional_files)
-  pkg.version = BIORUBY_VERSION || spec.version
+  pkg.version = (BIORUBY_VERSION || spec.version) + BIORUBY_EXTRA_VERSION.to_s
 end
 
 Rake::GemPackageTask.new(spec) do |pkg|
@@ -102,3 +105,39 @@ Rake::RDocTask.new do |r|
   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)
+  sh "rd2 -r rd/rd2html-lib.rb --with-css=bioruby.css #{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
+  end
+end
+

data/bin/br_pmfetch.rb

@@ -6,15 +6,16 @@
 #               Toshiaki Katayama <k@bioruby.org>
 # License::     The Ruby License
 #
-# $Id: br_pmfetch.rb,v 1.7 2007/04/05 23:35:39 trevor Exp $
+# $Id:$
 #
 
-PROG_VER  = '$Id: br_pmfetch.rb,v 1.7 2007/04/05 23:35:39 trevor Exp $'
+require 'bio'
+
+PROG_VER  = "Powered by BioRuby #{Bio::BIORUBY_VERSION_ID}"
 PROG_NAME = File.basename($0)
 
 
 require 'getoptlong'
-require 'bio'
 
 
 ### formatting

data/bioruby.gemspec

@@ -3,7 +3,7 @@
 # 
 Gem::Specification.new do |s|
   s.name = 'bio'
-  s.version = "1.2.9.9501"
+  s.version = "1.3.0"
 
   s.author = "BioRuby project"
   s.email = "staff@bioruby.org"
@@ -31,7 +31,10 @@ Gem::Specification.new do |s|
     "doc/KEGG_API.rd",
     "doc/KEGG_API.rd.ja",
     "doc/Tutorial.rd",
+    "doc/Tutorial.rd.html",
     "doc/Tutorial.rd.ja",
+    "doc/Tutorial.rd.ja.html",
+    "doc/bioruby.css",
     "etc/bioinformatics/seqdatabase.ini",
     "extconf.rb",
     "lib/bio.rb",
@@ -202,6 +205,7 @@ Gem::Specification.new do |s|
     "lib/bio/io/registry.rb",
     "lib/bio/io/soapwsdl.rb",
     "lib/bio/io/sql.rb",
+    "lib/bio/io/togows.rb",
     "lib/bio/location.rb",
     "lib/bio/map.rb",
     "lib/bio/pathway.rb",
@@ -235,6 +239,7 @@ Gem::Specification.new do |s|
     "lib/bio/shell/plugin/psort.rb",
     "lib/bio/shell/plugin/seq.rb",
     "lib/bio/shell/plugin/soap.rb",
+    "lib/bio/shell/plugin/togows.rb",
     "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/bioruby_generator.rb",
     "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_classes.rhtml",
     "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_log.rhtml",
@@ -290,6 +295,7 @@ Gem::Specification.new do |s|
     "lib/bio/util/restriction_enzyme/single_strand_complement.rb",
     "lib/bio/util/restriction_enzyme/string_formatting.rb",
     "lib/bio/util/sirna.rb",
+    "lib/bio/version.rb",
     "rdoc.zsh",
     "sample/any2fasta.rb",
     "sample/biofetch.rb",
@@ -354,6 +360,7 @@ Gem::Specification.new do |s|
     "test/functional/bio/appl/test_pts1.rb",
     "test/functional/bio/io/test_ensembl.rb",
     "test/functional/bio/io/test_soapwsdl.rb",
+    "test/functional/bio/io/test_togows.rb",
     "test/functional/bio/sequence/test_output_embl.rb",
     "test/functional/bio/test_command.rb",
     "test/runner.rb",
@@ -403,6 +410,7 @@ Gem::Specification.new do |s|
     "test/unit/bio/io/test_fastacmd.rb",
     "test/unit/bio/io/test_flatfile.rb",
     "test/unit/bio/io/test_soapwsdl.rb",
+    "test/unit/bio/io/test_togows.rb",
     "test/unit/bio/sequence/test_aa.rb",
     "test/unit/bio/sequence/test_common.rb",
     "test/unit/bio/sequence/test_compat.rb",
@@ -443,11 +451,11 @@ Gem::Specification.new do |s|
 
   s.has_rdoc = true
   s.extra_rdoc_files = [ 
+    "ChangeLog",
     "KNOWN_ISSUES.rdoc",
     "README.rdoc",
     "README_DEV.rdoc",
-    "doc/Changes-1.3.rdoc",
-    "ChangeLog"
+    "doc/Changes-1.3.rdoc"
   ]
   s.rdoc_options << '--main' << 'README.rdoc'
   s.rdoc_options << '--title' << 'BioRuby API documentation'

data/bioruby.gemspec.erb

@@ -1,6 +1,41 @@
 Gem::Specification.new do |s|
   s.name = 'bio'
-  s.version = "1.2.9.9501"
+  s.version = "<% ###### Below is executed in ERB environment ######
+    # Version can be specified by the environment variable
+    env_ver = ENV['BIORUBY_GEM_VERSION']
+    env_ver = nil if env_ver.to_s.strip.empty?
+
+    # By default, determined from lib/bio/version.rb
+    load "./lib/bio/version.rb" unless defined?(BIO_VERSION_RB_LOADED)
+    case Bio::BIORUBY_EXTRA_VERSION
+    when nil
+      suffix = nil
+    when /\A\.(\d+)\z/
+      suffix = $1
+    when /\-alpha(\d+)/
+      decrement = true
+      suffix = 9000 + $1.to_i
+    when /\-pre(\d+)/
+      decrement = true
+      suffix = 9500 + $1.to_i
+    when /\-rc(\d+)/
+      decrement = true
+      suffix = 9900 + $1.to_i
+    else
+      suffix = "0000"
+    end
+    ver = Bio::BIORUBY_VERSION.reverse.collect do |i|
+            if decrement then
+              i -= 1
+              i < 0 ? (i += 10) : decrement = false
+            end
+            i
+          end.reverse
+    ver.push suffix if suffix
+    %><%= 
+    (env_ver || ver.join('.'))
+       ###### Above is executed in ERB environment ######
+    %>"
 
   s.author = "BioRuby project"
   s.email = "staff@bioruby.org"
@@ -16,7 +51,7 @@ Gem::Specification.new do |s|
     files = (`git ls-files` rescue nil).to_s.split(/\r?\n/)
     files.delete_if { |x| x.empty? }
     # When git-ls-files isn't available, creates a list from current files.
-    unless $?.success? or files.size <= 0 then
+    if !($?.success?) or files.size <= 0 then
       files =
         [ "README.rdoc", "README_DEV.rdoc", 
           "ChangeLog", "KNOWN_ISSUES.rdoc",
@@ -33,7 +68,7 @@ Gem::Specification.new do |s|
             end
     end
     %><%= 
-    files.collect { |x| x.dump }.join(",\n    ")
+    files.sort.collect { |x| x.dump }.join(",\n    ")
        ###### Above is executed in ERB environment ######
     %>
   ]
@@ -49,7 +84,7 @@ Gem::Specification.new do |s|
                          'doc/Changes-1.3.rdoc' ]
         end
         rdoc_files.push "ChangeLog" unless rdoc_files.include?("ChangeLog")
-        rdoc_files.collect { |x| x.dump }.join(",\n    ")
+        rdoc_files.sort.collect { |x| x.dump }.join(",\n    ")
         ###### Above is executed in ERB environment ######
     %>
   ]
@@ -74,7 +109,7 @@ Gem::Specification.new do |s|
         if exec_files.empty? then
             exec_files = [ "bioruby", "br_biofetch.rb", "br_biogetseq.rb", "br_bioflat.rb", "br_pmfetch.rb" ]
         end
-        exec_files.collect { |x| x.dump }.join(",\n    ")
+        exec_files.sort.collect { |x| x.dump }.join(",\n    ")
         ###### Above is executed in ERB environment ######
     %>
   ]

data/doc/Changes-0.7.rd

@@ -338,6 +338,13 @@ In 1.1.0:
   instead of a string or nil: score, percent_identity, percent_positive,
   percent_gaps.
 
+--- BioRuby Shell
+
+In 1.1.0:
+
+* Shell commands seq, ent, obj are renamed to getseq, getent, getobj,
+  respectively.
+
 === Deleted files
 
 : lib/bio/db/genbank.rb

data/doc/Changes-1.3.rdoc

@@ -58,6 +58,11 @@ particular use cases.
 
 New method Bio::Locations#to_s is added to support output of features.
 
+=== Bio::TogoWS::REST
+
+TogoWS REST client class is newly added. Information about TogoWS REST service
+can be found on http://togows.dbcls.jp/site/en/rest.html.
+
 == Deprecated classes
 
 === Bio::Features
@@ -74,6 +79,18 @@ will soon be removed in the future.
 
 == Incompatible changes
 
+=== Bio::BIORUBY_VERSION
+
+Definition of the constant Bio::BIORUBY_VERSION is moved from lib/bio.rb to
+lib/bio/version.rb. Normally, the autoload mechanism of Ruby correctly loads
+the version.rb, but special scripts directly using bio.rb may be needed to
+be changed.
+
+Bio::BIORUBY_VERSION is changed to be frozen.
+
+New constants Bio::BIORUBY_EXTRA_VERSION and Bio::BIORUBY_VERSION_ID are
+added. See their RDoc for details.
+
 === Bio::Sequence
 
 Bio::Sequence#date is removed.  Alternatively, date_created or date_modified