Commit 6047d6a3 authored by Lucas Nussbaum's avatar Lucas Nussbaum

Imported Upstream version 1.4.2

parent 6ef6e6ce
commit 3acc1e098839cacbe85b5c23367ab14e0c4fe3ea
Author: Naohisa Goto <ng@bioruby.org>
Date: Fri Aug 26 15:01:49 2011 +0900
Preparation for bioruby-1.4.2 release.
bioruby.gemspec | 2 +-
lib/bio/version.rb | 2 +-
2 files changed, 2 insertions(+), 2 deletions(-)
commit bf69125192fa01ae3495e094e7ef1b5e895954ad
Author: Naohisa Goto <ng@bioruby.org>
Date: Fri Aug 26 14:42:02 2011 +0900
updated bioruby.gemspec
bioruby.gemspec | 3 +++
1 files changed, 3 insertions(+), 0 deletions(-)
commit e0a3ead917812199c6a0e495f3afa6a636bbf0c5
Author: Naohisa Goto <ng@bioruby.org>
Date: Fri Aug 26 14:39:54 2011 +0900
Added PLUGIN section to README.rdoc, and some changes made.
README.rdoc | 20 +++++++++++++++++---
1 files changed, 17 insertions(+), 3 deletions(-)
commit 1da0a1ce6eddcef8f8fc811b0a2cf8d58f880642
Author: Naohisa Goto <ng@bioruby.org>
Date: Fri Aug 26 14:38:13 2011 +0900
updated doc/Tutorial.rd.html
doc/Tutorial.rd.html | 41 ++++++++++++++++++++---------------------
1 files changed, 20 insertions(+), 21 deletions(-)
commit a8b90367b830e58b397536be3dada10cdde97aab
Author: Naohisa Goto <ng@bioruby.org>
Date: Fri Aug 26 14:36:24 2011 +0900
Removed sections contain obsolete (404 Not Found) URL in Tutorial.rd.
doc/Tutorial.rd | 12 ------------
1 files changed, 0 insertions(+), 12 deletions(-)
commit e17546cb90a012cd1f51674ceb4c8da5dd516bdf
Author: Michael O'Keefe <okeefm@rpi.edu>
Date: Tue Aug 23 20:15:44 2011 -0400
Updated tutorial
* Updated tutorial
(original commit id: 7b9108657961cf2354278e04971c32059b3ed4e2
and some preceding commits)
doc/Tutorial.rd | 55 ++++++++++++++++++++++++++++++++-----------------------
1 files changed, 32 insertions(+), 23 deletions(-)
commit de8a394129c752a0b9a5975a73c5eb582d9681d3
Author: Naohisa Goto <ng@bioruby.org>
Date: Fri Aug 26 13:24:27 2011 +0900
fix typo and change order of lines
RELEASE_NOTES.rdoc | 6 +++---
1 files changed, 3 insertions(+), 3 deletions(-)
commit 1cf2a11199655e4c9f5fc49c5a588b99c18ab7ca
Author: Naohisa Goto <ng@bioruby.org>
Date: Fri Aug 26 13:16:11 2011 +0900
RELEASE_NOTE.rdoc modified to reflect recent changes
RELEASE_NOTES.rdoc | 14 ++++++++++++++
1 files changed, 14 insertions(+), 0 deletions(-)
commit b44871a5866eeb2d379f080b39b09693c9e9e3cc
Author: Naohisa Goto <ng@bioruby.org>
Date: Fri Aug 26 13:15:14 2011 +0900
In BioRuby Shell, getent() fails when EMBOSS seqret does not found.
lib/bio/shell/plugin/entry.rb | 10 +++++++---
1 files changed, 7 insertions(+), 3 deletions(-)
commit 179e7506b008a220d5dd42ce1a6c7ce589c3fcda
Author: Naohisa Goto <ng@bioruby.org>
Date: Fri Aug 26 12:26:52 2011 +0900
New methods Bio::NCBI::REST::EFetch.nucleotide and protein
* New methods Bio::NCBI::REST::EFetch.nucleotide and protein,
to get data from "nucleotide" and "protein" database respectively.
Because NCBI changed not to accept "gb" format for the database
"sequence", the two new methods are added for convenience.
* In BioRuby Shell, efetch method uses the above new methods.
lib/bio/io/ncbirest.rb | 122 +++++++++++++++++++++++++++++++++++++-
lib/bio/shell/plugin/ncbirest.rb | 6 ++-
2 files changed, 126 insertions(+), 2 deletions(-)
commit 99b31379bb41c7cad34c1e7dc00f802da37de1cd
Author: Naohisa Goto <ng@bioruby.org>
Date: Thu Aug 25 19:03:43 2011 +0900
New method Bio::Fastq#to_s
* New method Bio::Fastq#to_s.
Thanks to Tomoaki NISHIYAMA who wrote a patch.
(https://github.com/bioruby/bioruby/pull/37)
lib/bio/db/fastq.rb | 14 ++++++++++++++
test/unit/bio/db/test_fastq.rb | 14 ++++++++++++++
2 files changed, 28 insertions(+), 0 deletions(-)
commit 8ab772b37850c3874b55cf37d091046394cda5bd
Author: Naohisa Goto <ng@bioruby.org>
Date: Thu Aug 25 15:23:00 2011 +0900
RELEASE_NOTES.rdoc changed to reflect recent changes.
RELEASE_NOTES.rdoc | 16 ++++++++++++++++
1 files changed, 16 insertions(+), 0 deletions(-)
commit 8db6abdcc81db6a58bdd99e7f8d410b1a74496b1
Author: Naohisa Goto <ng@bioruby.org>
Date: Thu Aug 25 14:28:42 2011 +0900
A test connecting to DDBJ BLAST web service is enabled.
test/functional/bio/appl/test_blast.rb | 2 +-
1 files changed, 1 insertions(+), 1 deletions(-)
commit 121ad93c0c1f018ee389972ac5e5e8cc395f00d1
Author: Naohisa Goto <ng@bioruby.org>
Date: Thu Aug 25 14:15:23 2011 +0900
Bio::DDBJ::REST::*. new classes for DDBJ REST web services.
* Bio::DDBJ::REST::*: new classes for DDBJ REST web services (WABI).
Currently not all services are covered. (lib/bio/io/ddbjrest.rb)
* autoload of the above (lib/bio/db/genbank/ddbj.rb, lib/bio.rb)
* Tests for the above (but still incomplete)
(test/functional/bio/io/test_ddbjrest.rb)
* Remote BLAST using DDBJ server now uses REST interface instead
of SOAP, for Ruby 1.9.x support.
(lib/bio/appl/blast/ddbj.rb)
lib/bio.rb | 1 +
lib/bio/appl/blast/ddbj.rb | 33 +---
lib/bio/db/genbank/ddbj.rb | 3 +-
lib/bio/io/ddbjrest.rb | 344 +++++++++++++++++++++++++++++++
test/functional/bio/io/test_ddbjrest.rb | 47 +++++
5 files changed, 399 insertions(+), 29 deletions(-)
create mode 100644 lib/bio/io/ddbjrest.rb
create mode 100644 test/functional/bio/io/test_ddbjrest.rb
commit 7e8ba7c1388204daa5245d2128d01f6f40298185
Author: Naohisa Goto <ng@bioruby.org>
Date: Thu Aug 18 00:08:51 2011 +0900
In Fastq formatter, default width value changed to nil
* In Bio::Sequence#output(:fastq) (Fastq output formatter),
default width value is changed from 70 to nil, which means
"without wrapping". close [Feature #3191]
(https://redmine.open-bio.org/issues/3191)
RELEASE_NOTES.rdoc | 8 ++++++--
lib/bio/db/fastq/format_fastq.rb | 4 ++--
test/unit/bio/db/test_fastq.rb | 12 ++++++++++++
3 files changed, 20 insertions(+), 4 deletions(-)
commit 0fb65211519febff18413c589fe7af753ee2e61d
Author: Naohisa Goto <ng@bioruby.org>
Date: Wed Aug 17 22:02:03 2011 +0900
Bug fix: Bio::SPTR follow-up of UniProtKB format changes
* Bug fix: Bio::SPTR follow-up of UniProtKB format changes.
* Tests are added about the fix.
* Bug fix: Bio::SPTR#cc_web_resource should be private.
* Incompatible changes in Bio::SPTR#cc("WEB RESOURCE") is
documented in RELEASE_NOTES.rdoc.
* KNOWN_ISSUES.rdoc: description about incompleteness of the fix.
* Thanks to Nicholas Letourneau who reports the issue.
(https://github.com/bioruby/bioruby/pull/36)
KNOWN_ISSUES.rdoc | 5 +
RELEASE_NOTES.rdoc | 20 ++-
lib/bio/db/embl/sptr.rb | 214 +++++++++++++++++++++---
test/unit/bio/db/embl/test_sptr.rb | 12 +-
test/unit/bio/db/embl/test_uniprot_new_part.rb | 208 +++++++++++++++++++++++
5 files changed, 430 insertions(+), 29 deletions(-)
create mode 100644 test/unit/bio/db/embl/test_uniprot_new_part.rb
commit 0d066ab6b8fc19f1cf6e66e07c2065775739cccd
Author: Naohisa Goto <ng@bioruby.org>
Date: Sat Aug 13 00:58:51 2011 +0900
preparation for release: alpha test version 1.4.2-alpha1
bioruby.gemspec | 23 +++++++++++++++++++++--
lib/bio/version.rb | 4 ++--
2 files changed, 23 insertions(+), 4 deletions(-)
commit 55ece17775f5d24cf62f93d54ded5dc6eed53584
Author: Naohisa Goto <ng@bioruby.org>
Date: Fri Aug 12 21:57:25 2011 +0900
Test bug fix: use sort command in PATH
* Test bug fix: FuncTestCommandQuery: use sort command in PATH.
Thanks to Tomoaki Nishiyama who reports the issue.
(https://github.com/bioruby/bioruby/pull/13)
test/functional/bio/test_command.rb | 6 +++---
1 files changed, 3 insertions(+), 3 deletions(-)
commit 2f464aae016387cd50031f9d9664e78e220e2d01
Author: Naohisa Goto <ng@bioruby.org>
Date: Fri Aug 12 20:37:18 2011 +0900
RELEASE_NOTES.rdoc is updated following recent changes.
RELEASE_NOTES.rdoc | 21 ++++++++++++++-------
1 files changed, 14 insertions(+), 7 deletions(-)
commit d1a193684afdfd4c632ef75a978d4f3680d1bdf3
Author: Naohisa Goto <ng@bioruby.org>
Date: Fri Aug 12 20:30:53 2011 +0900
README.rdoc: changed required Ruby version etc.
* README.rdoc: now Ruby 1.8.6 or later is required.
* README.rdoc: removed old obsolete descriptions.
* README.rdoc: modified about RubyGems.
* KNOWN_ISSUES.rdoc: moved descriptions about older RubyGems and CVS
from README.rdoc.
* KNOWN_ISSUES.rdoc: modified about end-of-life Ruby versions.
KNOWN_ISSUES.rdoc | 40 ++++++++++++++++++++++++++++++----
README.rdoc | 61 ++++++++++++++++++++--------------------------------
2 files changed, 59 insertions(+), 42 deletions(-)
commit b5cbdc6ab7e81aae4db9aeb708fac57ffbce5636
Author: Naohisa Goto <ng@bioruby.org>
Date: Sat Jul 16 00:12:17 2011 +0900
Added topics for the release notes
RELEASE_NOTES.rdoc | 39 ++++++++++++++++++++++++++++++++++++++-
1 files changed, 38 insertions(+), 1 deletions(-)
commit f062b5f37a6d8ad35b5b10c942fd61e1a4d37e08
Author: Naohisa Goto <ng@bioruby.org>
Date: Sat Jul 2 01:05:42 2011 +0900
Speedup of Bio::RestrictionEnzyme::Analysis.cut.
* Speedup of Bio::RestrictionEnzyme::Analysis.cut. The new code
is 50 to 80 fold faster than the previous code when cutting
1Mbp sequence running on Ruby 1.9.2p180.
* Thanks to Tomoaki NISHIYAMA who wrote the first version of the
patch. Thanks to ray1729 (on GitHub) who reports the issue.
(https://github.com/bioruby/bioruby/issues/10)
lib/bio/util/restriction_enzyme.rb | 3 +
.../restriction_enzyme/range/sequence_range.rb | 14 ++--
.../range/sequence_range/calculated_cuts.rb | 75 +++++++++++++++-----
.../range/sequence_range/fragment.rb | 4 +-
4 files changed, 69 insertions(+), 27 deletions(-)
commit 735379421d9d6b7ceb06b91dcfcca6d5ff841236
Author: Naohisa Goto <ng@bioruby.org>
Date: Sat Jul 2 00:59:58 2011 +0900
New classes (for internal use only) for restriction enzyme classes
* New classes Bio::RestrictionEnzyme::SortedNumArray and
Bio::RestrictionEnzyme::DenseIntArray. Both of them are for
Bio::RestrictionEnzyme internal use only. They will be used
for the speedup of restriction enzyme analysis.
lib/bio/util/restriction_enzyme/dense_int_array.rb | 195 ++++++++++++++
.../util/restriction_enzyme/sorted_num_array.rb | 219 +++++++++++++++
.../restriction_enzyme/test_dense_int_array.rb | 201 ++++++++++++++
.../restriction_enzyme/test_sorted_num_array.rb | 281 ++++++++++++++++++++
4 files changed, 896 insertions(+), 0 deletions(-)
create mode 100644 lib/bio/util/restriction_enzyme/dense_int_array.rb
create mode 100644 lib/bio/util/restriction_enzyme/sorted_num_array.rb
create mode 100644 test/unit/bio/util/restriction_enzyme/test_dense_int_array.rb
create mode 100644 test/unit/bio/util/restriction_enzyme/test_sorted_num_array.rb
commit 6cbb0c230d1a0bf3125c3b0fdb9ec3333d9564f8
Author: Naohisa Goto <ng@bioruby.org>
Date: Thu Jun 30 20:47:26 2011 +0900
A sample benchmark script for Bio::RestrictionEnzyme::Analysis.cut
sample/test_restriction_enzyme_long.rb | 4403 ++++++++++++++++++++++++++++++++
1 files changed, 4403 insertions(+), 0 deletions(-)
create mode 100644 sample/test_restriction_enzyme_long.rb
commit 413442bd7424f837c73d8170ced8e01a01f87a59
Author: Naohisa Goto <ng@bioruby.org>
Date: Tue May 24 23:26:41 2011 +0900
Added a test for Bio::FastaFormat#entry_overrun etc.
* Added a test for Bio::FastaFormat#entry_overrun.
* Removed a void test class.
test/unit/bio/db/test_fasta.rb | 24 ++++++++++++------------
1 files changed, 12 insertions(+), 12 deletions(-)
commit b74020ff9b5c9fc8531c584898a329987008870e
Author: Naohisa Goto <ng@bioruby.org>
Date: Tue May 24 22:21:17 2011 +0900
Bug fix: Bio::FastaFormat#query passes nil to the given factory
* Bug fix: Bio::FastaFormat#query passes nil to the given factory
object. Thanks to Philipp Comans who reports the bug.
(https://github.com/bioruby/bioruby/issues/35)
* Test method for Bio::FastaFormat#query is added.
lib/bio/db/fasta.rb | 2 +-
test/unit/bio/db/test_fasta.rb | 22 ++++++++++++++++++++++
2 files changed, 23 insertions(+), 1 deletions(-)
commit 80e49373e0e9013442680ba33499be80c58471db
Author: Naohisa Goto <ng@bioruby.org>
Date: Tue May 17 22:33:56 2011 +0900
Changed database name in the example.
* Changed database name in the example.
Thanks to Philipp Comans who reports the issue.
lib/bio/appl/blast.rb | 2 +-
1 files changed, 1 insertions(+), 1 deletions(-)
commit 7427d1f1355a6c190c6bf8522978e462dea64134
Author: Naohisa Goto <ng@bioruby.org>
Date: Thu May 12 22:15:37 2011 +0900
Bug fix: changed GenomeNet remote BLAST URL.
* Bug fix: changed GenomeNet remote BLAST host name and path.
Thanks to Philipp Comans who reports the bug.
( https://github.com/bioruby/bioruby/issues/34 )
lib/bio/appl/blast/genomenet.rb | 6 +++---
1 files changed, 3 insertions(+), 3 deletions(-)
commit c1c231b0a17c06ec042534245ed903e0256a59ed
Author: Naohisa Goto <ng@bioruby.org>
Date: Tue May 10 20:57:17 2011 +0900
updated doc/Tutorial.rd.html
doc/Tutorial.rd.html | 34 ++++++++++++++++++----------------
1 files changed, 18 insertions(+), 16 deletions(-)
commit 5261c926cae8dac890d7d0380e84f2eb88912417
Author: Pjotr Prins <pjotr.public01@thebird.nl>
Date: Thu May 5 12:07:54 2011 +0200
Tutorial: Fixed URL and the intro
doc/Tutorial.rd | 34 ++++++++++++++++++++--------------
1 files changed, 20 insertions(+), 14 deletions(-)
commit 71de394053376f4759d705c52e6f16eca3da9d62
Author: Pjotr Prins <pjotr.public01@thebird.nl>
Date: Wed Mar 9 10:26:53 2011 +0100
Tutorial: Added a commnet for rubydoctest, changed Ruby version
* Added a comment for rubydoctest
* Changed example Ruby version representation
* This is part of commit ba5b9c2d29223860252451110a99d4ff0250395d
and modified to merge with the current HEAD.
doc/Tutorial.rd | 4 ++--
1 files changed, 2 insertions(+), 2 deletions(-)
commit 1d27153065b8e8595a470b2201961b0a39bf8ca1
Author: Naohisa Goto <ng@bioruby.org>
Date: Thu Apr 28 23:58:57 2011 +0900
updated doc/Tutorial.rd.html
doc/Tutorial.rd.html | 2 +-
1 files changed, 1 insertions(+), 1 deletions(-)
commit ae9beff3bc43db3724a292b10a214583d9fbc111
Author: Michael O'Keefe <okeemf@rpi.edu>
Date: Wed Apr 6 11:46:54 2011 -0400
Updated through the section on Homology searching with BLAST
doc/Tutorial.rd | 64 ++++++++++++++++++++--------------------------
doc/Tutorial.rd.html | 68 ++++++++++++++++++++++----------------------------
2 files changed, 58 insertions(+), 74 deletions(-)
commit 971da799b16628a927abd7dd6c218994506f8fd8
Author: Michael O'Keefe <okeemf@rpi.edu>
Date: Thu Mar 24 18:29:20 2011 -0400
Updated the html file generated from the RDoc
doc/Tutorial.rd.html | 224 ++++++++++++++++++++++++++------------------------
1 files changed, 117 insertions(+), 107 deletions(-)
commit c6afd7eeed121926b56d300cb4170b5024f29eb0
Author: Michael O'Keefe <okeemf@rpi.edu>
Date: Thu Mar 24 18:08:17 2011 -0400
Finished updating the tutorial
doc/Tutorial.rd | 16 ++++++++--------
1 files changed, 8 insertions(+), 8 deletions(-)
commit 7349ac550ec03e2c5266496297becbdb3f4e0edd
Author: Michael O'Keefe <okeemf@rpi.edu>
Date: Thu Mar 24 15:56:37 2011 -0400
Edited tutorial up through the extra stuff section
doc/Tutorial.rd | 28 ++++++++++++++--------------
1 files changed, 14 insertions(+), 14 deletions(-)
commit 32ba3b15ad00d02b12ef2b44636505e23caaf620
Author: Michael O'Keefe <okeemf@rpi.edu>
Date: Thu Mar 24 15:26:48 2011 -0400
Updated tutorial up through BioSQL
doc/Tutorial.rd | 172 ++++++++++++++++++-------------------------------------
1 files changed, 57 insertions(+), 115 deletions(-)
commit 249580edb49a13545708fdcb559104217e37f162
Author: Michael O'Keefe <okeemf@rpi.edu>
Date: Thu Mar 24 12:09:03 2011 -0400
Updated tutorial through the section on alignments
doc/Tutorial.rd | 40 +++++++++++++++++++++++++++++++++-------
1 files changed, 33 insertions(+), 7 deletions(-)
commit 54f7b54044bb245ec5953dc7426f1c434b41f24f
Author: Michael O'Keefe <okeemf@rpi.edu>
Date: Thu Mar 24 11:51:23 2011 -0400
Updated the tutorial (mostly grammar fixes) up until GenBank
doc/Tutorial.rd | 31 +++++++++++++++----------------
1 files changed, 15 insertions(+), 16 deletions(-)
commit f046a52081a8af0e9afbf65fd2673c29689be769
Author: Naohisa Goto <ng@bioruby.org>
Date: Tue Feb 8 12:58:50 2011 +0900
Added a test protein sequence data for BLAST test.
test/data/fasta/EFTU_BACSU.fasta | 8 ++++++++
1 files changed, 8 insertions(+), 0 deletions(-)
create mode 100644 test/data/fasta/EFTU_BACSU.fasta
commit f61a5f4bdde16fa051f43cbe3efef4570b415a6a
Author: Anthony Underwood <email2ants@gmail.com>
Date: Mon Jan 31 12:44:55 2011 +0000
Bug fix: GenBank sequence output should format date as 27-JAN-2011
* Bug fix: GenBank sequence output should format date as 27-JAN-2011
rather than 2011-01-27 as specified by offical GenBank specs.
lib/bio/db/genbank/format_genbank.rb | 2 +-
1 files changed, 1 insertions(+), 1 deletions(-)
commit be144e75a059058ab000a55d7bf535597e7e2617
Author: Naohisa Goto <ng@bioruby.org>
Date: Thu Feb 3 20:28:03 2011 +0900
Added tests for remote BLAST execution via GenomeNet and DDBJ.
* Added tests for remote BLAST execution via GenomeNet and DDBJ.
Currently, a test for DDBJ BLAST web API is disabled because
it takes relatively long time.
* Tests to retrieve remote BLAST database information for GenomeNet
and DDBJ servers are also added.
test/functional/bio/appl/blast/test_remote.rb | 93 +++++++++++++++++++++++++
test/functional/bio/appl/test_blast.rb | 61 ++++++++++++++++
2 files changed, 154 insertions(+), 0 deletions(-)
create mode 100644 test/functional/bio/appl/blast/test_remote.rb
create mode 100644 test/functional/bio/appl/test_blast.rb
commit 67314f1f1a248954c030f7ffe048faf862bf07d2
Author: Naohisa Goto <ng@bioruby.org>
Date: Thu Feb 3 20:19:11 2011 +0900
Updated _parse_databases following the changes in the DDBJ server
* Updated _parse_databases following the changes in the DDBJ server.
Changed to use (NT) or (AA) in the tail of each description.
Thanks to DDBJ to improve their web service API.
lib/bio/appl/blast/ddbj.rb | 29 ++++++++++++++++++++---------
1 files changed, 20 insertions(+), 9 deletions(-)
commit d6aad2f4cc53c1227c86b6b573644cca15c9ed82
Author: Naohisa Goto <ng@bioruby.org>
Date: Wed Feb 2 00:02:32 2011 +0900
Release notes for the next release is added.
RELEASE_NOTES.rdoc | 38 ++++++++++++++++++++++++++++++++++++++
1 files changed, 38 insertions(+), 0 deletions(-)
create mode 100644 RELEASE_NOTES.rdoc
commit b4a30cc8ac9472b9e1c2a298afc624d0229c64c9
Author: Naohisa Goto <ng@bioruby.org>
Date: Tue Feb 1 23:33:18 2011 +0900
Bug fix: Execution failure due to the changes of DDBJ BLAST server
lib/bio/appl/blast/ddbj.rb | 4 +++-
1 files changed, 3 insertions(+), 1 deletions(-)
commit d30cb5975febd8b526088612c4fb9689a6cc46ba
Author: Naohisa Goto <ng@bioruby.org>
Date: Tue Feb 1 23:01:34 2011 +0900
Support for database "mine-aa" and "mine-nt" with KEGG organism codes
* Added support for database "mine-aa" and "mine-nt" combined with
KEGG organism codes. When database name starts with mine-aa or
mine-nt, space-separated list of KEGG organism codes can be given.
For example, "mine-aa eco bsu hsa".
lib/bio/appl/blast/genomenet.rb | 11 +++++++++++
1 files changed, 11 insertions(+), 0 deletions(-)
commit abcba798ccf57894dcd570a6578ef78db30a3e25
Author: Naohisa Goto <ng@bioruby.org>
Date: Tue Feb 1 22:20:02 2011 +0900
RELEASE_NOTES.rdoc is renamed to doc/RELEASE_NOTES-1.4.1.rdoc
RELEASE_NOTES.rdoc | 104 ------------------------------------------
doc/RELEASE_NOTES-1.4.1.rdoc | 104 ++++++++++++++++++++++++++++++++++++++++++
2 files changed, 104 insertions(+), 104 deletions(-)
delete mode 100644 RELEASE_NOTES.rdoc
create mode 100644 doc/RELEASE_NOTES-1.4.1.rdoc
commit 8719cf4e06fc8a8cd0564aeb0b95372a7a0bcefb
Author: Naohisa Goto <ng@bioruby.org>
Date: Tue Feb 1 22:07:32 2011 +0900
Bug: Options "-v" and "-b" should be used for the limit of hits.
* Bug: Options "-v" and "-b" should be used for the limit of hits,
and "-V" and "-B" should not be used for the purpose.
lib/bio/appl/blast/genomenet.rb | 8 ++++----
1 files changed, 4 insertions(+), 4 deletions(-)
commit 974b640badae9837fe9fc173d690b27c9b045454
Author: Naohisa Goto <ng@bioruby.org>
Date: Tue Feb 1 20:34:50 2011 +0900
Bug fix: Workaround for a change in the GenomeNet BLAST site.
* Bug fix: Workaround for a change in the GenomeNet BLAST site.
Thanks to the anonymous reporter. The patch was originally made
by Toshiaki Katyama.
lib/bio/appl/blast/genomenet.rb | 7 +++----
1 files changed, 3 insertions(+), 4 deletions(-)
commit 001d3e3570c77185cece4aed1be5be2ed6f94f7e
Author: Naohisa Goto <ng@bioruby.org>
Date: Thu Jan 6 23:39:19 2011 +0900
Added tests to check the previous Bio::Reference#endnote fix.
test/unit/bio/test_reference.rb | 30 ++++++++++++++++++++++++++++++
1 files changed, 30 insertions(+), 0 deletions(-)
commit e1cd766abe24dbcc08a42103127c75ad0ab929aa
Author: Naohisa Goto <ng@bioruby.org>
Date: Thu Jan 6 23:07:35 2011 +0900
Bio::Reference#pubmed_url is updated to follow recent NCBI changes.
lib/bio/reference.rb | 5 ++---
test/unit/bio/test_reference.rb | 5 +++++
2 files changed, 7 insertions(+), 3 deletions(-)
commit 48024313a7568a38f4291618708541ae1dac312c
Author: Naohisa Goto <ng@bioruby.org>
Date: Thu Jan 6 22:56:37 2011 +0900
Bug fix: Bio::Reference#endnote fails when url is not set
* Bug fix: Bio::Reference#endnote fails when url is not set.
Thanks to Warren Kibbe who reports the bug.
(https://github.com/bioruby/bioruby/issues#issue/15)
lib/bio/reference.rb | 2 +-
1 files changed, 1 insertions(+), 1 deletions(-)
commit 577278a95340abfa32d3e67415d3a10bc74b82c0
Author: Pjotr Prins <pjotr.public01@thebird.nl>
Date: Fri Dec 17 12:16:31 2010 +0100
Bug fix: In Bio::MEDLINE#reference, doi field should be filled.
* Bug fix: In Bio::MEDLINE#reference, doi field should be filled.
(https://github.com/bioruby/bioruby/issues#issue/29)
lib/bio/db/medline.rb | 1 +
test/unit/bio/db/test_medline.rb | 1 +
2 files changed, 2 insertions(+), 0 deletions(-)
commit daa20c85681576d3bfbdc8f87580a4b6227b122c
Author: Naohisa Goto <ng@bioruby.org>
Date: Thu Jan 6 20:25:03 2011 +0900
Bug fix: Bio::Newick#reparse failure
* Bug fix: Bio::Newick#reparse failure.
Thanks to jdudley who reports the bug.
(https://github.com/bioruby/bioruby/issues#issue/28)
* Tests are added to confirm the bug fix.
lib/bio/db/newick.rb | 4 +++-
test/unit/bio/db/test_newick.rb | 12 ++++++++++++
2 files changed, 15 insertions(+), 1 deletions(-)
commit 16117aefdf57ac3ae16b5568f462f7b919ef005f
Author: Naohisa Goto <ng@bioruby.org>
Date: Thu Jan 6 20:14:18 2011 +0900
Use setup for the preparation of adding more test methods.
test/unit/bio/db/test_newick.rb | 14 ++++++++++----
1 files changed, 10 insertions(+), 4 deletions(-)
commit e5dc5896a5c6249e2a6cb03d63a3c2ade36b67e7
Author: Naohisa Goto <ng@bioruby.org>
Date: Fri Nov 19 21:07:13 2010 +0900
Ruby 1.9 support: suppressed warning "mismatched indentations"
test/unit/bio/db/pdb/test_pdb.rb | 4 ++--
1 files changed, 2 insertions(+), 2 deletions(-)
commit 1bce41c7ebed46ac6cf433b047fe6a4c3a538089
Author: Naohisa Goto <ng@bioruby.org>
Date: Fri Nov 19 21:05:06 2010 +0900
Ruby 1.9 support: Suppressed warning "shadowing outer local variable"
lib/bio/db/pdb/residue.rb | 4 ++--
1 files changed, 2 insertions(+), 2 deletions(-)
commit 0f31727769833ccf9d6891ae192da1bc180223e0
Author: Naohisa Goto <ng@bioruby.org>
Date: Fri Nov 19 21:04:07 2010 +0900
Ruby 1.9 support: Suppressed warning "shadowing outer local variable"
lib/bio/location.rb | 4 ++--
1 files changed, 2 insertions(+), 2 deletions(-)
commit 70c1135b171fcf47dd9dc1bc396d15d1c3acfa62
Author: Naohisa Goto <ng@bioruby.org>
Date: Fri Nov 19 21:02:57 2010 +0900
Ruby 1.9 support: Suppressed warning "shadowing outer local variable"
lib/bio/db/pdb/pdb.rb | 14 +++++++-------
1 files changed, 7 insertions(+), 7 deletions(-)
commit a77e4ab78211a85aa052ca6645a2051a4f3b76d8
Author: Naohisa Goto <ng@bioruby.org>
Date: Fri Nov 19 20:42:22 2010 +0900
Ruby 1.9 support: use Array#join instead of Array#to_s
lib/bio/db/pdb/pdb.rb | 4 ++--
1 files changed, 2 insertions(+), 2 deletions(-)
commit 734c2e54613e3ed5efd95e1212feab8f014d5f19
Author: Naohisa Goto <ng@bioruby.org>
Date: Fri Nov 19 20:38:11 2010 +0900
Changed to use assert_instance_of
* Changed to use assert_instance_of(klass, obj) instead of
assert_equal(klass, obj.class).
test/unit/bio/db/pdb/test_pdb.rb | 16 ++++++++--------
1 files changed, 8 insertions(+), 8 deletions(-)
commit 490286018c8ce314da441c646ea9c5fb3f765c95
Author: Naohisa Goto <ng@bioruby.org>
Date: Fri Nov 19 20:24:36 2010 +0900
Float::EPSILON was too small for the delta tolerance.
test/unit/bio/db/pdb/test_pdb.rb | 20 ++++++++++----------
1 files changed, 10 insertions(+), 10 deletions(-)
commit e92d225cadabe63fe23c7c32a4d1d50a371366cc
Author: Naohisa Goto <ng@bioruby.org>
Date: Fri Nov 19 20:16:30 2010 +0900
Ruby 1.9 support: use assert_in_delta
test/unit/bio/db/pdb/test_pdb.rb | 24 +++++++++++++++---------
1 files changed, 15 insertions(+), 9 deletions(-)
commit 41452971a132ef55de3486022962fa2c333b4c85
Author: Naohisa Goto <ng@bioruby.org>
Date: Fri Nov 19 13:19:39 2010 +0900
Fixed Object#id problem and suppressed warning messages.
* Changed not to call nil.id (==4) invoked from chain.id.
* Suppressed warning message about useless use of a variable.
* Suppressed waring about conflict of IDs when testing
addResidue, addLigand and addChain methods.
test/unit/bio/db/pdb/test_pdb.rb | 119 +++++++++++++++++++-------------------
1 files changed, 59 insertions(+), 60 deletions(-)
commit b4af5826f77002933de9d3c2ddfcc5a7cb5629db
Author: Naohisa Goto <ng@bioruby.org>
Date: Wed Nov 17 22:26:26 2010 +0900
Adjusted copyright line
test/unit/bio/db/pdb/test_pdb.rb | 4 ++--
1 files changed, 2 insertions(+), 2 deletions(-)
commit 06fd989072b2287a3accbb60684b8a029bfc0ac3
Author: Naohisa Goto <ng@bioruby.org>
Date: Wed Nov 17 21:54:05 2010 +0900
A module name is changed to avoid potential name conflict.
* A module name is changed to avoid potential name conflict.
* Removed a Shift_JIS character (Zenkaku space) in a comment line.
test/unit/bio/db/pdb/test_pdb.rb | 4 ++--
1 files changed, 2 insertions(+), 2 deletions(-)
commit 09007f93abe8c9c5e7561f082b55ca307a7d4a1e
Author: Kazuhiro Hayashi <k.hayashi.info@gmail.com>
Date: Thu Jul 15 21:06:28 2010 +0900
Added more unit tests for Bio::PDB
* Added more unit tests for Bio::PDB.
* This is part of combinations of the 13 commits:
* 555f7b49a43e7c35c82cd48b199af96ca93d4179
* 2b5c87a9ada248597e0517e22191bb4c88be2a42
* a16e24fa35debdcacd11cf36fdf0e60fe82b3684
* e3607c0f7154a4156fd53ed17470aa3628cd2586