bio 2.0.1 → 2.0.4

checksums.yaml

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data/ChangeLog

@@ -1,3 +1,316 @@
+commit 1bc877e557e165b42eea992d89f19a63996cb586
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Tue Sep 13 21:19:01 2022 +0900
+
+    regenerate bioruby.gemspec with rake regemspec
+
+ bioruby.gemspec | 4 +++-
+ 1 file changed, 3 insertions(+), 1 deletion(-)
+
+commit 190e4751b84cc45cbce636c4414482a8169b08df
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Tue Sep 13 21:18:06 2022 +0900
+
+    prepare for BioRuby 2.0.4 release
+
+ lib/bio/version.rb | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+commit a666639e0393e96b2de0bbcb447c13f8a14ad06d
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Tue Sep 13 21:17:11 2022 +0900
+
+    update release notes for upcoming BioRuby 2.0.4
+
+ RELEASE_NOTES.rdoc | 14 ++++++++++++++
+ 1 file changed, 14 insertions(+)
+
+commit c0d197343dd7fd8999d04083c9e8f24fa37a2f93
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Tue Sep 13 21:13:40 2022 +0900
+
+    License of UniProt data is CC BY 4.0
+
+ LEGAL | 9 +++++++++
+ 1 file changed, 9 insertions(+)
+
+commit e670102e6d4deb04c1fcae62459cc02861132d25
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Tue Sep 13 21:01:50 2022 +0900
+
+    Bug fix: Bio::UniProtKB#protein_name and #synonyms may raise error
+    
+     * Bug fix: Bio::UniProtKB#protein_name and #synonyms may raise error
+       after calling Bio::UniProtKB#de method.
+
+ lib/bio/db/embl/uniprotkb.rb                   | 25 ++++++++++++++++++-------
+ test/unit/bio/db/embl/test_uniprotkb_P28907.rb | 11 +++++++++++
+ 2 files changed, 29 insertions(+), 7 deletions(-)
+
+commit 9c04e08e8d1316ffd7fc15ab311cea5dd6937d36
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Tue Sep 13 20:44:46 2022 +0900
+
+    Supports format change of FT lines since UniProt release 2019_11
+    
+     * Bio::UniProtKB#ft: Supports text format change of FT lines since
+       UniProt release 2019_11. (Details of the format changes:
+       https://www.uniprot.org/release-notes/2019-12-18-release#text%5Fft )
+    
+       This closes https://github.com/bioruby/bioruby/issues/147 .
+    
+     * Tests are added with a new test data
+
+ lib/bio/db/embl/uniprotkb.rb                   | 122 +++++-
+ test/data/uniprot/P28907.uniprot               | 551 +++++++++++++++++++++++++
+ test/unit/bio/db/embl/test_uniprotkb_P28907.rb | 314 ++++++++++++++
+ 3 files changed, 983 insertions(+), 4 deletions(-)
+ create mode 100644 test/data/uniprot/P28907.uniprot
+ create mode 100644 test/unit/bio/db/embl/test_uniprotkb_P28907.rb
+
+commit b18ee463d4328b5ef619733b46f568b18459be7a
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Fri Nov 5 23:49:18 2021 +0900
+
+    BioRuby 2.0.3 is released
+
+ ChangeLog | 136 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ 1 file changed, 136 insertions(+)
+
+commit c16e230d15cf30478a3739563b4e4745dc57ef82
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Fri Nov 5 23:44:45 2021 +0900
+
+    regenerate bioruby.gemspec with rake regemspec
+
+ bioruby.gemspec | 3 ++-
+ 1 file changed, 2 insertions(+), 1 deletion(-)
+
+commit 1a8c44dc5b8d24342550273a594e5f75e41f41df
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Fri Nov 5 23:41:29 2021 +0900
+
+    prepare for BioRuby 2.0.3 release
+
+ lib/bio/version.rb | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+commit 863242cdb9a748ba9efb3be3b39f92c17ed3ea84
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Fri Nov 5 23:36:27 2021 +0900
+
+    update release notes for upcoming BioRuby 2.0.3
+
+ RELEASE_NOTES.rdoc | 26 ++++++++++++++++++++++++++
+ 1 file changed, 26 insertions(+)
+
+commit b97794d632c73dc45639cec000fb11238740eb30
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Fri Nov 5 23:26:20 2021 +0900
+
+    Ruby 3.0 compatibility fix: Bio::Sequence::*#partition, #rpartiton
+    
+     * Behaviors of Bio::Sequence::*#partition and #rpartition in Ruby 3.0
+       are changed to mimic those in Ruby 2.x.
+
+ lib/bio/sequence/common.rb           | 17 +++++++
+ test/unit/bio/sequence/test_ruby3.rb | 94 ++++++++++++++++++++++++++++++++++++
+ 2 files changed, 111 insertions(+)
+
+commit 7ff79cd449ee03e0063120fb9abec50d9b08e979
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Fri Nov 5 22:24:16 2021 +0900
+
+    remove resolved Ruby 3.0 issue
+
+ KNOWN_ISSUES.rdoc | 8 --------
+ 1 file changed, 8 deletions(-)
+
+commit 24bb3c3cf417837ad63a27913db7237aef1414c6
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Fri Nov 5 21:24:26 2021 +0900
+
+    Bio::Sequence::NA,AA,Generic: workaround for Ruby 3.0.0 incompatible change
+    
+     * Since Ruby 3.0.0, over 30 methods in subclass of String class are
+       changed to return/yield String instance instead of the subclass
+       instance. (https://github.com/ruby/ruby/blob/v3_0_0/NEWS.md )
+    
+     * In this commit, workaround is made for the following methods:
+       * *
+       * capitalize
+       * center
+       * chomp
+       * chop
+       * delete
+       * delete_prefix
+       * delete_suffix
+       * downcase
+       * each_char
+       * each_grapheme_cluster
+       * each_line
+       * gsub
+       * gsub!
+       * ljust
+       * lstrip
+       * revserse
+       * rjust
+       * rstrip
+       * slice!
+       * slice / []
+       * split
+       * squeeze
+       * strip
+       * sub
+       * sub!
+       * succ / next
+       * swapcase
+       * tr
+       * tr_s
+       * upcase
+     * Note: sub! and gsub! are not described in the NEWS.md
+       but are also affected by this Ruby 3.0.0 incompatible changes.
+    
+     * The following methods are not patched i.e. they return/yield
+       String instances.
+       * dump
+       * partition
+       * rpartition
+       * scrub
+     * Note: In Ruby 2.7 or earlier, Bio::Sequence::NA#partition
+       and #rpartition methods return an array that may contain
+       mixture of Bio::Sequence::NA instances and String instances.
+    
+     * test/unit/bio/sequence/test_ruby3.rb: unit tests for the
+       above methods.
+    
+     * Close https://github.com/bioruby/bioruby/issues/137
+
+ lib/bio/sequence/common.rb           |  95 +++++++++
+ test/unit/bio/sequence/test_ruby3.rb | 368 +++++++++++++++++++++++++++++++++++
+ 2 files changed, 463 insertions(+)
+ create mode 100644 test/unit/bio/sequence/test_ruby3.rb
+
+commit 0efc0a54685d43645daa9c53d7140bfb81577777
+Author: kojix2 <2xijok@gmail.com>
+Date:   Tue Aug 31 19:39:25 2021 +0900
+
+    Fix typos: Retrun -> Return
+
+ lib/bio/appl/iprscan/report.rb | 6 +++---
+ lib/bio/appl/sosui/report.rb   | 2 +-
+ lib/bio/db/embl/uniprotkb.rb   | 2 +-
+ lib/bio/db/go.rb               | 4 ++--
+ lib/bio/tree.rb                | 2 +-
+ 5 files changed, 8 insertions(+), 8 deletions(-)
+
+commit a291b5a72da12a5cc8b006d1dd63d002fda5dff3
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Thu Dec 31 23:52:54 2020 +0900
+
+    BioRuby 2.0.2 is released
+
+ ChangeLog | 98 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ 1 file changed, 98 insertions(+)
+
+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

data/LEGAL

@@ -114,6 +114,15 @@ test/data/uniprot/p53_human.uniprot:
    removed.
 
 
+test/data/uniprot/P28907.uniprot:
+
+   Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
+   Distributed under the Creative Commons Attribution (CC BY 4.0) License
+
+   https://www.uniprot.org/help/license
+   https://creativecommons.org/licenses/by/4.0/
+
+
 GPL:
 
  Copyright (C) 1989, 1991 Free Software Foundation, Inc.

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 +1,62 @@
+= BioRuby 2.0.4 RELEASE NOTES
+
+Some fixes have been made in BioRuby 2.0.4 after the release of 2.0.3.
+
+== Fixes
+
+* Bio::UniProtKB#ft: Supports text format change of FT lines since
+  UniProt release 2019_11.
+  (https://github.com/bioruby/bioruby/issues/147 )
+* Bio::UniProtKB#protein_name and #synonyms methods may raise error
+  after calling Bio::UniProtKB#de method.
+
+
+
+= BioRuby 2.0.3 RELEASE NOTES
+
+Some bug fixes have been made in BioRuby 2.0.3 after the release of 2.0.2.
+
+== Bug fixes
+
+* Fix Ruby 3.0.0 Bio::Sequence::* issue.
+  (https://github.com/bioruby/bioruby/issues/137 )
+* Fix typo (https://github.com/bioruby/bioruby/pull/145 )
+
+== Incompatible changes
+
+=== Bio::Sequence::* incompatible changes since Ruby 3.0.0
+
+Since Ruby 3.0.0, the following methods in Bio::Sequence::NA,
+Bio::Sequence::AA, and Bio::Sequence::Generic return or yield
+String instance, instead of the Bio::Sequence::* instance.
+
+* dump
+* scrub
+
+For details about Ruby 3.0.0 incompatible changes, see
+{News for Ruby 3.0.0}[https://github.com/ruby/ruby/blob/v3_0_0/NEWS.md].
+
+
+
+= 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 = "2.0.4"
 
   s.author = "BioRuby project"
   s.email = "staff@bioruby.org"
@@ -454,6 +454,7 @@ Gem::Specification.new do |s|
     "test/data/sim4/simple2-A4.sim4",
     "test/data/soft/GDS100_partial.soft",
     "test/data/soft/GSE3457_family_partial.soft",
+    "test/data/uniprot/P28907.uniprot",
     "test/data/uniprot/p53_human.uniprot",
     "test/functional/bio/sequence/test_output_embl.rb",
     "test/functional/bio/test_command.rb",
@@ -498,6 +499,7 @@ Gem::Specification.new do |s|
     "test/unit/bio/db/embl/test_embl_to_bioseq.rb",
     "test/unit/bio/db/embl/test_uniprot.rb",
     "test/unit/bio/db/embl/test_uniprotkb.rb",
+    "test/unit/bio/db/embl/test_uniprotkb_P28907.rb",
     "test/unit/bio/db/embl/test_uniprotkb_new_part.rb",
     "test/unit/bio/db/fasta/test_defline.rb",
     "test/unit/bio/db/fasta/test_defline_misc.rb",
@@ -546,6 +548,7 @@ Gem::Specification.new do |s|
     "test/unit/bio/sequence/test_dblink.rb",
     "test/unit/bio/sequence/test_na.rb",
     "test/unit/bio/sequence/test_quality_score.rb",
+    "test/unit/bio/sequence/test_ruby3.rb",
     "test/unit/bio/sequence/test_sequence_masker.rb",
     "test/unit/bio/test_alignment.rb",
     "test/unit/bio/test_command.rb",
@@ -580,7 +583,6 @@ 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/appl/iprscan/report.rb

@@ -83,7 +83,7 @@ module Bio
         yield Bio::Iprscan::Report.parse_raw_entry(entry) if entry != ''
       end
     
-      # Parser method for a raw formated entry. Retruns a Bio::Iprscan::Report 
+      # Parser method for a raw formated entry. Returns a Bio::Iprscan::Report 
       # object.
       def self.parse_raw_entry(str)
         report = self.new
@@ -113,7 +113,7 @@ module Bio
 
 
 
-      # Parser method for a xml formated entry. Retruns a Bio::Iprscan::Report 
+      # Parser method for a xml formated entry. Returns a Bio::Iprscan::Report 
       # object.
 #      def self.parse_xml(str)
 #      end
@@ -196,7 +196,7 @@ module Bio
         end
       end
 
-      # Parser method for a pseudo-txt formated entry. Retruns a Bio::Iprscan::Report 
+      # Parser method for a pseudo-txt formated entry. Returns a Bio::Iprscan::Report 
       # object.
       # 
       # == Usage

data/lib/bio/appl/sosui/report.rb

@@ -78,7 +78,7 @@ module Bio
         # Returns aRng of transmembrane helix
         attr_reader :range
         
-        # Retruns ``PRIMARY'' or ``SECONDARY'' of helix.
+        # Returns ``PRIMARY'' or ``SECONDARY'' of helix.
         attr_reader :grade
 
         # Returns the sequence. of transmembrane helix.