bio 2.0.1 → 2.0.2

checksums.yaml

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data/ChangeLog

@@ -1,3 +1,101 @@
+commit fd420b713ca364e677ef3551919ec907791df86d
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Thu Dec 31 23:51:08 2020 +0900
+
+    RELEASE_NOTES.rdoc: change some description
+
+ RELEASE_NOTES.rdoc | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+commit 0ed9b37f38fa1b00dcc1d422914e4cbdbbc5f6ab
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Thu Dec 31 23:46:46 2020 +0900
+
+    regenerate bioruby.gemspec with rake regemspec
+
+ bioruby.gemspec | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+commit fa84b8fac653c26b9f8db429321ef49202554a69
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Thu Dec 31 23:45:38 2020 +0900
+
+    prepare for BioRuby 2.0.2 release
+
+ lib/bio/version.rb | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+commit 32c5efccbad4e0d3440726383f863520ee242cc5
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Thu Dec 31 23:39:18 2020 +0900
+
+    update release notes for upcoming BioRuby 2.0.2
+
+ RELEASE_NOTES.rdoc | 19 +++++++++++++++++++
+ 1 file changed, 19 insertions(+)
+
+commit c2f6e62ab64bc532f442bccc0d76ced5380664ec
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Thu Dec 31 23:38:43 2020 +0900
+
+    add a known issue about Ruby 3.0
+
+ KNOWN_ISSUES.rdoc | 10 +++++++++-
+ 1 file changed, 9 insertions(+), 1 deletion(-)
+
+commit a733c0816da7c97ca0c23016b473b004fb755f54
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Thu Dec 31 23:04:55 2020 +0900
+
+    remove deprecation warning of Gem::Specification#has_rdoc=
+    
+    Gem::Specification#has_rdoc= have been deprecated since RubyGems 1.3.3
+    in 2009. (https://blog.rubygems.org/2009/05/04/1.3.3-released.html )
+    RDoc is always generated regardless of the value, and the line is
+    safely removed.
+    
+    This fixes https://github.com/bioruby/bioruby/issues/138 .
+    Thanks to @jaysonvirissimo for reporting the issue.
+
+ bioruby.gemspec     | 1 -
+ bioruby.gemspec.erb | 1 -
+ 2 files changed, 2 deletions(-)
+
+commit bed6746ce62059795996eeb6e5ac65655bab12b5
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Thu Dec 31 22:51:56 2020 +0900
+
+    require ruby's date library to avoid NameError for Date
+    
+    In Bio::Sequence#output(:embl), NameError (uninitialized constant
+    Bio::Sequence::Format::INSDFeatureHelper::Date) is observed.
+    The error message is misleading because Date is provided by Ruby's
+    standard date library.
+    
+    This fixes https://github.com/bioruby/bioruby/issues/135 .
+    Thanks to Dr. Mark Wilkinson for reporting the issue.
+
+ lib/bio/sequence/format.rb | 1 +
+ 1 file changed, 1 insertion(+)
+
+commit 5f3aa79fdaf6dd5551d51663ca2e9b6f5e56d855
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Fri Nov 6 17:45:12 2020 +0900
+
+    fix mistaken URLs
+
+ README.rdoc | 6 +++---
+ 1 file changed, 3 insertions(+), 3 deletions(-)
+
+commit d5e1670ee4863cc60d3aa08432a7ee3b1e445439
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Fri Sep 6 15:48:45 2019 +0900
+
+    BioRuby 2.0.1 is released
+
+ ChangeLog | 185 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ 1 file changed, 185 insertions(+)
+
 commit 21bf51a1ec8c18c9cdf8528ffc3c59c503cef042
 Author: Naohisa Goto <ng@bioruby.org>
 Date:   Fri Sep 6 15:45:47 2019 +0900

data/KNOWN_ISSUES.rdoc

@@ -1,5 +1,5 @@
 = KNOWN_ISSUES.rdoc - Known issues and bugs in BioRuby
-Copyright:: Copyright (C) 2009-2019 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
@@ -12,6 +12,14 @@ they are not BioRuby's issues and/or it is very difficult to fix them.
 
 == 1. Ruby version specific issues
 
+==== Ruby 3.0
+
+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
 
 Currently, BioRuby do not care string encodings. In some cases,

data/README.rdoc

@@ -206,9 +206,9 @@ 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/bioruby-shell]
-* {bio-executables}[https://rubygems.org/gems/bioruby-executables]
-* {bio-blast-xmlparser}[https://rubygems.org/gems/bioruby-blast-xmlparser]
+* {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

data/RELEASE_NOTES.rdoc

@@ -1,3 +1,22 @@
+= 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
+
+* 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
+
+== Known issues
+
+A known issue about Ruby 3.0 is added to KNOWN_ISSUES.rdoc.
+The issue will be fixed in the near future.
+
+
+
 = BioRuby 2.0.1 RELEASE NOTES
 
 Some bug fixes and improvements have been made to the BioRuby 2.0.1 after

data/bioruby.gemspec

@@ -3,7 +3,7 @@
 # 
 Gem::Specification.new do |s|
   s.name = 'bio'
-  s.version = "2.0.1"
+  s.version = "2.0.2"
 
   s.author = "BioRuby project"
   s.email = "staff@bioruby.org"
@@ -580,7 +580,6 @@ Gem::Specification.new do |s|
     "test/unit/bio/util/test_sirna.rb"
   ]
 
-  s.has_rdoc = true
   s.extra_rdoc_files = [ 
     "KNOWN_ISSUES.rdoc",
     "README.rdoc",

data/bioruby.gemspec.erb

@@ -63,7 +63,6 @@ Gem::Specification.new do |s|
     %>
   ]
 
-  s.has_rdoc = true
   s.extra_rdoc_files = [ 
     <%= ###### Below is executed in ERB environment ######
         # Files whose suffix are .rdoc are selected.

data/lib/bio/sequence/format.rb

@@ -10,6 +10,7 @@
 #
 
 require 'erb'
+require 'date'
 
 module Bio
 

data/lib/bio/version.rb

@@ -10,7 +10,7 @@
 module Bio
 
   # BioRuby version (Array containing Integer)
-  BIORUBY_VERSION = [2, 0, 1].extend(Comparable).freeze
+  BIORUBY_VERSION = [2, 0, 2].extend(Comparable).freeze
 
   # Extra version specifier (String or nil).
   # Existance of the value indicates development version.

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bio
 version: !ruby/object:Gem::Version
-  version: 2.0.1
+  version: 2.0.2
 platform: ruby
 authors:
 - BioRuby project
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-09-06 00:00:00.000000000 Z
+date: 2020-12-31 00:00:00.000000000 Z
 dependencies: []
 description: BioRuby is a library for bioinformatics (biology + information science).
 email: staff@bioruby.org