ChangeLog in bio-1.4.2 vs ChangeLog in bio-1.4.3
- old
+ new
@@ -1,5004 +1,1469 @@
-commit 3acc1e098839cacbe85b5c23367ab14e0c4fe3ea
+commit 51ab2dec144c99a14ca9009c7b589b500f1cad5f
Author: Naohisa Goto <ng@bioruby.org>
-Date: Fri Aug 26 15:01:49 2011 +0900
+Date: Wed Aug 22 00:12:47 2012 +0900
- Preparation for bioruby-1.4.2 release.
+ Preparation to re-release BioRuby 1.4.3
- bioruby.gemspec | 2 +-
- lib/bio/version.rb | 2 +-
- 2 files changed, 2 insertions(+), 2 deletions(-)
+ ChangeLog | 22 ++++++++++++++++++++++
+ 1 files changed, 22 insertions(+), 0 deletions(-)
-commit bf69125192fa01ae3495e094e7ef1b5e895954ad
+commit 5ff159d12252393ff04afe52b59a315d15c63d18
Author: Naohisa Goto <ng@bioruby.org>
-Date: Fri Aug 26 14:42:02 2011 +0900
+Date: Wed Aug 22 00:00:40 2012 +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
+ Bug fix: bin/bioruby failed to save object
- * Updated tutorial
- (original commit id: 7b9108657961cf2354278e04971c32059b3ed4e2
- and some preceding commits)
+ * Bug fix: bin/bioruby: Failed to save object with error message
+ "can't convert Symbol into String" on Ruby 1.9.
- doc/Tutorial.rd | 55 ++++++++++++++++++++++++++++++++-----------------------
- 1 files changed, 32 insertions(+), 23 deletions(-)
+ RELEASE_NOTES.rdoc | 2 ++
+ lib/bio/shell/core.rb | 1 +
+ 2 files changed, 3 insertions(+), 0 deletions(-)
-commit de8a394129c752a0b9a5975a73c5eb582d9681d3
+commit 74c6ce09413e7ddde1431d74e10cc9c4cdbb95ba
Author: Naohisa Goto <ng@bioruby.org>
-Date: Fri Aug 26 13:24:27 2011 +0900
+Date: Tue Aug 21 22:35:18 2012 +0900
- fix typo and change order of lines
+ BioRuby 1.4.3 is released.
- RELEASE_NOTES.rdoc | 6 +++---
- 1 files changed, 3 insertions(+), 3 deletions(-)
+ ChangeLog | 21 +++++++++++++++++++++
+ 1 files changed, 21 insertions(+), 0 deletions(-)
-commit 1cf2a11199655e4c9f5fc49c5a588b99c18ab7ca
+commit 61af85b6cfc7bb1f3668ed68232113eb0751e7ea
Author: Naohisa Goto <ng@bioruby.org>
-Date: Fri Aug 26 13:16:11 2011 +0900
+Date: Tue Aug 21 22:33:30 2012 +0900
- RELEASE_NOTE.rdoc modified to reflect recent changes
+ preparation for BioRuby 1.4.3 release version
- RELEASE_NOTES.rdoc | 14 ++++++++++++++
- 1 files changed, 14 insertions(+), 0 deletions(-)
+ bioruby.gemspec | 2 +-
+ lib/bio/version.rb | 2 +-
+ 2 files changed, 2 insertions(+), 2 deletions(-)
-commit b44871a5866eeb2d379f080b39b09693c9e9e3cc
+commit 1ec68beac42a06e9ef0a9c953650ef4d599e4e65
Author: Naohisa Goto <ng@bioruby.org>
-Date: Fri Aug 26 13:15:14 2011 +0900
+Date: Tue Aug 21 20:53:04 2012 +0900
- In BioRuby Shell, getent() fails when EMBOSS seqret does not found.
+ ChangeLog modified; release candidate version 1.4.3-rc2
- lib/bio/shell/plugin/entry.rb | 10 +++++++---
- 1 files changed, 7 insertions(+), 3 deletions(-)
+ ChangeLog | 1353 ++++++++++++++++++++++++++++++++++++++++++++++++++++
+ bioruby.gemspec | 2 +-
+ lib/bio/version.rb | 4 +-
+ 3 files changed, 1356 insertions(+), 3 deletions(-)
-commit 179e7506b008a220d5dd42ce1a6c7ce589c3fcda
+commit e0d570b237a8b96ae0c1e7b1ad72c7333be07c52
Author: Naohisa Goto <ng@bioruby.org>
-Date: Fri Aug 26 12:26:52 2011 +0900
+Date: Mon Aug 20 20:35:58 2012 +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.
+ version changed to 1.4.3-rc1
- lib/bio/io/ncbirest.rb | 122 +++++++++++++++++++++++++++++++++++++-
- lib/bio/shell/plugin/ncbirest.rb | 6 ++-
- 2 files changed, 126 insertions(+), 2 deletions(-)
+ bioruby.gemspec | 3 ++-
+ lib/bio/version.rb | 2 +-
+ 2 files changed, 3 insertions(+), 2 deletions(-)
-commit 99b31379bb41c7cad34c1e7dc00f802da37de1cd
+commit 511c81ba67f7b8dc9cff85cf68db654d2feaf52e
Author: Naohisa Goto <ng@bioruby.org>
-Date: Thu Aug 25 19:03:43 2011 +0900
+Date: Mon Aug 20 20:17:14 2012 +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)
+ document JRUBY-5678 (resolved) and related issue with the workaround.
- lib/bio/db/fastq.rb | 14 ++++++++++++++
- test/unit/bio/db/test_fastq.rb | 14 ++++++++++++++
- 2 files changed, 28 insertions(+), 0 deletions(-)
+ KNOWN_ISSUES.rdoc | 9 +++++++++
+ RELEASE_NOTES.rdoc | 9 +++++++++
+ 2 files changed, 18 insertions(+), 0 deletions(-)
-commit 8ab772b37850c3874b55cf37d091046394cda5bd
+commit 2fdd7a3b3555a33dead31181c9526af22f24916f
Author: Naohisa Goto <ng@bioruby.org>
-Date: Thu Aug 25 15:23:00 2011 +0900
+Date: Mon Aug 20 19:44:39 2012 +0900
- RELEASE_NOTES.rdoc changed to reflect recent changes.
+ update recommended Ruby versions and the year in copyright lines
- RELEASE_NOTES.rdoc | 16 ++++++++++++++++
- 1 files changed, 16 insertions(+), 0 deletions(-)
+ README.rdoc | 7 +++----
+ 1 files changed, 3 insertions(+), 4 deletions(-)
-commit 8db6abdcc81db6a58bdd99e7f8d410b1a74496b1
+commit b156227749e5ada74330e837c9ce48a16e6a6a2f
Author: Naohisa Goto <ng@bioruby.org>
-Date: Thu Aug 25 14:28:42 2011 +0900
+Date: Mon Aug 20 19:16:25 2012 +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.
+ Bug fix: Bio::EMBL#os raises error, with incompatible change
- * 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)
+ * Bug fix: Bio::EMBL#os raises error. The bug is reported by
+ Marc P. Hoeppner in the BioRuby mailing list
+ (https://redmine.open-bio.org/issues/3294).
+ * Incompatible change: Bio::EMBL#os no longer splits the content with
+ comma, and it no longer raises error even if the OS line is not in
+ the "Genus species (name)" format. The changes may affect the parsing
+ of old EMBL files which contain two or more species names in an OS line.
+ * Unit tests are modified to catch up the above incompatible changes.
- 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
+ RELEASE_NOTES.rdoc | 14 ++++++
+ lib/bio/db/embl/embl.rb | 74 ++++++++++++++++++++++++++++++
+ test/unit/bio/db/embl/test_embl.rb | 9 +---
+ test/unit/bio/db/embl/test_embl_rel89.rb | 9 +---
+ 4 files changed, 92 insertions(+), 14 deletions(-)
-commit 7e8ba7c1388204daa5245d2128d01f6f40298185
+commit 31c8b4cb6ce2364aacee8137ddec3aa5f7d2d0d8
Author: Naohisa Goto <ng@bioruby.org>
-Date: Thu Aug 18 00:08:51 2011 +0900
+Date: Mon Aug 20 19:04:50 2012 +0900
- In Fastq formatter, default width value changed to nil
+ Workaround for jruby-1.7.0.preview2 bugs JRUBY-6195, JRUBY-6818
- * 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)
+ * Workaroud for jruby-1.7.0.preview2 bugs JRUBY-6195 and JRUBY-6818.
+ * Refactoring of call_command_popen: split _call_command_popen_ruby18
+ and _call_command_popen_ruby19, add _call_command_popen_jruby19.
+ Note that _call_command_popen_jruby19 will be removed in the future
+ after the bugs are fixed.
- 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(-)
+ lib/bio/command.rb | 98 ++++++++++++++++++++++++++++++++++++++++++++++-----
+ 1 files changed, 88 insertions(+), 10 deletions(-)
-commit 0fb65211519febff18413c589fe7af753ee2e61d
+commit 05f51fa2e871e71c2b20559eb05e456768a4f7d6
Author: Naohisa Goto <ng@bioruby.org>
-Date: Wed Aug 17 22:02:03 2011 +0900
+Date: Sat Aug 18 00:32:31 2012 +0900
- Bug fix: Bio::SPTR follow-up of UniProtKB format changes
+ New default etc/bioinformatics/seqdatabase.ini
- * 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)
+ * New default etc/bioinformatics/seqdatabase.ini, with currently
+ available services.
- 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
+ etc/bioinformatics/seqdatabase.ini | 27 +++++++++++++++++++++++++++
+ 1 files changed, 27 insertions(+), 0 deletions(-)
+ create mode 100644 etc/bioinformatics/seqdatabase.ini
-commit 0d066ab6b8fc19f1cf6e66e07c2065775739cccd
+commit a4264cc3667b98289c09efc7ccba9c8e86f6d89c
Author: Naohisa Goto <ng@bioruby.org>
-Date: Sat Aug 13 00:58:51 2011 +0900
+Date: Sat Aug 18 00:31:10 2012 +0900
- preparation for release: alpha test version 1.4.2-alpha1
+ etc/bioinformatics/seqdatabase.ini is moved to sample/
- bioruby.gemspec | 23 +++++++++++++++++++++--
- lib/bio/version.rb | 4 ++--
- 2 files changed, 23 insertions(+), 4 deletions(-)
+ etc/bioinformatics/seqdatabase.ini | 210 ------------------------------------
+ sample/seqdatabase.ini | 210 ++++++++++++++++++++++++++++++++++++
+ 2 files changed, 210 insertions(+), 210 deletions(-)
+ delete mode 100644 etc/bioinformatics/seqdatabase.ini
+ create mode 100644 sample/seqdatabase.ini
-commit 55ece17775f5d24cf62f93d54ded5dc6eed53584
+commit 04b7a27b557576f5325b3ee420262922ab66ca3b
Author: Naohisa Goto <ng@bioruby.org>
-Date: Fri Aug 12 21:57:25 2011 +0900
+Date: Sat Aug 18 00:30:38 2012 +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)
+ known issue about http://bioruby.org/cgi-bin/biofetch.rb server down
- test/functional/bio/test_command.rb | 6 +++---
- 1 files changed, 3 insertions(+), 3 deletions(-)
+ KNOWN_ISSUES.rdoc | 9 +++++++++
+ 1 files changed, 9 insertions(+), 0 deletions(-)
-commit 2f464aae016387cd50031f9d9664e78e220e2d01
+commit 4a8193f7b91ff703c8f3dc6e6a6ae0c981a404e6
Author: Naohisa Goto <ng@bioruby.org>
-Date: Fri Aug 12 20:37:18 2011 +0900
+Date: Fri Aug 17 23:45:41 2012 +0900
- RELEASE_NOTES.rdoc is updated following recent changes.
+ Update descriptions about JRuby and Rubinius bugs
- RELEASE_NOTES.rdoc | 21 ++++++++++++++-------
- 1 files changed, 14 insertions(+), 7 deletions(-)
+ KNOWN_ISSUES.rdoc | 14 ++++++++++----
+ RELEASE_NOTES.rdoc | 14 ++++++++++----
+ 2 files changed, 20 insertions(+), 8 deletions(-)
-commit d1a193684afdfd4c632ef75a978d4f3680d1bdf3
+commit a2d8dd8ccebde84e91f82c59e531cc08fbf0f3fe
Author: Naohisa Goto <ng@bioruby.org>
-Date: Fri Aug 12 20:30:53 2011 +0900
+Date: Fri Aug 17 17:19:22 2012 +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.
+ Remove the suffix .rb in require, to avoid potential multiple loading.
- KNOWN_ISSUES.rdoc | 40 ++++++++++++++++++++++++++++++----
- README.rdoc | 61 ++++++++++++++++++++--------------------------------
- 2 files changed, 59 insertions(+), 42 deletions(-)
+ test/unit/bio/db/fasta/test_defline.rb | 2 +-
+ test/unit/bio/db/genbank/test_genpept.rb | 2 +-
+ test/unit/bio/db/kegg/test_drug.rb | 2 +-
+ test/unit/bio/db/kegg/test_genome.rb | 2 +-
+ test/unit/bio/db/kegg/test_glycan.rb | 2 +-
+ test/unit/bio/util/test_restriction_enzyme.rb | 2 +-
+ 6 files changed, 6 insertions(+), 6 deletions(-)
-commit b5cbdc6ab7e81aae4db9aeb708fac57ffbce5636
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Sat Jul 16 00:12:17 2011 +0900
+commit 1d2e8b02db3699c2cd4f4890abc078ffd2b503aa
+Author: Ben J. Woodcroft <donttrustben near gmail.com>
+Date: Wed Aug 8 09:41:20 2012 +1000
- Added topics for the release notes
+ fill in missing piece of documentation in FastaFormat
- 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 +-
+ lib/bio/db/fasta.rb | 2 +-
1 files changed, 1 insertions(+), 1 deletions(-)
-commit 7427d1f1355a6c190c6bf8522978e462dea64134
+commit 83bf09d4d81803c8d06e0d45ca25e7c09016161c
Author: Naohisa Goto <ng@bioruby.org>
-Date: Thu May 12 22:15:37 2011 +0900
+Date: Wed Aug 8 00:08:26 2012 +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 )
+ RELEASE_NOTE.rdoc modified to reflect recent changes
- lib/bio/appl/blast/genomenet.rb | 6 +++---
- 1 files changed, 3 insertions(+), 3 deletions(-)
+ RELEASE_NOTES.rdoc | 107 ++++++++++++++++++++++++++++++++++++++++++++-------
+ 1 files changed, 92 insertions(+), 15 deletions(-)
-commit c1c231b0a17c06ec042534245ed903e0256a59ed
+commit c3afb1eb98cf8777ee021624c3d2eab92b3543f2
Author: Naohisa Goto <ng@bioruby.org>
-Date: Tue May 10 20:57:17 2011 +0900
+Date: Wed Aug 8 00:06:09 2012 +0900
- updated doc/Tutorial.rd.html
+ Descriptions about JRuby, Rubinius, DDBJ Web API, SOAP4R etc.
- doc/Tutorial.rd.html | 34 ++++++++++++++++++----------------
- 1 files changed, 18 insertions(+), 16 deletions(-)
+ KNOWN_ISSUES.rdoc | 45 +++++++++++++++++++++++++++++++++++++++++++--
+ 1 files changed, 43 insertions(+), 2 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
+commit 01da7401a011aa519c43a021f89f6e7f769b4649
Author: Naohisa Goto <ng@bioruby.org>
-Date: Thu Apr 28 23:58:57 2011 +0900
+Date: Tue Aug 7 23:55:09 2012 +0900
- updated doc/Tutorial.rd.html
+ regenerate bioruby.gemspec with rake regemspec
- doc/Tutorial.rd.html | 2 +-
- 1 files changed, 1 insertions(+), 1 deletions(-)
+ bioruby.gemspec | 3 +--
+ 1 files changed, 1 insertions(+), 2 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
+commit 9f70c27d9b75408fddae8384a2a09715b959dcb5
Author: Naohisa Goto <ng@bioruby.org>
-Date: Tue Feb 8 12:58:50 2011 +0900
+Date: Tue Aug 7 23:51:56 2012 +0900
- Added a test protein sequence data for BLAST test.
+ improve documentation; version changed to 1.4.3-pre1
- test/data/fasta/EFTU_BACSU.fasta | 8 ++++++++
- 1 files changed, 8 insertions(+), 0 deletions(-)
- create mode 100644 test/data/fasta/EFTU_BACSU.fasta
+ lib/bio/version.rb | 13 +++++++++++--
+ 1 files changed, 11 insertions(+), 2 deletions(-)
-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
+commit c11f12c8aa56b8509cd082f3478e96374210e5d7
Author: Naohisa Goto <ng@bioruby.org>
-Date: Thu Feb 3 20:28:03 2011 +0900
+Date: Tue Aug 7 23:31:41 2012 +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.
+ Remove autorequire which have been deprecated
- 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
+ bioruby.gemspec.erb | 1 -
+ 1 files changed, 0 insertions(+), 1 deletions(-)
-commit 67314f1f1a248954c030f7ffe048faf862bf07d2
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Thu Feb 3 20:19:11 2011 +0900
+commit 7792b092033d2c819f2bcad0e206f27608481db5
+Author: Ben J Woodcroft <donttrustben@gmail.com>
+Date: Mon Aug 6 09:40:55 2012 +1000
- 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.
+ flesh out FastaFormat documentation
- lib/bio/appl/blast/ddbj.rb | 29 ++++++++++++++++++++---------
- 1 files changed, 20 insertions(+), 9 deletions(-)
+ lib/bio/db/fasta.rb | 102 ++++++++++++++++++++++++-------------------
+ lib/bio/db/fasta/defline.rb | 2 +-
+ 2 files changed, 58 insertions(+), 46 deletions(-)
-commit d6aad2f4cc53c1227c86b6b573644cca15c9ed82
+commit 9a2fe67c247cdc7c9ddc9f8b8de771515ba76ac1
Author: Naohisa Goto <ng@bioruby.org>
-Date: Wed Feb 2 00:02:32 2011 +0900
+Date: Fri Aug 3 22:36:12 2012 +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
+ .travis.yml: restructure matrix, add allow_failures lines
- * 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".
+ * Add allow_failures lines
+ * Restructure matrix: remove many exclude lines and add some
+ include lines.
+ * When running jruby, Set TMPDIR to avoid known issue about
+ FileUtils#remove_entry_secure.
- lib/bio/appl/blast/genomenet.rb | 11 +++++++++++
- 1 files changed, 11 insertions(+), 0 deletions(-)
+ .travis.yml | 52 ++++++++++++++++++----------------------------------
+ 1 files changed, 18 insertions(+), 34 deletions(-)
-commit abcba798ccf57894dcd570a6578ef78db30a3e25
+commit 553fd102c533c42675f93895557e3e00d36fd3e7
Author: Naohisa Goto <ng@bioruby.org>
-Date: Tue Feb 1 22:20:02 2011 +0900
+Date: Fri Aug 3 22:05:39 2012 +0900
- RELEASE_NOTES.rdoc is renamed to doc/RELEASE_NOTES-1.4.1.rdoc
+ Improve tests for BLAST "-m 8" tabular format parser
- 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
+ test/unit/bio/appl/blast/test_report.rb | 119 +++++++++++++++++++++++++++++++
+ 1 files changed, 119 insertions(+), 0 deletions(-)
-commit 8719cf4e06fc8a8cd0564aeb0b95372a7a0bcefb
+commit 3e1c062dbc168bd558ca8408a6da115aa570f3a7
Author: Naohisa Goto <ng@bioruby.org>
-Date: Tue Feb 1 22:07:32 2011 +0900
+Date: Fri Aug 3 22:05:07 2012 +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.
+ Improve test and suppress warning: assigned but unused variable
- lib/bio/appl/blast/genomenet.rb | 8 ++++----
- 1 files changed, 4 insertions(+), 4 deletions(-)
+ test/unit/bio/io/flatfile/test_buffer.rb | 1 +
+ 1 files changed, 1 insertions(+), 0 deletions(-)
-commit 974b640badae9837fe9fc173d690b27c9b045454
+commit 7e29ce1f050e9e5b23299372d8ddfae781447dc3
Author: Naohisa Goto <ng@bioruby.org>
-Date: Tue Feb 1 20:34:50 2011 +0900
+Date: Fri Aug 3 22:02:21 2012 +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.
+ Improve test and suppress warning: assigned but unused variable
- lib/bio/appl/blast/genomenet.rb | 7 +++----
- 1 files changed, 3 insertions(+), 4 deletions(-)
+ test/unit/bio/db/test_newick.rb | 2 ++
+ 1 files changed, 2 insertions(+), 0 deletions(-)
-commit 001d3e3570c77185cece4aed1be5be2ed6f94f7e
+commit 1053b62069df74f336934e4ed0f3f217e4ad3312
Author: Naohisa Goto <ng@bioruby.org>
-Date: Thu Jan 6 23:39:19 2011 +0900
+Date: Fri Jul 27 13:56:53 2012 +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
+ Suppress warnings: shadowing outer local variable
- * 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)
+ * Suppress warnings: shadowing outer local variable.
+ Thanks to Andrew Grimm: https://github.com/bioruby/bioruby/pull/64
- 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
- * 4e74c9107f09c5eb3fc7fc9ec38d9d773fe89367
- * 605fb0a222f70eeaa1e576d31af484a9a6a2ac27
- * 2c8b2b5496fee04b886bfcbd11fb99948816cc28
- * 202cf2b1b57fbcac215aa135cf6343af6a49d2ef
- * f13c070c763c9035451c3639e6e29c9a156947cd
- * 843378e608bd1ef27a713d9be2d50f0f56915b0b
- * a9078b8a586b66d8026af612d9a5999c6c77de33
- * f0174a8ca3ee136271c51047fce12597d3fbb58c
- * 6675fd930718e41ad009f469b8167f81c9b2ad52
-
- test/unit/bio/db/pdb/test_pdb.rb | 3281 +++++++++++++++++++++++++++++++++++++-
- 1 files changed, 3276 insertions(+), 5 deletions(-)
-
-commit 2f6a1d29b14d89ac39b408582c9865ad06560ae1
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Sat Nov 6 00:41:21 2010 +0900
-
- Adjusted test data file path, required files and header descriptions.
-
- test/unit/bio/db/test_litdb.rb | 8 ++++----
+ lib/bio/db/gff.rb | 8 ++++----
1 files changed, 4 insertions(+), 4 deletions(-)
-commit d3394e69c98b3be63c8287af84dc530830fb977a
-Author: Kazuhiro Hayashi <k.hayashi.info@gmail.com>
-Date: Fri Jun 18 17:11:25 2010 +0900
-
- added unit test for Bio::LITDB with a sample file
-
- test/data/litdb/1717226.litdb | 13 +++++
- test/unit/bio/db/test_litdb.rb | 95 ++++++++++++++++++++++++++++++++++++++++
- 2 files changed, 108 insertions(+), 0 deletions(-)
- create mode 100644 test/data/litdb/1717226.litdb
- create mode 100644 test/unit/bio/db/test_litdb.rb
-
-commit cef1d2c824f138fe268d20eaa9ffd85223c85ef9
+commit e55794f65b3fb45c99e61d45220fe42f718426a3
Author: Naohisa Goto <ng@bioruby.org>
-Date: Fri Nov 5 23:54:31 2010 +0900
+Date: Wed Jul 25 23:29:17 2012 +0900
- Adjusted test data file path, required files and header descriptions.
-
- test/unit/bio/db/test_nbrf.rb | 8 ++++----
- 1 files changed, 4 insertions(+), 4 deletions(-)
-
-commit e892e7f9b9b4daadeff44c9e479e6f51f02e383e
-Author: Kazuhiro Hayashi <k.hayashi.info@gmail.com>
-Date: Fri Jun 25 13:20:46 2010 +0900
-
- Added unit tests for Bio::NBRF with test data.
+ Suppress warnings in lib/bio/alignment.rb:2322
- * Added unit tests for Bio::NBRF with test data.
- * This is part of combinations of the two commits:
- * 53873a82182e072e738da20381dcb2bfd8bc9e96
- (Modified the unit test for Bio::NBRF)
- * 4675cf85aa9c0b4de9f527f9c6bb80804fdaaaa9
- (Modified Bio::TestNBRF and Bio::TestTRANSFAC.)
+ * A space is inserted to suppress warnings in lib/bio/alignment.rb:2322.
+ * warning: :' after local variable is interpreted as binary operator
+ * warning: even though it seems like symbol literal
- test/data/pir/CRAB_ANAPL.pir | 6 +++
- test/unit/bio/db/test_nbrf.rb | 82 +++++++++++++++++++++++++++++++++++++++++
- 2 files changed, 88 insertions(+), 0 deletions(-)
- create mode 100644 test/data/pir/CRAB_ANAPL.pir
- create mode 100644 test/unit/bio/db/test_nbrf.rb
-
-commit 4922d5151138312d5a09ac60a06419c23978ba3c
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Fri Nov 5 23:07:13 2010 +0900
-
- Mock class for testing is moved under the test class
-
- * Mock class for testing is moved under the test class, to avoid
- potential name conflicts.
-
- test/unit/bio/db/genbank/test_common.rb | 25 ++++++++++++-------------
- 1 files changed, 12 insertions(+), 13 deletions(-)
-
-commit 8f630700bc6dd8c183d08291c66c665394873586
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Fri Nov 5 23:01:32 2010 +0900
-
- Adjusted header descriptions.
-
- test/unit/bio/db/genbank/test_common.rb | 4 ++--
- 1 files changed, 2 insertions(+), 2 deletions(-)
-
-commit ab3d6384ca721fb6004efb5988461eecefad4d6b
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Fri Nov 5 22:58:21 2010 +0900
-
- Adjusted test data file path and header descriptions.
-
- test/unit/bio/db/genbank/test_genpept.rb | 8 ++++----
- 1 files changed, 4 insertions(+), 4 deletions(-)
-
-commit 1d24aecfac9dbc190cdc3eef0956451cc88cfe4f
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Fri Nov 5 22:54:19 2010 +0900
-
- Adjusted test data file path, required files and header descriptions.
-
- test/unit/bio/db/genbank/test_genbank.rb | 12 ++++++++----
- 1 files changed, 8 insertions(+), 4 deletions(-)
-
-commit 09275d8661f3d49a7e40be59a086ba33659b2448
-Author: Kazuhiro Hayashi <k.hayashi.info@gmail.com>
-Date: Thu Jun 17 22:08:15 2010 +0900
-
- Added unit tests for Bio::GenPept newly.
-
- * Added unit tests for Bio::GenPept newly.
- * This is part of the commit 8e46ff42b627791f259033d5a20c1610e32cfa62
- (Added unit tests for NBRF and GenPept newly.)
-
- test/data/genbank/CAA35997.gp | 48 ++++++++++++++++++
- test/unit/bio/db/genbank/test_genpept.rb | 81 ++++++++++++++++++++++++++++++
- 2 files changed, 129 insertions(+), 0 deletions(-)
- create mode 100644 test/data/genbank/CAA35997.gp
- create mode 100644 test/unit/bio/db/genbank/test_genpept.rb
-
-commit 2cde22cb358a2b7ec8197866fe35a0b46ebf9b00
-Author: Kazuhiro Hayashi <k.hayashi.info@gmail.com>
-Date: Thu Jun 24 18:52:37 2010 +0900
-
- Added unit tests for Bio::NCBIDB::Common
-
- * Added unit tests for Bio::NCBIDB::Common.
- * This is part of combination of the 4 commits:
- * 7da8d557e8ee53da9d93c6fadfd0d8f493977c81
- (added test/unit/bio/db/genbank/test_common.rb newly)
- * 2b5c87a9ada248597e0517e22191bb4c88be2a42
- (Modified a few lines of Bio::NCBIDB::TestCommon,
- Bio::TestPDBRecord and Bio::TestPDB)
- * 10c043535dd7bf5b9682b4060183f494742c53df
- (Modified unit test for Bio::GenBank::Common)
- * 0af08fb988e08948a54e33273861b5460b7f6b2d
- (Modified the unit test for Bio::GenBank)
-
- test/unit/bio/db/genbank/test_common.rb | 275 +++++++++++++++++++++++++++++++
- 1 files changed, 275 insertions(+), 0 deletions(-)
- create mode 100644 test/unit/bio/db/genbank/test_common.rb
-
-commit f775d9b7f7deda2e30d4196d4cf507b59936a654
-Author: Kazuhiro Hayashi <k.hayashi.info@gmail.com>
-Date: Sat Jun 26 17:54:32 2010 +0900
-
- Added unit tests for Bio::GenBank with test data.
-
- * Added unit tests for Bio::GenBank with test data.
- * This is part of combination of the two commits:
- * 555f7b49a43e7c35c82cd48b199af96ca93d4179
- (added test_genbank.rb and test_go.rb with the test files.
- modified test_pdb.rb)
- * a46f895bf378ce08143ff031ddda302f970c270a
- (Modified Bio::GenBank and Bio::Nexus)
-
- test/data/genbank/SCU49845.gb | 167 +++++++++++++
- test/unit/bio/db/genbank/test_genbank.rb | 397 ++++++++++++++++++++++++++++++
- 2 files changed, 564 insertions(+), 0 deletions(-)
- create mode 100644 test/data/genbank/SCU49845.gb
- create mode 100644 test/unit/bio/db/genbank/test_genbank.rb
-
-commit 33621c1f4c16173efd05861759f577b2c4733a53
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Fri Oct 29 16:45:22 2010 +0900
-
- Bio::BIORUBY_EXTRA_VERSION is changed to ".5000".
-
- bioruby.gemspec | 2 +-
- lib/bio/version.rb | 2 +-
- 2 files changed, 2 insertions(+), 2 deletions(-)
-
-commit cfb2c744f3762689077f5bf2092f715d25e066ed
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Fri Oct 22 13:02:03 2010 +0900
-
- BioRuby 1.4.1 is released.
-
- ChangeLog | 55 +++++++++++++++++++++++++++++++++++++++++++++++++++++++
- 1 files changed, 55 insertions(+), 0 deletions(-)
-
-commit 92cfda14c08b270ed1beca33153125141f88510e
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Fri Oct 22 13:00:09 2010 +0900
-
- Preparation for bioruby-1.4.1 release.
-
- bioruby.gemspec | 2 +-
- lib/bio/version.rb | 2 +-
- 2 files changed, 2 insertions(+), 2 deletions(-)
-
-commit d7999539392bba617b041e3120b5b2d785301f24
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Fri Oct 22 10:27:02 2010 +0900
-
- Newly added issue is copied from KNOWN_ISSUES.rdoc to the release note.
-
- RELEASE_NOTES.rdoc | 15 +++++++++++++++
- 1 files changed, 15 insertions(+), 0 deletions(-)
-
-commit a9f287658441038a4e9bb220502523de039417f9
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Fri Oct 22 10:26:44 2010 +0900
-
- updated description of an issue
-
- KNOWN_ISSUES.rdoc | 12 +++++++-----
- 1 files changed, 7 insertions(+), 5 deletions(-)
-
-commit bb946d1c97d1eb0de62c8b509bbfb02d67efffeb
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Thu Oct 21 23:17:25 2010 +0900
-
- Added an issue about command-line string escaping on Windows with Ruby 1.9.
-
- KNOWN_ISSUES.rdoc | 8 ++++++++
- 1 files changed, 8 insertions(+), 0 deletions(-)
-
-commit fe7d26516cc6b9a3cf8c16e6f8204a4d5eb5e5ae
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Thu Oct 21 20:34:32 2010 +0900
-
- Added descriptions.
-
- RELEASE_NOTES.rdoc | 52 ++++++++++++++++++++++++++++++++++++++++++++++++++++
- 1 files changed, 52 insertions(+), 0 deletions(-)
-
-commit fd5da3b47ebce1df46922f20d013439faef483e9
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Thu Oct 21 18:27:44 2010 +0900
-
- ChangeLog is updated.
-
- ChangeLog | 1657 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- 1 files changed, 1657 insertions(+), 0 deletions(-)
-
-commit fab16977d23bb3a5fdfc976eece14dfdabdcac4d
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Thu Oct 21 18:07:43 2010 +0900
-
- preparation for release candidate 1.4.1-rc1
-
- bioruby.gemspec | 40 ++++++++++++++++++++++++++++++++++++++--
- lib/bio/version.rb | 4 ++--
- 2 files changed, 40 insertions(+), 4 deletions(-)
-
-commit 119cc3bf5582735a5df574450ec685fd2f989b5d
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Thu Oct 21 18:05:13 2010 +0900
-
- Temporarily removed for packaging new version. It will be reverted later.
-
- doc/howtos/sequence_codon.txt | 38 --------------------------------------
- 1 files changed, 0 insertions(+), 38 deletions(-)
- delete mode 100644 doc/howtos/sequence_codon.txt
-
-commit 1b1b3752e3c98a29caf837bfc12c1ed79a04dba2
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Thu Oct 21 16:48:43 2010 +0900
-
- Fixed typo, reported by Tomoaki NISHIYAMA.
-
- KNOWN_ISSUES.rdoc | 2 +-
+ lib/bio/alignment.rb | 2 +-
1 files changed, 1 insertions(+), 1 deletions(-)
-commit 47ed7e5eaca4a261ef0fd4f76909c930e52aadd5
-Merge: c002142 548cb58
+commit 174a38ea8c4ecea70724bf6ec8e72b2e4259853b
Author: Naohisa Goto <ng@bioruby.org>
-Date: Thu Oct 21 16:17:59 2010 +0900
+Date: Wed Jul 25 23:12:51 2012 +0900
- Merge branch 'test-defline-by-jtprince'
+ Modified to follow changes of GenomeNet BLAST site
-commit 548cb58aaad06bb9161e09f7b4ae45729898ca5e
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Thu Oct 21 16:16:28 2010 +0900
-
- adjusted filename in header
-
- test/unit/bio/db/fasta/test_defline_misc.rb | 2 +-
- 1 files changed, 1 insertions(+), 1 deletions(-)
-
-commit 95be260708ef21be7848a5d4b7c494cc6bb3d81f
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Thu Oct 21 16:14:58 2010 +0900
-
- Renamed to test_defline_misc.rb to resolve the file name conflict.
-
- test/unit/bio/db/fasta/test_defline.rb | 490 ---------------------------
- test/unit/bio/db/fasta/test_defline_misc.rb | 490 +++++++++++++++++++++++++++
- 2 files changed, 490 insertions(+), 490 deletions(-)
- delete mode 100644 test/unit/bio/db/fasta/test_defline.rb
- create mode 100644 test/unit/bio/db/fasta/test_defline_misc.rb
-
-commit 1e7628e2c396330743d4904b100d62d2c2773bf0
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Thu Oct 21 16:11:14 2010 +0900
-
- Test bug fix: mistake in test_get method in two classes.
-
- test/unit/bio/db/fasta/test_defline.rb | 4 ++--
- 1 files changed, 2 insertions(+), 2 deletions(-)
-
-commit c479f56f14fb531e31c7e5fdd02f6c934ac468fa
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Thu Oct 21 16:06:46 2010 +0900
-
- Test bug fix: test classes should inherit Test::Unit::TestCase.
-
- test/unit/bio/db/fasta/test_defline.rb | 10 +++++-----
- 1 files changed, 5 insertions(+), 5 deletions(-)
-
-commit 0e8ea46e5a239df5c1da3c63e602376c04191ef4
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Thu Oct 21 15:55:02 2010 +0900
-
- Bug fix: syntax error in Ruby 1.8.7 due to a comma.
-
- test/unit/bio/db/fasta/test_defline.rb | 2 +-
- 1 files changed, 1 insertions(+), 1 deletions(-)
-
-commit 62a2c1d7c47fbef7a7e7c4f1c079f98fa74e5099
-Author: John Prince <jtprince@gmail.com>
-Date: Tue Oct 19 11:20:16 2010 -0600
-
- added individual unit tests for Bio::FastaDefline
-
- test/unit/bio/db/fasta/test_defline.rb | 490 ++++++++++++++++++++++++++++++++
- 1 files changed, 490 insertions(+), 0 deletions(-)
- create mode 100644 test/unit/bio/db/fasta/test_defline.rb
-
-commit c002142cdb478b0ad08b7bd5e3331c7b643222f1
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Thu Oct 21 15:36:58 2010 +0900
-
- Adjusted file paths and the copyright line.
-
- test/unit/bio/db/fasta/test_defline.rb | 6 +++---
+ lib/bio/appl/blast/genomenet.rb | 6 +++---
1 files changed, 3 insertions(+), 3 deletions(-)
-commit a5818c5f8ae07e4ec4bdcc2229df9a59bded63f0
-Author: Kazuhiro Hayashi <k.hayashi.info@gmail.com>
-Date: Thu Jun 17 11:54:15 2010 +0900
-
- Newly added unit tests for Bio::FastaDefline
-
- * Newly added unit tests for Bio::FastaDefline.
- * This is part of combination of the two commits:
- bd2452caf0768e7000d19d462465b1772e3c030b
- (modified test file for Bio::FastaDefline)
- cae1b6c00cdb9044cb0dfb4db58e6acfe9b7d246
- (Added test/unit/bio/db/fasta/test_defline.rb and
- test/unit/bio/db/kegg/test_kgml.rb with the sample file newly.)
-
- test/unit/bio/db/fasta/test_defline.rb | 160 ++++++++++++++++++++++++++++++++
- 1 files changed, 160 insertions(+), 0 deletions(-)
- create mode 100644 test/unit/bio/db/fasta/test_defline.rb
-
-commit 4addb906df442adf4ed20275428070b651abbf07
+commit 93e24935840dcdec76984313719700134d69daf2
Author: Naohisa Goto <ng@bioruby.org>
-Date: Thu Oct 21 15:08:46 2010 +0900
+Date: Wed Jul 25 15:21:32 2012 +0900
- Added note for a dead link, updated a URL, and added a new reference.
+ suppress warnings: instance variable @comment not initialized
- lib/bio/db/fasta/defline.rb | 8 ++++++--
- 1 files changed, 6 insertions(+), 2 deletions(-)
+ lib/bio/db/gff.rb | 6 ++++--
+ 1 files changed, 4 insertions(+), 2 deletions(-)
-commit e636f123adf28688748cc5bbbc6e0c817358d475
-Author: John Prince <jtprince@gmail.com>
-Date: Thu Oct 14 15:38:07 2010 -0600
-
- included TREMBL prefix to list of NSIDs (tr|)
-
- * Included TREMBL prefix to list of NSIDs (tr|).
- This is a standard prefix found in UniprotKB FASTA files.
-
- lib/bio/db/fasta/defline.rb | 1 +
- 1 files changed, 1 insertions(+), 0 deletions(-)
-
-commit 5277eb0b5376a0dc217dc051c49993c505956400
+commit 0ad3818fedb707a26e849877bde1f8dab006b848
Author: Naohisa Goto <ng@bioruby.org>
-Date: Thu Oct 21 14:16:03 2010 +0900
+Date: Wed Jul 25 00:54:02 2012 +0900
- Bug fix: Bio::ClustalW::Report#get_sequence may fail
-
- * Bug fix: Bio::ClustalW::Report#get_sequence may fail when the second
- argument of Bio::ClustalW::Report.new is specified.
+ suppress warnings: URI.escape/URI.unescape is obsolete
- lib/bio/appl/clustalw/report.rb | 5 +++--
- 1 files changed, 3 insertions(+), 2 deletions(-)
+ lib/bio/db/gff.rb | 39 +++++++++++++++++++++++++++++++++------
+ 1 files changed, 33 insertions(+), 6 deletions(-)
-commit 81b9238abb643573a4051dc0f10c4f9a2cff40fa
+commit 1263938742e7eeedb4a877aff7314e304320eca9
Author: Naohisa Goto <ng@bioruby.org>
-Date: Thu Oct 21 14:21:52 2010 +0900
+Date: Mon Jul 23 21:15:52 2012 +0900
- Added a test class to test the second argument of Bio::ClustalW::Report.new.
-
- test/unit/bio/appl/clustalw/test_report.rb | 19 +++++++++++++++++++
- 1 files changed, 19 insertions(+), 0 deletions(-)
-
-commit 3e9b149aec91585732a34efaa960c96bcec2eef8
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Thu Oct 21 13:22:38 2010 +0900
-
- Ruby 1.9.2 support: defined Bio::RestrictionEnzyme::DoubleStranded::AlignedStrands#initialize
+ Added link to blastall options reference
- * Bio::RestrictionEnzyme::DoubleStranded::AlignedStrands#initialize
- is explicitly defined, due to the behavior change of argument number
- check in the default initialize method in Ruby 1.9.2.
+ * Added link to blastall options reference.
+ Thanks to Gareth Rees who sent a pull request.
+ (https://github.com/bioruby/bioruby/pull/49)
- .../double_stranded/aligned_strands.rb | 5 +++++
+ lib/bio/appl/blast/genomenet.rb | 5 +++++
1 files changed, 5 insertions(+), 0 deletions(-)
-commit cfe31c02d4bd0d97e588d25dc30188da6be81e85
+commit 2ec5f4fd5abd0db7ec79ab3a9fd4adde7c9384a8
Author: Naohisa Goto <ng@bioruby.org>
-Date: Thu Oct 21 11:49:08 2010 +0900
+Date: Mon Jul 23 17:26:45 2012 +0900
- Ruby 1.9.2 support: assert_in_delta for a float value.
+ Next bioruby release version will be 1.4.3.
- test/unit/bio/db/test_aaindex.rb | 2 +-
+ RELEASE_NOTES.rdoc | 2 +-
1 files changed, 1 insertions(+), 1 deletions(-)
-commit 3f5d2ccb9ac8bc44febc88d441f47aeddf7f12ff
+commit 6cf1318507a5d82bb93acdfe33e96723a2e742fc
Author: Naohisa Goto <ng@bioruby.org>
-Date: Thu Oct 21 11:41:38 2010 +0900
+Date: Mon Jul 23 17:25:35 2012 +0900
- Ruby 1.9.2 support: using assert_in_delta for float values.
-
- * Ruby 1.9.2 support: using assert_in_delta for float values.
- The patch is written by Tomoaki NISHIYAMA during BH2010.10.
+ fix typo
- test/unit/bio/util/test_contingency_table.rb | 14 +++++++-------
- 1 files changed, 7 insertions(+), 7 deletions(-)
+ README.rdoc | 2 +-
+ 1 files changed, 1 insertions(+), 1 deletions(-)
-commit f357929bc5dcf8295b0a11a09b4025e3592d9eda
+commit 2fd71cac315affe6e4d90b03dadac782f11553a5
Author: Naohisa Goto <ng@bioruby.org>
-Date: Thu Oct 21 11:16:37 2010 +0900
+Date: Mon Jul 23 17:21:57 2012 +0900
- Small changes for README.rdoc.
+ Bug fix: Genomenet remote blast: catch up changes of the server
- README.rdoc | 5 +++--
- 1 files changed, 3 insertions(+), 2 deletions(-)
+ lib/bio/appl/blast/genomenet.rb | 33 +++++++++++++++++++++++----------
+ 1 files changed, 23 insertions(+), 10 deletions(-)
-commit c6c567fe9602ae8d7d343a5773f51d8aa22c8876
+commit 69d9717da11b2fe81a8f840bbafcc5fbb0dbe688
Author: Naohisa Goto <ng@bioruby.org>
-Date: Thu Oct 21 11:12:17 2010 +0900
+Date: Fri Jul 20 11:24:37 2012 +0900
- Shows message when running "ruby setup.rb test" with Ruby1.9.
+ regenerate bioruby.gemspec with rake regemspec
- setup.rb | 5 +++++
- 1 files changed, 5 insertions(+), 0 deletions(-)
+ bioruby.gemspec | 2 ++
+ 1 files changed, 2 insertions(+), 0 deletions(-)
-commit 9b66463c4150a679e63289e0cee3c4d1200c7d0f
+commit 9683da186579dbfa5da1bb1a32edc49cfdc026b8
Author: Naohisa Goto <ng@bioruby.org>
-Date: Wed Oct 20 17:53:36 2010 +0900
+Date: Wed Jul 18 23:19:33 2012 +0900
- Added description about incompatible the change in Bio::AAindex2.
-
- RELEASE_NOTES.rdoc | 6 ++++++
- 1 files changed, 6 insertions(+), 0 deletions(-)
-
-commit 327ea878d4e15b99711d8121a54698da29d4b0aa
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Wed Oct 20 17:35:53 2010 +0900
-
- Changed the expected return values in the unit tests, following the last change to Bio::AAindex2.
+ Incompatible changes in Bio::KEGG::KGML are documented.
- * Changed the expected return values in the unit tests,
- following the last change to Bio::AAindex2.
- * The patch is written by Tomoaki NISHIYAMA during BH2010.10.
+ * Incompatible changes in Bio::KEGG::KGML are documented.
+ * Next BioRuby release version will be 1.4.3.
- test/unit/bio/db/test_aaindex.rb | 15 ++++++++-------
- 1 files changed, 8 insertions(+), 7 deletions(-)
+ RELEASE_NOTES.rdoc | 44 +++++++++++++++++++++++++++++++++++++++++---
+ 1 files changed, 41 insertions(+), 3 deletions(-)
-commit 31963b43daab2801087f5f6d23b04e357bb7b1e2
+commit 6cab377ae760d1abfda06caafe4a04ecd549e21d
Author: Naohisa Goto <ng@bioruby.org>
-Date: Wed Oct 20 17:32:26 2010 +0900
+Date: Wed Jul 18 22:56:00 2012 +0900
- Ruby 1.9.2 support: Incompatible change: the symmetric elements for triangular matrix should be copied
+ Incompatible changes: Bio::KEGG::KGML::Reaction#substrates, products
- * Ruby 1.9.2 support: Incompatible change: the symmetric elements
- for triangular matrix should be copied. The patch is written by
- Tomoaki NISHIYAMA during BH2010.10.
+ * Incompatible changes: Bio::KEGG::KGML::Reaction#substrates and
+ Bio::KEGG::KGML::Reaction#products are changed to return an array
+ containing Bio::KEGG::KGML::Substrate and Bio::KEGG::KGML::Product
+ objects, respectively. The aim of these changes are to store ID
+ of substrates and products that were thrown away in the previous
+ versions.
- lib/bio/db/aaindex.rb | 12 +++++++++++-
- 1 files changed, 11 insertions(+), 1 deletions(-)
+ lib/bio/db/kegg/kgml.rb | 48 ++++++++++++++--
+ test/unit/bio/db/kegg/test_kgml.rb | 104 +++++++++++++++++++++++++++++++++++-
+ 2 files changed, 144 insertions(+), 8 deletions(-)
-commit e8a1d65984781466eff9d5a262f18cb1c3e01056
+commit 3cb1e09709d3c6b934028e28f9cafed149c9c751
Author: Naohisa Goto <ng@bioruby.org>
-Date: Wed Oct 20 16:10:51 2010 +0900
+Date: Wed Jul 18 22:16:46 2012 +0900
- Test bug fix: confusion between assert and assert_equal
+ Bio::KEGG::KGML#parse_* :use new attribute names
- * Test bug fix: the assert should be assert_equal. The bug was
- found with Ruby 1.9.2-p0.
+ * In Bio::KEGG::KGML#parse_* (private methods) new attribute method
+ names should be used instead of deprecated old names.
- test/unit/bio/db/embl/test_sptr.rb | 2 +-
- 1 files changed, 1 insertions(+), 1 deletions(-)
+ lib/bio/db/kegg/kgml.rb | 18 +++++++++---------
+ 1 files changed, 9 insertions(+), 9 deletions(-)
-commit feb2cda47beab91e2fc3dddf99d5cc1cacf3fbae
+commit c5ef981db6add98dc6778cd9809aff38a7071593
Author: Naohisa Goto <ng@bioruby.org>
-Date: Wed Oct 20 14:59:40 2010 +0900
+Date: Wed Jul 18 22:14:33 2012 +0900
- Test bug fix: confusion between assert and assert_equal, and apparently wrong expected values.
-
- * Test bug fix: the assert should be assert_equal. The bug was found
- with Ruby 1.9.2-p0.
- * In the test_rates_hundred_and_fiftieth_position method, the index
- for @example_rates and the expected value of the third assertion
- were apparently wrong.
- * Reported by Tomoaki NISHIYAMA during BH2010.10.
+ modified documentation for Bio::KEGG::KGML
- test/unit/bio/appl/paml/codeml/test_rates.rb | 12 ++++++------
- 1 files changed, 6 insertions(+), 6 deletions(-)
+ lib/bio/db/kegg/kgml.rb | 73 +++++++++++++++++++++++++++--------------------
+ 1 files changed, 42 insertions(+), 31 deletions(-)
-commit ffc03a11a4ef7b36ea78de58d4c8d4e9259093c4
+commit 5416b84eaa37b5abf15f905586a5eee65c4026f0
Author: Naohisa Goto <ng@bioruby.org>
-Date: Sat Oct 16 01:06:36 2010 +0900
+Date: Wed Jul 18 15:01:58 2012 +0900
- Tests for Bio::KEGG::PATHWAY are improved with new test data.
-
- test/data/KEGG/ec00072.pathway | 23 +
- test/data/KEGG/hsa00790.pathway | 59 ++
- test/data/KEGG/ko00312.pathway | 16 +
- test/data/KEGG/rn00250.pathway | 114 ++++
- test/unit/bio/db/kegg/test_pathway.rb | 1055 +++++++++++++++++++++++++++++++++
- 5 files changed, 1267 insertions(+), 0 deletions(-)
- create mode 100644 test/data/KEGG/ec00072.pathway
- create mode 100644 test/data/KEGG/hsa00790.pathway
- create mode 100644 test/data/KEGG/ko00312.pathway
- create mode 100644 test/data/KEGG/rn00250.pathway
-
-commit 1e1d974c2c72ddf5a45e41c6f2510729fb65a4ad
-Author: Toshiaki Katayama <k@bioruby.org>
-Date: Tue Jul 20 11:46:52 2010 +0900
-
- Added methods for parsing KEGG PATHWAY fields.
+ New class Bio::KEGG::KGML::Graphics with tests for Bio::KEGG::KGML
- * Added methods for parsing KEGG PATHWAY fields.
- * This is part of commit e2abe5764f3ded91c82689245f19a0412d3a7afb
- and modified to merge with the current HEAD (original commit
- message: Changes for TogoWS).
+ * New class Bio::KEGG::KGML::Graphics for storing a graphics element.
+ This fixes https://github.com/bioruby/bioruby/issues/51.
+ * Unit tests for Bio::KEGG::KGML are added with mock test data.
+ * Improve rdoc documentation for Bio::KEGG::KGML.
+ * New method Bio::KEGG::KGML::Reaction#id
+ * Attribute methods that were different from the KGML attribute
+ names are renamed to the names of the KGML attribute names.
+ Old method names are deprecated and are changed to aliases
+ and will be removed in the future.
+ * Bio::KEGG::KGML::Entry#id (old name: entry_id)
+ * Bio::KEGG::KGML::Entry#type (old name: category)
+ * Bio::KEGG::KGML::Entry#entry1 (old name: node1)
+ * Bio::KEGG::KGML::Entry#entry2 (old name: node2)
+ * Bio::KEGG::KGML::Entry#type (old name: rel)
+ * Bio::KEGG::KGML::Reaction#name (old name: entry_id)
+ * Bio::KEGG::KGML::Reaction#type (old name: direction)
+ * Following attribute methods are deprecated because two or more
+ graphics elements may exist in an entry element. They will be
+ removed in the future.
+ * Bio::KEGG::KGML::Entry#label
+ * Bio::KEGG::KGML::Entry#shape
+ * Bio::KEGG::KGML::Entry#x
+ * Bio::KEGG::KGML::Entry#y
+ * Bio::KEGG::KGML::Entry#width
+ * Bio::KEGG::KGML::Entry#height
+ * Bio::KEGG::KGML::Entry#fgcolor
+ * Bio::KEGG::KGML::Entry#bgcolor
- lib/bio/db/kegg/pathway.rb | 146 +++++++++++++++++++++++++++++++++++++++++++-
- 1 files changed, 145 insertions(+), 1 deletions(-)
+ lib/bio/db/kegg/kgml.rb | 321 ++++++++++---
+ test/data/KEGG/test.kgml | 37 ++
+ test/unit/bio/db/kegg/test_kgml.rb | 922 ++++++++++++++++++++++++++++++++++++
+ 3 files changed, 1223 insertions(+), 57 deletions(-)
+ create mode 100644 test/data/KEGG/test.kgml
+ create mode 100644 test/unit/bio/db/kegg/test_kgml.rb
-commit 957c8ee630538a8c49c52339cb3c0364e5328378
+commit e5478363ef6969ec14c4e09c2bd7c6d27c12cf5b
Author: Naohisa Goto <ng@bioruby.org>
-Date: Sat Oct 16 00:50:42 2010 +0900
+Date: Tue Jul 17 22:23:28 2012 +0900
- Private method strings_as_hash is moved to Bio::KEGG::Common::StringsAsHash.
+ rdoc documentation for Bio::KEGG::KGML
- lib/bio/db/kegg/common.rb | 18 ++++++++++++++++++
- lib/bio/db/kegg/module.rb | 19 +++++--------------
- 2 files changed, 23 insertions(+), 14 deletions(-)
+ lib/bio/db/kegg/kgml.rb | 166 ++++++++++++++++++++++++++++++++++++++++++++---
+ 1 files changed, 157 insertions(+), 9 deletions(-)
-commit b7fd85382bccceaa29958d5daf98ca0a513e5a9a
+commit 4a97e7034cae835b3bbc8ef918b9c6c48910dec5
Author: Naohisa Goto <ng@bioruby.org>
-Date: Fri Oct 15 22:01:05 2010 +0900
+Date: Wed Jul 11 15:16:49 2012 +0900
- Renamed Bio::KEGG::*#pathway_modules to modules, etc.
-
- * Renamed following methods in Bio::KEGG::ORTHOLOGY and
- Bio::KEGG:PATHWAY classes: pathway_modules to modules,
- pathway_modules_as_strings to modules_as_strings, and
- pathway_modules_as_hash to modules_as_hash.
- * Unit tests are also modified.
+ autoload should not be used for libraries outside bio
- lib/bio/db/kegg/common.rb | 18 +++++++++---------
- lib/bio/db/kegg/orthology.rb | 10 +++++-----
- lib/bio/db/kegg/pathway.rb | 10 +++++-----
- test/unit/bio/db/kegg/test_orthology.rb | 12 ++++++------
- test/unit/bio/db/kegg/test_pathway.rb | 20 ++++++++++----------
- 5 files changed, 35 insertions(+), 35 deletions(-)
+ lib/bio/db/kegg/kgml.rb | 3 +--
+ 1 files changed, 1 insertions(+), 2 deletions(-)
-commit 02aea9f18ff6e3079309a76d04d02ea1f2902e7b
+commit 338d4cd9913d70041349c5201f80f7a65e7135a6
Author: Naohisa Goto <ng@bioruby.org>
-Date: Fri Oct 15 00:20:48 2010 +0900
+Date: Fri Jul 6 00:50:01 2012 +0900
- Modified tests for Bio::KEGG::GENES following the changes of the class.
+ remove unnecessary require "bio/db" in lib/bio/db/pdb.rb
- test/unit/bio/db/kegg/test_genes.rb | 30 +++++++++++++++++++++++++++++-
- 1 files changed, 29 insertions(+), 1 deletions(-)
+ lib/bio/db/pdb.rb | 5 +----
+ 1 files changed, 1 insertions(+), 4 deletions(-)
-commit f4b45ea629734ecff820483475d83fef6cbe068e
+commit 87c806a480fcacb0fc610c9669de19e4cb661a9c
Author: Naohisa Goto <ng@bioruby.org>
-Date: Thu Oct 14 23:57:18 2010 +0900
+Date: Fri Jul 6 00:47:20 2012 +0900
- Reverted Bio::KEGG::GENES#genes, gene and motif methods and modified.
-
- * Reverted Bio::KEGG::GENES#genes, gene and motif methods which are
- removed in the last commit. To avoid code duplication, they are
- also modified to use other methods, and RDoc is added about the
- deprecation or change of the methods.
- * Modified RDoc.
+ workaround to avoid circular require about Bio::PDB
- lib/bio/db/kegg/genes.rb | 32 +++++++++++++++++++++++++++++++-
- 1 files changed, 31 insertions(+), 1 deletions(-)
+ lib/bio/db/pdb/atom.rb | 5 +++--
+ lib/bio/db/pdb/chain.rb | 5 ++---
+ lib/bio/db/pdb/chemicalcomponent.rb | 5 +++--
+ lib/bio/db/pdb/model.rb | 4 ++--
+ lib/bio/db/pdb/pdb.rb | 3 ++-
+ lib/bio/db/pdb/residue.rb | 4 ++--
+ lib/bio/db/pdb/utils.rb | 11 +++++++----
+ 7 files changed, 21 insertions(+), 16 deletions(-)
-commit dd987911cb4a84e23565bb37707611d054c22101
-Author: Toshiaki Katayama <k@bioruby.org>
-Date: Tue Jul 20 11:46:52 2010 +0900
-
- New methods Bio::KEGG::GENES#keggclass etc.
-
- * New methods and aliases are added: Bio::KEGG::GENES#keggclass,
- keggclasses, names_as_array, names, motifs_as_strings,
- motifs_as_hash, motifs.
- * Removed Bio::KEGG::GENES#genes, gene and motif methods.
- * Added a comment about deprecation of CODON_USAGE lines.
- * This is part of commit e2abe5764f3ded91c82689245f19a0412d3a7afb
- (original commit message: Changes for TogoWS).
-
- lib/bio/db/kegg/genes.rb | 41 ++++++++++++++++++++++++++---------------
- 1 files changed, 26 insertions(+), 15 deletions(-)
-
-commit b2575f5acfeca269c93a35baa3809fdac17a7271
+commit 874f35c3930506fa029b419aa84677d1fea6681a
Author: Naohisa Goto <ng@bioruby.org>
-Date: Wed Oct 13 23:12:33 2010 +0900
+Date: Fri Jul 6 00:24:24 2012 +0900
- Release notes for the upcoming release version.
+ regenerate bioruby.gemspec with rake regemspec
- RELEASE_NOTES.rdoc | 31 +++++++++++++++++++++++++++++++
- 1 files changed, 31 insertions(+), 0 deletions(-)
- create mode 100644 RELEASE_NOTES.rdoc
-
-commit 83992875c45a1fdd54d042c923dee51119026e49
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Wed Oct 13 23:11:21 2010 +0900
-
- Renamed RELEASE_NOTES.rdoc to doc/RELEASE_NOTES-1.4.0.rdoc.
-
- RELEASE_NOTES.rdoc | 167 ------------------------------------------
- doc/RELEASE_NOTES-1.4.0.rdoc | 167 ++++++++++++++++++++++++++++++++++++++++++
- 2 files changed, 167 insertions(+), 167 deletions(-)
- delete mode 100644 RELEASE_NOTES.rdoc
- create mode 100644 doc/RELEASE_NOTES-1.4.0.rdoc
-
-commit f649629eb6216aeabbd2020bcac9b7f870b12395
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Wed Oct 13 21:58:58 2010 +0900
-
- Added acknowledgement to Kozo Nishida for KEGG parsers.
-
- RELEASE_NOTES.rdoc | 1 +
+ bioruby.gemspec | 1 +
1 files changed, 1 insertions(+), 0 deletions(-)
-commit 379f177edc0f95dee1ec0c2d2cf679c27918e41b
+commit 090d4edb5698135f87df450a963ef35a307349c4
Author: Naohisa Goto <ng@bioruby.org>
-Date: Fri Oct 8 16:31:58 2010 +0900
+Date: Fri Jul 6 00:19:54 2012 +0900
- Fixed a variable name mistake in Bio::Command, and English grammer fix.
+ Tree output (formatter) methods moved to lib/bio/tree/output.rb
- * Fixed a variable name mistake in Bio::Command#no_fork?.
- * English grammer fix for comments. Thanks to Andrew Grimm who
- reports the fix.
+ * To avoid circular require about bio/tree, phylogenetic tree output
+ (formatter) methods are moved to lib/bio/tree/output.rb.
- lib/bio/command.rb | 6 +++---
- 1 files changed, 3 insertions(+), 3 deletions(-)
+ lib/bio/db/newick.rb | 244 --------------------------------------------
+ lib/bio/tree.rb | 3 +-
+ lib/bio/tree/output.rb | 264 ++++++++++++++++++++++++++++++++++++++++++++++++
+ 3 files changed, 265 insertions(+), 246 deletions(-)
+ create mode 100644 lib/bio/tree/output.rb
-commit 1344c27c90438d8c8840ee507d0ab43224f89054
+commit b3d12b63097a5141b029bbfb3690870cd1935a60
Author: Naohisa Goto <ng@bioruby.org>
-Date: Wed Oct 6 23:47:26 2010 +0900
+Date: Fri Jul 6 00:18:44 2012 +0900
- Bug fix: fork(2) is called on platforms that do not support it.
-
- * Bug fix: fork(2) is called on platforms that do not support it.
- Thanks to Andrew Grimm who reports the bug
- (fork() is called on platforms that do not support it;
- http://github.com/bioruby/bioruby/issues#issue/6).
- * Bio::Command#call_command and query_command can now fall back
- into using popen when fork(2) is not implemented.
- * Detection of Windows platform is improved. The idea of the code
- is taken from Redmine's platform.rb.
+ Workaround to avoid circular require for Bio::Blast
- lib/bio/command.rb | 98 +++++++++++++++++++++++++++++------
- test/functional/bio/test_command.rb | 9 +--
- 2 files changed, 84 insertions(+), 23 deletions(-)
+ lib/bio/appl/bl2seq/report.rb | 6 +++---
+ lib/bio/appl/blast/ddbj.rb | 3 ---
+ lib/bio/appl/blast/format0.rb | 3 +++
+ lib/bio/appl/blast/genomenet.rb | 2 --
+ lib/bio/appl/blast/ncbioptions.rb | 11 ++++++++---
+ lib/bio/appl/blast/remote.rb | 11 ++++++-----
+ lib/bio/appl/blast/report.rb | 16 ++++++++++------
+ lib/bio/appl/blast/rpsblast.rb | 5 +++--
+ lib/bio/appl/blast/wublast.rb | 6 +++---
+ 9 files changed, 36 insertions(+), 27 deletions(-)
-commit 0bfa1c3a8d7b8d03919d54a2a241ca96a79bad83
+commit 8f6c906c7b0d65b93ebf0a1e1307259e6eab8465
Author: Naohisa Goto <ng@bioruby.org>
-Date: Wed Oct 6 15:49:51 2010 +0900
+Date: Thu Jul 5 23:29:42 2012 +0900
- Bug fix: Bio::MEDLINE#reference is changed not to put empty values
-
- * Bug fix: Bio::MEDLINE#reference is changed not to put empty values
- in the returned Bio::Reference object. I think the original bahavior
- is a bug. This is an incompatible change but the effect is very small.
+ remove old require lines that are commented out
- lib/bio/db/medline.rb | 2 +-
- 1 files changed, 1 insertions(+), 1 deletions(-)
+ lib/bio/appl/blast/format0.rb | 5 -----
+ 1 files changed, 0 insertions(+), 5 deletions(-)
-commit 8e0bc03d79a1f20743c29f0a44e273d362eaa2cd
+commit c632fbf2d0320860eadfacb196d51d80ed3a2b34
Author: Naohisa Goto <ng@bioruby.org>
-Date: Wed Oct 6 15:39:34 2010 +0900
+Date: Thu Jul 5 23:16:49 2012 +0900
- Bug fix: Bio::MEDLINE#initialize should handle continuation of lines.
-
- * Bug fix: Bio::MEDLINE#initialize should handle continuation of lines.
- Thanks to Steven Bedrick who reports the bug
- (Bio::MEDLINE#initialize handles multi-line MeSH terms incorrectly;
- http://github.com/bioruby/bioruby/issues#issue/7).
+ Remove old workaround of strscan.so for Ruby 1.7 or earlier
- lib/bio/db/medline.rb | 6 +++++-
- 1 files changed, 5 insertions(+), 1 deletions(-)
+ lib/bio/appl/blast/format0.rb | 18 +-----------------
+ 1 files changed, 1 insertions(+), 17 deletions(-)
-commit 728de78b438108e44066a7ce7490632c81108fb6
+commit c81dce87f53d3ea7c7d2335e077fa609f2737779
Author: Naohisa Goto <ng@bioruby.org>
-Date: Wed Oct 6 15:29:10 2010 +0900
+Date: Thu Jul 5 23:03:40 2012 +0900
- Added unit tests for Bio::MEDLINE with test data.
-
- * Added unit tests for Bio::MEDLINE with test data. The data is
- taken from NCBI and the abstract was removed to avoid possible
- copyright problem. The choice of the data (PMID: 20146148) is
- suggested by Steven Bedrick in a bug report (Bio::MEDLINE#initialize
- handles multi-line MeSH terms incorrectly).
+ .travis.yml: include ruby 1.9.2 test
- test/data/medline/20146148_modified.medline | 54 ++++++++++
- test/unit/bio/db/test_medline.rb | 148 +++++++++++++++++++++++++++
- 2 files changed, 202 insertions(+), 0 deletions(-)
- create mode 100644 test/data/medline/20146148_modified.medline
-
-commit 930095817ce60793ac909a4d01731d1f97bc4fa5
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Wed Sep 29 20:51:12 2010 +0900
-
- Bug fix: NoMethodError in Bio::Tree#collect_edge!
-
- * Bug fix: NoMethodError in Bio::Tree#collect_edge!.
- Thanks to Kazuhiro Hayashi who reports the bug.
-
- lib/bio/tree.rb | 2 +-
- 1 files changed, 1 insertions(+), 1 deletions(-)
-
-commit c7927ec4743ddc4ec4501790bbed097b69f616e7
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Wed Sep 29 20:49:44 2010 +0900
-
- Modified and improved tests for Bio::Tree.
-
- test/unit/bio/test_tree.rb | 393 +++++++++++++++++++++++++++-----------------
- 1 files changed, 240 insertions(+), 153 deletions(-)
-
-commit 0161148c9b4d9ea404af92b4baf8241239a283de
-Author: Kazuhiro Hayashi <k.hayashi.info@gmail.com>
-Date: Fri Jul 16 00:09:39 2010 +0900
-
- Modified unit tests for Bio::Tree
-
- * Modified unit tests for Bio::Tree.
- * This is part of combination of the two commits:
- * 6675fd930718e41ad009f469b8167f81c9b2ad52
- (Modified unit tests and classes)
- * a6dc63ffe3460ea8d8980b3d6c641356881e0862
- (Modified unit test for Bio::Tree)
-
- test/unit/bio/test_tree.rb | 174 +++++++++++++++++++++++++++++++++++++++++++-
- 1 files changed, 173 insertions(+), 1 deletions(-)
-
-commit 31ded691a9329e45fe563e5f70138648d3b30bbf
-Author: Kazuhiro Hayashi <k.hayashi.info@gmail.com>
-Date: Thu Jul 15 21:06:28 2010 +0900
-
- Bug fix: Bio::Tree#remove_edge_if did not work.
-
- * Bug fix: Bio::Tree#remove_edge_if did not work.
- * This is part of commit 6675fd930718e41ad009f469b8167f81c9b2ad52
- (original commit message: Modified unit tests and classes)
- and removed a comment line.
-
- lib/bio/tree.rb | 6 +++---
- 1 files changed, 3 insertions(+), 3 deletions(-)
-
-commit d0a3af23c74004688a8fc0b5be3d09f7144e33a1
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Wed Sep 22 19:23:50 2010 +0900
-
- Renamed test/data/go/part_of_* to avoid possible confusion
-
- * Renamed test/data/go/part_of_* to selected_* to avoid possible
- confusion: The word "part_of" is a keyword in Gene Ontology.
-
- test/data/go/part_of_component.ontology | 12 ----------
- test/data/go/part_of_gene_association.sgd | 31 ----------------------------
- test/data/go/part_of_wikipedia2go | 13 -----------
- test/data/go/selected_component.ontology | 12 ++++++++++
- test/data/go/selected_gene_association.sgd | 31 ++++++++++++++++++++++++++++
- test/data/go/selected_wikipedia2go | 13 +++++++++++
- test/unit/bio/db/test_go.rb | 6 ++--
- 7 files changed, 59 insertions(+), 59 deletions(-)
- delete mode 100644 test/data/go/part_of_component.ontology
- delete mode 100644 test/data/go/part_of_gene_association.sgd
- delete mode 100644 test/data/go/part_of_wikipedia2go
- create mode 100644 test/data/go/selected_component.ontology
- create mode 100644 test/data/go/selected_gene_association.sgd
- create mode 100644 test/data/go/selected_wikipedia2go
-
-commit e4f82da52402f8175bd92b50209b09bc83bfddd6
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Wed Sep 22 19:21:36 2010 +0900
-
- Removed unused test/data/go/wikipedia2go.txt.
-
- test/data/go/wikipedia2go.txt | 728 -----------------------------------------
- 1 files changed, 0 insertions(+), 728 deletions(-)
- delete mode 100644 test/data/go/wikipedia2go.txt
-
-commit 5003fd53b0a3852fa23b76ad6ec8e9e76d5850fc
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Thu Sep 16 22:37:31 2010 +0900
-
- Adjusted test data file paths and header lines in test_go.rb.
-
- * Adjusted test data file paths.
- * Adjusted copyright and description in the header.
-
- test/unit/bio/db/test_go.rb | 26 +++++++++++++++++---------
- 1 files changed, 17 insertions(+), 9 deletions(-)
-
-commit 540cb7ab27e79634f5436476cce51cc20ca0f70f
-Author: Kazuhiro Hayashi <k.hayashi.info@gmail.com>
-Date: Thu Jul 15 21:06:28 2010 +0900
-
- Added tests for Bio::GO classes.
-
- * Added tests for Bio::GO classes.
- * This is part of combination of the three commits:
- * 555f7b49a43e7c35c82cd48b199af96ca93d4179
- (added test_genbank.rb and test_go.rb with the test files.
- modified test_pdb.rb)
- * e966f17546427b8ad39cb9942807ceb8a068d746
- (modified test/unit/bio/db/test_go.rb and added the test files
- for each GO class)
- * 6675fd930718e41ad009f469b8167f81c9b2ad52
- (Modified unit tests and classes)
-
- test/unit/bio/db/test_go.rb | 163 +++++++++++++++++++++++++++++++++++++++++++
- 1 files changed, 163 insertions(+), 0 deletions(-)
- create mode 100644 test/unit/bio/db/test_go.rb
-
-commit 5ff01f7dfbc3661d8c66b44874a2ba4ff2f96b56
-Author: Kazuhiro Hayashi <k.hayashi.info@gmail.com>
-Date: Fri Jun 11 21:02:29 2010 +0900
-
- Added test data for Bio::GO classes.
-
- * Added test data for Bio::GO classes.
- * This is part of combination of the three commits:
- * 555f7b49a43e7c35c82cd48b199af96ca93d4179
- (added test_genbank.rb and test_go.rb with the test files.
- modified test_pdb.rb)
- * e966f17546427b8ad39cb9942807ceb8a068d746
- (modified test/unit/bio/db/test_go.rb and added the test files
- for each GO class)
- * 6675fd930718e41ad009f469b8167f81c9b2ad52
- (Modified unit tests and classes)
- * License for the test data is the public domain.
- ( http://wiki.geneontology.org/index.php/Legal_FAQ )
-
- test/data/go/part_of_component.ontology | 12 +
- test/data/go/part_of_gene_association.sgd | 31 ++
- test/data/go/part_of_wikipedia2go | 13 +
- test/data/go/wikipedia2go.txt | 728 +++++++++++++++++++++++++++++
- 4 files changed, 784 insertions(+), 0 deletions(-)
- create mode 100644 test/data/go/part_of_component.ontology
- create mode 100644 test/data/go/part_of_gene_association.sgd
- create mode 100644 test/data/go/part_of_wikipedia2go
- create mode 100644 test/data/go/wikipedia2go.txt
-
-commit d4210673a1a696bfb02c93b7743e60dea1a5fcc8
-Author: Kazuhiro Hayashi <k.hayashi.info@gmail.com>
-Date: Thu Jul 15 21:06:28 2010 +0900
-
- Bug fix: Typo and missing field in Bio::GO::GeneAssociation#to_str.
-
- * Bug fix: Typo and missing field in Bio::GO::GeneAssociation#to_str.
- * This is part of commit 6675fd930718e41ad009f469b8167f81c9b2ad52
- (original commit message: Modified unit tests and classes)
- and modified. The bug is also reported by Ralf Stephan
- ([BioRuby] [PATCH] GO annotations fixes and improvements).
-
- lib/bio/db/go.rb | 4 ++--
- 1 files changed, 2 insertions(+), 2 deletions(-)
-
-commit acab0bb4a4e0f970f8f6be3aea2c371f63a49fa7
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Wed Aug 25 22:58:42 2010 +0900
-
- Database names used in tests are changed, following the change of TogoWS.
-
- * Database names used in tests are changed, following the change of
- TogoWS: "gene" to "kegg-genes" and "enzyme" to "kegg-enzyme".
-
- test/functional/bio/io/test_togows.rb | 6 +++---
- 1 files changed, 3 insertions(+), 3 deletions(-)
-
-commit 1fb1f1cc5ca3edb42de03874b3527ce0cf0de294
-Author: Toshiaki Katayama <k@bioruby.org>
-Date: Tue Jul 20 11:46:52 2010 +0900
-
- Database name used in tests is changed, following the change of TogoWS.
-
- * The database name "genbank" is changed to "nucleotide", following
- the change in TogoWS.
- * This is part of commit e2abe5764f3ded91c82689245f19a0412d3a7afb.
- (Original commit message: Changes for TogoWS)
-
- test/functional/bio/io/test_togows.rb | 10 +++++-----
- 1 files changed, 5 insertions(+), 5 deletions(-)
-
-commit 1db4b8011f4fee158aeb78ec2d76c76688714788
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Wed Aug 11 23:33:49 2010 +0900
-
- New method Bio::Fastq#mask for masking low score regions.
-
- * New method Bio::Fastq#mask for masking low score regions is added
- with unit tests. This method is implemented as a shortcut of
- Bio::Sequence#mask_with_quality_score method.
-
- lib/bio/db/fastq.rb | 15 +++++++++++++++
- test/unit/bio/db/test_fastq.rb | 36 ++++++++++++++++++++++++++++++++++++
- 2 files changed, 51 insertions(+), 0 deletions(-)
-
-commit 72b47b2391a01c5f4214fd188abe0857cd3ed166
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Wed Aug 11 23:04:57 2010 +0900
-
- New module Bio::Sequence::SequenceMasker to help masking a sequence.
-
- * New module Bio::Sequence::SequenceMasker to help masking a sequence.
- The module is only expected to be included in Bio::Sequence.
- In the future, methods in this module might be moved to
- Bio::Sequence or other module and this module might be removed.
- * Unit tests for Bio::Sequence::SequenceMasker are also added.
-
- lib/bio/sequence.rb | 2 +
- lib/bio/sequence/sequence_masker.rb | 95 +++++++++++++
- test/unit/bio/sequence/test_sequence_masker.rb | 169 ++++++++++++++++++++++++
- 3 files changed, 266 insertions(+), 0 deletions(-)
- create mode 100644 lib/bio/sequence/sequence_masker.rb
- create mode 100644 test/unit/bio/sequence/test_sequence_masker.rb
-
-commit a2b21fa31c87fc47ae375380fb34958460414107
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Wed Aug 11 22:59:46 2010 +0900
-
- New method Bio::Sequence#output_fasta, a replacement for to_fasta.
-
- * New method Bio::Sequence#output_fasta, a replacement for
- Bio::Sequence#to_fasta. This is also implemented as a shortcut of
- Bio::Sequence#output(:fasta).
-
- lib/bio/sequence/format.rb | 14 ++++++++++++++
- 1 files changed, 14 insertions(+), 0 deletions(-)
-
-commit d139a1e3e7f77317102eaa24649515541761a212
-Author: Toshiaki Katayama <k@bioruby.org>
-Date: Tue Jul 20 11:46:52 2010 +0900
-
- File format autodetection for Bio::KEGG::PATHWAY and Bio::KEGG::MODULE.
-
- * Added file format autodetection for Bio::KEGG::PATHWAY and
- Bio::KEGG::MODULE.
- * This is part of commit e2abe5764f3ded91c82689245f19a0412d3a7afb.
- (Original commit message: Changes for TogoWS)
-
- lib/bio/io/flatfile/autodetection.rb | 6 ++++++
- 1 files changed, 6 insertions(+), 0 deletions(-)
-
-commit 920d92c13b44921a3f58ddbd8566e7a90dd59996
-Author: Toshiaki Katayama <k@bioruby.org>
-Date: Tue Jul 20 11:46:52 2010 +0900
-
- Added autoload for Bio::KEGG::PATHWAY and Bio::KEGG::MODULE.
-
- * Added autoload for Bio::KEGG::PATHWAY and Bio::KEGG::MODULE.
- * This is part of commit e2abe5764f3ded91c82689245f19a0412d3a7afb.
- (Original commit message: Changes for TogoWS)
-
- lib/bio.rb | 2 ++
+ .travis.yml | 2 ++
1 files changed, 2 insertions(+), 0 deletions(-)
-commit bf342c28e0c75c9b48770144f421dd12babd9d0e
+commit 34709d114089c722b5da796028ffb91021761fdd
Author: Naohisa Goto <ng@bioruby.org>
-Date: Tue Aug 17 23:19:47 2010 +0900
+Date: Thu Jul 5 23:00:37 2012 +0900
- Unit tests for Bio::KEGG::MODULE is modified and improved.
+ Remove old comment lines
- test/unit/bio/db/kegg/test_module.rb | 194 ++++++++++++++++++++++++++++++----
- 1 files changed, 173 insertions(+), 21 deletions(-)
+ lib/bio/sequence/format.rb | 6 ------
+ 1 files changed, 0 insertions(+), 6 deletions(-)
-commit 1742568a4f27e75a19441e4a4437ca3f1c0251f8
+commit e0d5ed61e0101e2e72ad024dccd58c8c90def2b9
Author: Naohisa Goto <ng@bioruby.org>
-Date: Tue Aug 17 23:15:44 2010 +0900
+Date: Thu Jul 5 22:42:17 2012 +0900
- In Bio::KEGG::MODULE, an internal-only method is changed to private.
-
- lib/bio/db/kegg/module.rb | 4 ++++
- 1 files changed, 4 insertions(+), 0 deletions(-)
-
-commit 8f5ff66cca678ac6be75a7dda1ff840ac3111f42
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Tue Aug 17 23:10:39 2010 +0900
-
- Removed unused comments.
-
- lib/bio/db/kegg/module.rb | 32 --------------------------------
- 1 files changed, 0 insertions(+), 32 deletions(-)
-
-commit f9d23fb32eeb15dc57580e25653d3f2fff5fa1dc
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Tue Aug 17 22:59:18 2010 +0900
-
- Reverted Bio::KEGG::MODULE#keggclass.
+ Finalizer for Bio::Command::Tmpdir is changed to suppress test failure
- * Reverted Bio::KEGG::MODULE#keggclass.
- * Removed keggclasses and keggclasses_as_array methods, because
- they are inconsistent with Bio::KEGG::ORTHOLOGY#keggclasses.
+ * New class Bio::Command::Tmpdir::Remover for removing temporary
+ directory in finilizer. This class is BioRuby internal use only.
+ Users should not use this class.
+ * Finalizer for Bio::Command::Tmpdir is changed from a Proc object
+ to an instance of the Remover class.
+ * Test failure fix: In some environment, with Ruby 1.9.2,
+ test_output_embl(Bio::FuncTestSequenceOutputEMBL) was failed with
+ "<#<ArgumentError: wrong number of arguments (1 for 0)>" that was
+ raised in the finalizer callback of Bio::Command::Tmpdir. This
+ commit fixes the problem.
- lib/bio/db/kegg/module.rb | 6 +-----
- 1 files changed, 1 insertions(+), 5 deletions(-)
+ lib/bio/command.rb | 56 +++++++++++++++++++++++++++------------------------
+ 1 files changed, 30 insertions(+), 26 deletions(-)
-commit 94188d23ad843c7cb998c99f46371e540ce457dc
-Author: Toshiaki Katayama <k@bioruby.org>
-Date: Tue Jul 20 11:41:50 2010 +0900
-
- For Bio::KEGG::MODULE, methods are added and modified.
-
- * For Bio::KEGG::MODULE, methods are added and modified.
- * New methods: definition, etc.
- * Removed methods: pathway, orthologies, keggclass, etc.
- * Changed methods: reactions, compounds, etc.
- * (Original commit message: Changes for TogoWS)
-
- lib/bio/db/kegg/module.rb | 136 +++++++++++++++++++++++++++++++++++++++++---
- 1 files changed, 126 insertions(+), 10 deletions(-)
-
-commit 92efc03707a49fa0b2c02e7b2f8b53749a75ad59
-Author: Kozo Nishida <kozo-ni@cg04.naist.jp>
-Date: Thu Feb 4 22:59:20 2010 +0900
-
- New class Bio::KEGG::MODULE, parser for KEGG MODULE (Pathway Module).
-
- lib/bio/db/kegg/module.rb | 83 ++++++++++++++++++++++++++++++
- test/data/KEGG/M00118.module | 44 ++++++++++++++++
- test/unit/bio/db/kegg/test_module.rb | 94 ++++++++++++++++++++++++++++++++++
- 3 files changed, 221 insertions(+), 0 deletions(-)
- create mode 100644 lib/bio/db/kegg/module.rb
- create mode 100644 test/data/KEGG/M00118.module
- create mode 100644 test/unit/bio/db/kegg/test_module.rb
-
-commit b7c75cc6023d5dc9096111fde99a6e89db2e4bdc
+commit cca98d1378ce66d6db84cc9c1beadd39ed0e0fee
Author: Naohisa Goto <ng@bioruby.org>
-Date: Wed May 12 01:13:52 2010 +0900
+Date: Thu Jul 5 22:21:34 2012 +0900
- Improvement of tests for Bio::KEGG::ORTHOLOGY using updated test data.
-
- test/unit/bio/db/kegg/test_orthology.rb | 95 +++++++++++++++++++++++++++++++
- 1 files changed, 95 insertions(+), 0 deletions(-)
-
-commit f61c232371f6f673044960b0626486b2e8e160b8
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Wed May 12 01:11:16 2010 +0900
-
- Updated test data K02338.orthology to follow KEGG format changes.
-
- test/data/KEGG/K02338.orthology | 232 ++++++++++++++++++++++++++++++---------
- 1 files changed, 180 insertions(+), 52 deletions(-)
-
-commit 2aa060f42263392877683a47ef9bd744ef4de7f8
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Wed May 12 01:03:18 2010 +0900
-
- Incompatible change of Bio::KEGG::ORTHOLOGY#pathways, and added new methods
+ Workaround to avoid circular require and JRuby autoload bug
- * Incompatible change of Bio::KEGG::ORTHOLOGY#pathways due to the
- changes of KEGG ORTHOLOGY format changes: Because PATHWAY field
- is added, the method is changed to return a hash. The pathway
- method of old behavior is renamed to pathways_in_keggclass
- for compatibility.
- * New methods are added to Bio::KEGG::ORTHOLOGY: references,
- pathways_as_strings, pathways_as_hash, pathway_modules,
- pathway_modules_as_hash, pathway_modules_as_strings.
+ * "require" lines are modified to avoid circular require.
+ * In files that would be required directly from outside bio/sequence
+ (aa.rb, adapter.rb, common.rb, compat.rb, dblink.rb, generic.rb,
+ na.rb, quality_score.rb, sequence_masker.rb), because of avoiding
+ potential mismatch of superclass and/or lack of some methods,
+ bio/sequence.rb is required when Bio::Sequence is not defined.
+ * workaround to avoid JRuby autoload bug
- lib/bio/db/kegg/orthology.rb | 41 ++++++++++++++++++++++++++++++++++++++++-
- 1 files changed, 40 insertions(+), 1 deletions(-)
+ lib/bio/sequence.rb | 10 ++++++----
+ lib/bio/sequence/aa.rb | 8 +++-----
+ lib/bio/sequence/adapter.rb | 12 ++++++------
+ lib/bio/sequence/common.rb | 2 ++
+ lib/bio/sequence/compat.rb | 9 ++-------
+ lib/bio/sequence/dblink.rb | 11 ++++++-----
+ lib/bio/sequence/generic.rb | 7 +++----
+ lib/bio/sequence/na.rb | 10 ++++------
+ lib/bio/sequence/quality_score.rb | 2 ++
+ lib/bio/sequence/sequence_masker.rb | 3 +++
+ 10 files changed, 37 insertions(+), 37 deletions(-)
-commit 2e6754f2598f66f29afb573c3dc83592089b411c
+commit d2915c33ae7f330837688195a58c1e60fe78402a
Author: Naohisa Goto <ng@bioruby.org>
-Date: Wed May 12 00:59:26 2010 +0900
+Date: Thu Jul 5 21:04:28 2012 +0900
- Changed to use Bio::KEGG::Common::PathwayModulesAsHash.
-
- lib/bio/db/kegg/pathway.rb | 25 ++++++++-----------------
- 1 files changed, 8 insertions(+), 17 deletions(-)
-
-commit 527920da990f4374e20333d6852b810ea73ead02
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Wed May 12 00:55:10 2010 +0900
-
- New module Bio::KEGG::Common::PathwayModulesAsHash (internal use only)
+ workaround to avoid circular require in Bio::RestrictionEnzyme
- * New module Bio::KEGG::Common::PathwayModulesAsHash is added,
- based on Bio::KEGG::PATHWAY#pathway_modules_as_hash method.
- Note that the method is Bio::KEGG::* internal use only.
+ * Workaround to avoid circular require in Bio::RestrictionEnzyme
+ * Special care was needed for Bio::RestrictionEnzyme::Analysis
+ because its method definitions are divided into two files:
+ analysis.rb, analysis_basic.rb.
- lib/bio/db/kegg/common.rb | 22 ++++++++++++++++++++++
- 1 files changed, 22 insertions(+), 0 deletions(-)
+ lib/bio/util/restriction_enzyme/analysis.rb | 13 ++++++++-----
+ lib/bio/util/restriction_enzyme/analysis_basic.rb | 7 ++++---
+ lib/bio/util/restriction_enzyme/cut_symbol.rb | 5 +++--
+ lib/bio/util/restriction_enzyme/dense_int_array.rb | 3 +++
+ lib/bio/util/restriction_enzyme/double_stranded.rb | 7 +++----
+ .../double_stranded/aligned_strands.rb | 7 +++----
+ .../double_stranded/cut_location_pair.rb | 7 +++----
+ .../cut_location_pair_in_enzyme_notation.rb | 7 +++----
+ .../double_stranded/cut_locations.rb | 7 +++----
+ .../cut_locations_in_enzyme_notation.rb | 7 +++----
+ lib/bio/util/restriction_enzyme/range/cut_range.rb | 7 +++----
+ .../util/restriction_enzyme/range/cut_ranges.rb | 7 +++----
+ .../range/horizontal_cut_range.rb | 7 +++----
+ .../restriction_enzyme/range/sequence_range.rb | 7 +++----
+ .../range/sequence_range/calculated_cuts.rb | 7 +++----
+ .../range/sequence_range/fragment.rb | 7 +++----
+ .../range/sequence_range/fragments.rb | 7 +++----
+ .../restriction_enzyme/range/vertical_cut_range.rb | 7 +++----
+ lib/bio/util/restriction_enzyme/single_strand.rb | 6 +++---
+ .../cut_locations_in_enzyme_notation.rb | 7 +++----
+ .../restriction_enzyme/single_strand_complement.rb | 7 +++----
+ .../util/restriction_enzyme/sorted_num_array.rb | 3 +++
+ .../util/restriction_enzyme/string_formatting.rb | 7 +++----
+ 23 files changed, 75 insertions(+), 81 deletions(-)
-commit 36041377dbafce642180eb1c664ee36ef21d3bfb
+commit 7df4843288ffde6d7132a5651fe978301f8ebd2b
Author: Naohisa Goto <ng@bioruby.org>
-Date: Fri Mar 19 23:25:56 2010 +0900
+Date: Thu Jul 5 20:18:08 2012 +0900
- New method Bio::KEGG::PATHWAY#references.
-
- * New method Bio::KEGG::PATHWAY#references.
- * Additional unit tests for Bio::KEGG::PATHWAY with test data.
+ workaround to avoid JRuby autoload bug
- lib/bio/db/kegg/pathway.rb | 8 ++
- test/data/KEGG/map00030.pathway | 37 ++++++++++
- test/unit/bio/db/kegg/test_pathway.rb | 120 ++++++++++++++++++++++++++++++++-
- 3 files changed, 162 insertions(+), 3 deletions(-)
- create mode 100644 test/data/KEGG/map00030.pathway
+ lib/bio/util/restriction_enzyme.rb | 4 +---
+ 1 files changed, 1 insertions(+), 3 deletions(-)
-commit d743892d298786eb9e88e2a51ac9f7774785848f
+commit 97d95f2b400006d4229a7ce69d7d8a5cdce42764
Author: Naohisa Goto <ng@bioruby.org>
-Date: Fri Mar 19 00:06:20 2010 +0900
+Date: Wed Jul 4 22:00:27 2012 +0900
- Improvement of Bio::KEGG::Common::References#references.
-
- * Improvement of Bio::KEGG::Common::References#references:
- added support for parsing "journal (year)" style.
+ changed require to autoload for the workaround of JRuby autoload bug
- lib/bio/db/kegg/common.rb | 4 ++++
- 1 files changed, 4 insertions(+), 0 deletions(-)
+ lib/bio/feature.rb | 5 ++---
+ 1 files changed, 2 insertions(+), 3 deletions(-)
-commit 35807ae22c9ad9a3ce37ed5c655d1c080f8d2334
+commit 530b82a45731c2a71a110826341be425de1271e0
Author: Naohisa Goto <ng@bioruby.org>
-Date: Fri Mar 19 00:02:10 2010 +0900
+Date: Wed Jul 4 22:00:06 2012 +0900
- Implementation of Bio::KEGG::GENOME#references is moved.
-
- * Implementation of Bio::KEGG::GENOME#references is moved to
- Bio::KEGG::Common::References#references, which will be
- shared with Bio::KEGG::Pathway and other classes.
+ workaround to avoid JRuby autoload bug
- lib/bio/db/kegg/common.rb | 61 +++++++++++++++++++++++++++++++++++++++++++-
- lib/bio/db/kegg/genome.rb | 62 +++++---------------------------------------
- 2 files changed, 67 insertions(+), 56 deletions(-)
+ lib/bio/sequence/common.rb | 4 +---
+ 1 files changed, 1 insertions(+), 3 deletions(-)
-commit 263c37a07203b87e3b33d35adef3aa3ddcf89601
+commit 8614f31b36fb93d6e49d109268d646ff3032cd1a
Author: Naohisa Goto <ng@bioruby.org>
-Date: Wed Mar 17 00:26:56 2010 +0900
+Date: Wed Jul 4 21:28:52 2012 +0900
- Bug fix: Bio::KEGG::GENES#pathway may fail, and other parse issues due to the format changes of KEGG GENES.
+ workaround to avoid JRuby autoload bug
- * Bug fix: Bio::KEGG::GENES#pathway may return unexpected value
- after calling pathways, pathways_as_hash or pathways_as_string
- methods.
- * Bio::KEGG::GENES#eclinks, Bio::KEGG::Common::PathwaysAsHash,
- and Bio::KEGG::Common::OrthologsAsHash are modified due to
- the file format changes of KEGG::GENES.
+ * Workaround to avoid JRuby autoload bug.
+ * Changed to require bio/db.rb because it is always loaded.
- lib/bio/db/kegg/common.rb | 9 +++++----
- lib/bio/db/kegg/genes.rb | 17 +++++++++++------
- 2 files changed, 16 insertions(+), 10 deletions(-)
+ lib/bio/db/kegg/genes.rb | 6 +++---
+ 1 files changed, 3 insertions(+), 3 deletions(-)
-commit 364cd405a10d0742091281c5a16b77cb54a8087e
+commit ea500006ed56857139c858bdfeb98773e5ca541e
Author: Naohisa Goto <ng@bioruby.org>
-Date: Wed Mar 17 00:25:51 2010 +0900
+Date: Thu Jun 28 21:36:35 2012 +0900
- New methods Bio::Location#== and Bio::Locations#==.
+ Rakefile: use own mktmpdir
- lib/bio/location.rb | 39 +++++++++++++++++++++++++++++++++++++++
- 1 files changed, 39 insertions(+), 0 deletions(-)
+ Rakefile | 59 +++++++++++++++++++++++++++++++++++++++++++----------------
+ 1 files changed, 43 insertions(+), 16 deletions(-)
-commit 2c7ffd6808e572cf35b82d6e74790447d44d08cc
+commit 452fadcab61083dcb9d01ee05d300eae5cb23fee
Author: Naohisa Goto <ng@bioruby.org>
-Date: Wed Mar 17 00:23:00 2010 +0900
+Date: Thu Jun 28 20:37:59 2012 +0900
- Improved unit tests for Bio::KEGG::GENES with new test data.
+ .travis.yml: remove "rake regemspec" from after_install
- test/data/KEGG/b0529.gene | 47 +++++++
- test/unit/bio/db/kegg/test_genes.rb | 254 ++++++++++++++++++++++++++++++++++-
- 2 files changed, 300 insertions(+), 1 deletions(-)
- create mode 100644 test/data/KEGG/b0529.gene
+ .travis.yml | 2 --
+ 1 files changed, 0 insertions(+), 2 deletions(-)
-commit 764869fd42d1e3f96885b3499844bf4fadde80f1
+commit 3fad822af3d7e558a58b71fd8ec2a7061b49f9f2
Author: Naohisa Goto <ng@bioruby.org>
-Date: Wed Mar 17 00:10:51 2010 +0900
+Date: Thu Jun 28 20:36:59 2012 +0900
- Bug fix: Bio::KEGG::GENOME parser issues for PLASMID, REFERENCE, and ORIGINAL_DB fields.
-
- * Bug fix: Fixed parse error for PLASMID fields due to the changes
- of the KEGG GENOME file format. For the bug fix, tag_get and
- tag_cut methods are redefined.
- * Bug fix: Fixed parse error for REFERENCE fields due to the changes
- of the file format.
- * New method Bio::KEGG::GENOME#original_databases is added to get
- ORIGINAL_DB record as an Array of String objects.
+ regenerate bioruby.gemspec with rake regemspec
- lib/bio/db/kegg/genome.rb | 69 +++++++++++++++++++++++++++++++++++++++-----
- 1 files changed, 61 insertions(+), 8 deletions(-)
+ bioruby.gemspec | 2 ++
+ 1 files changed, 2 insertions(+), 0 deletions(-)
-commit 75db7c6c7132f19e212be36d06643a0f48a7df44
+commit ea6e96fc654c797664b118a6326a84e4f9b1a8a3
Author: Naohisa Goto <ng@bioruby.org>
-Date: Wed Mar 17 00:09:09 2010 +0900
+Date: Thu Jun 28 20:35:49 2012 +0900
- New method Bio::Reference#==.
+ print message when doing Dir.chdir
- lib/bio/reference.rb | 24 ++++++++++++++++++++++++
- 1 files changed, 24 insertions(+), 0 deletions(-)
+ Rakefile | 17 +++++++++++------
+ 1 files changed, 11 insertions(+), 6 deletions(-)
-commit 64a6bfb52ca1bb27bd38c86c060e2925f38924fb
+commit c2fcd5e8cc71da38dc3c6d1f8c8d0233e47398b3
Author: Naohisa Goto <ng@bioruby.org>
-Date: Wed Mar 17 00:07:43 2010 +0900
+Date: Thu Jun 28 20:28:41 2012 +0900
- Newly added unit tests for Bio::KEGG::GENOME with test data.
+ In tar-install, removed dependency to regemspec
- test/data/KEGG/T00005.genome | 140 ++++++++++++
- test/data/KEGG/T00070.genome | 34 +++
- test/unit/bio/db/kegg/test_genome.rb | 408 ++++++++++++++++++++++++++++++++++
- 3 files changed, 582 insertions(+), 0 deletions(-)
- create mode 100644 test/data/KEGG/T00005.genome
- create mode 100644 test/data/KEGG/T00070.genome
- create mode 100644 test/unit/bio/db/kegg/test_genome.rb
-
-commit 21c92bb991c83dce27a4411382c456cdd6029a82
-Author: Naohisa Goto <ngoto@gen-info.osaka-u.ac.jp>
-Date: Tue Mar 9 23:24:15 2010 +0900
-
- Renamed Bio::KEGG::PATHWAY#keggmodules to pathway_modules_as_strings, etc.
-
- * Bio::KEGG::PATHWAY#keggmodules is renamed to
- pathway_modules_as_strings.
- * New method pathway_modules_as_hash and its alias method
- pathway_modules is added.
- * Bio::KEGG::PATHWAY#rel_pathways is renamed to
- rel_pathways_as_strings.
- * New method rel_pathways_as_hash is added, and rel_pathways
- is changed to be the alias of the rel_pathways_as_hash method.
- * Unit tests are also changed.
-
- lib/bio/db/kegg/pathway.rb | 42 +++++++++++++++++++++++++++++++-
- test/unit/bio/db/kegg/test_pathway.rb | 29 ++++++++++++++++++++--
- 2 files changed, 66 insertions(+), 5 deletions(-)
-
-commit fa10f38716ec2eecd6fa8e8b027085377e9ee421
-Author: Naohisa Goto <ngoto@gen-info.osaka-u.ac.jp>
-Date: Tue Mar 9 21:13:18 2010 +0900
-
- Fixed text indentations.
-
- lib/bio/db/kegg/pathway.rb | 4 ++--
- test/unit/bio/db/kegg/test_pathway.rb | 25 +++++++++++++------------
- 2 files changed, 15 insertions(+), 14 deletions(-)
-
-commit 0916b0cac5d17ce47ef5cc3382e3167293bcf4c2
-Author: Kozo Nishida <kozo-ni@cg04.naist.jp>
-Date: Tue Feb 2 17:34:17 2010 +0900
-
- Newly added Bio::KEGG::PATHWAY with test code and test data.
-
- lib/bio/db/kegg/pathway.rb | 73 +++++++++++++++++++++++++++++++++
- test/data/KEGG/map00052.pathway | 13 ++++++
- test/unit/bio/db/kegg/test_pathway.rb | 57 +++++++++++++++++++++++++
- 3 files changed, 143 insertions(+), 0 deletions(-)
- create mode 100644 lib/bio/db/kegg/pathway.rb
- create mode 100644 test/data/KEGG/map00052.pathway
- create mode 100644 test/unit/bio/db/kegg/test_pathway.rb
-
-commit c3ceea339164754071f03ce13da4f65e08230f40
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Fri Feb 19 00:43:38 2010 +0900
-
- Tutorial.rd.html is regenerated.
-
- doc/Tutorial.rd.html | 55 +++++++++++++++++++++++++++++++++++++++++++++++++-
- 1 files changed, 54 insertions(+), 1 deletions(-)
-
-commit 315da0213edfece696d22cc4648cb7a74f18ad34
-Author: Ra <ilpuccio.febo@gmail.com>
-Date: Sun Feb 7 10:38:36 2010 +0100
-
- Added BioSQL docs links
-
- doc/Tutorial.rd | 4 ++--
- 1 files changed, 2 insertions(+), 2 deletions(-)
-
-commit 22374415873906f4bcd3e84950c14b5f0b6c7e61
-Author: Ra <ilpuccio.febo@gmail.com>
-Date: Sun Feb 7 02:39:16 2010 +0100
-
- Added link to BioSQL install doc.
-
- doc/Tutorial.rd | 2 +-
+ Rakefile | 2 +-
1 files changed, 1 insertions(+), 1 deletions(-)
-commit 4d18dd2f5a3f18348e5f4aa07b14c104d3a65f5b
-Author: Ra <ilpuccio.febo@gmail.com>
-Date: Fri Feb 5 21:30:36 2010 +0100
-
- Added other examples about BioSQL
-
- doc/Tutorial.rd | 36 ++++++++++++++++++++++++++++--------
- 1 files changed, 28 insertions(+), 8 deletions(-)
-
-commit b704f01cd0799ab1a7e3975119e9d6139ddfbd51
-Author: Ra <ilpuccio.febo@gmail.com>
-Date: Wed Jan 27 21:08:25 2010 +0100
-
- BioSQL tutorial continue...
-
- doc/Tutorial.rd | 18 ++++++++++++++++--
- 1 files changed, 16 insertions(+), 2 deletions(-)
-
-commit 1993a1566b5ade937703d0291c4eaf2de673d170
-Author: Ra <ilpuccio.febo@gmail.com>
-Date: Wed Jan 27 20:32:23 2010 +0100
-
- BioSQL tutorial inital draft.
-
- doc/Tutorial.rd | 25 ++++++++++++++++++++++++-
- 1 files changed, 24 insertions(+), 1 deletions(-)
-
-commit 09047b664a03492d7546d92b619faacee72d0cd5
-Author: Jan Aerts <jan.aerts@gmail.com>
-Date: Sun Feb 7 17:58:59 2010 +0900
-
- Added code example that will serve as basis for sequence/codon howto
-
- doc/howtos/sequence_codon.txt | 38 ++++++++++++++++++++++++++++++++++++++
- 1 files changed, 38 insertions(+), 0 deletions(-)
- create mode 100644 doc/howtos/sequence_codon.txt
-
-commit c1e2165ba801cccd52135b13ed36713517e1fa8a
+commit 67a7e83d516aab5d60f8263525b359be8b0ffc0b
Author: Naohisa Goto <ng@bioruby.org>
-Date: Fri Feb 5 12:50:38 2010 +0900
+Date: Thu Jun 28 20:23:24 2012 +0900
- Suppressed "warning: parenthesize argument(s) for future version" in Ruby 1.8.5.
-
- lib/bio/appl/paml/codeml/report.rb | 2 +-
- 1 files changed, 1 insertions(+), 1 deletions(-)
-
-commit f7ce9ba6a2f4e680ee40017a21aa95d05baf34f4
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Thu Feb 4 20:26:00 2010 +0900
-
- Added :startdoc: and removed an empty line for RDoc.
-
- lib/bio/appl/paml/codeml/report.rb | 4 +++-
- 1 files changed, 3 insertions(+), 1 deletions(-)
-
-commit 6d4d2e1f37efb1e53091fbc9a0977568996788ff
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Thu Feb 4 16:58:10 2010 +0900
-
- New unit test for Bio::PAML::Codeml::Report.
+ Rakefile: give up using Dir.mktmpdir because of JRuby's behavior
- * New unit test for Bio::PAML::Codeml::Report and related classes.
- The test code is copied from the examples described in
- lib/bio/appl/paml/codeml/report.rb and modified for the unit test.
+ * Rakefile: give up using Dir.mktmpdir because of JRuby's behavior
+ that may be related with http://jira.codehaus.org/browse/JRUBY-5678
- test/unit/bio/appl/paml/codeml/test_report.rb | 253 +++++++++++++++++++++++++
- 1 files changed, 253 insertions(+), 0 deletions(-)
- create mode 100644 test/unit/bio/appl/paml/codeml/test_report.rb
+ Rakefile | 61 ++++++++++++++++++++++++++++++++++++++++++++++---------------
+ 1 files changed, 46 insertions(+), 15 deletions(-)
-commit 8418549811293c3e20b91d4e95da2cb2a282a064
+commit cff098034a338bbe9579d6c7b4380c7132a38ef5
Author: Naohisa Goto <ng@bioruby.org>
-Date: Thu Feb 4 16:47:37 2010 +0900
+Date: Thu Jun 28 19:23:57 2012 +0900
- Changes due to the rename to report_single.rb.
-
- .../bio/appl/paml/codeml/test_report_single.rb | 2 +-
- 1 files changed, 1 insertions(+), 1 deletions(-)
-
-commit 7bfb428da237709b243c8d0e4646bd41710d1519
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Thu Feb 4 16:39:10 2010 +0900
-
- Renamed codeml/test_report.rb to codeml/test_report_single.rb.
+ gem-integration-test, gem-install and gem-install-nodoc are removed
- * Renamed test/unit/bio/appl/paml/codeml/test_report.rb to
- test_report_single.rb.
+ * gem-integration-test, gem-install and gem-install-nodoc are removed
+ because they are useless with Bundler
- test/unit/bio/appl/paml/codeml/test_report.rb | 46 --------------------
- .../bio/appl/paml/codeml/test_report_single.rb | 46 ++++++++++++++++++++
- 2 files changed, 46 insertions(+), 46 deletions(-)
- delete mode 100644 test/unit/bio/appl/paml/codeml/test_report.rb
- create mode 100644 test/unit/bio/appl/paml/codeml/test_report_single.rb
+ Rakefile | 13 -------------
+ 1 files changed, 0 insertions(+), 13 deletions(-)
-commit 762d38b1564da7d846e3dcd461cf465aa685a1ae
-Author: Pjotr Prins <pjotr.public01@thebird.nl>
-Date: Tue Jan 12 10:13:35 2010 +0100
-
- Modified output of Bio::PAML::Codeml::PositiveSites#graph_to_s
-
- * Modified output of Bio::PAML::Codeml::PositiveSites#graph_to_s.
- (Part of commit ea350da85e5db2ba35cb8dd1e86e3d4323ee3fd1.
- Original commit message is:
- HtmlPaml: fixed some missing output
- use real greek omega in output)
-
- lib/bio/appl/paml/codeml/report.rb | 2 +-
- 1 files changed, 1 insertions(+), 1 deletions(-)
-
-commit f88645cd783b7027950133c0badb0a8da8e4fb95
-Author: Pjotr Prins <pjotr.public01@thebird.nl>
-Date: Tue Jan 12 09:24:46 2010 +0100
-
- Codeml: no negative gaps
-
- lib/bio/appl/paml/codeml/report.rb | 2 +-
- 1 files changed, 1 insertions(+), 1 deletions(-)
-
-commit 978b21cf90d0280e6e6c7d6e4fa65c49692bdd69
-Author: Pjotr Prins <pjotr.public01@thebird.nl>
-Date: Mon Jan 11 17:31:45 2010 +0100
-
- Codeml: always raise an error when significance can not be calculated
-
- lib/bio/appl/paml/codeml/report.rb | 15 ++++++++++-----
- 1 files changed, 10 insertions(+), 5 deletions(-)
-
-commit 12b5895f6f1819252d616bb0a38aa88a7828daff
-Author: Pjotr Prins <pjotr.public01@thebird.nl>
-Date: Mon Jan 11 17:22:34 2010 +0100
-
- Codeml: oops
-
- lib/bio/appl/paml/codeml/report.rb | 6 +++---
- 1 files changed, 3 insertions(+), 3 deletions(-)
-
-commit a8ff0a07fdbef72f72103f0bceb9c24a63162fc6
-Author: Pjotr Prins <pjotr.public01@thebird.nl>
-Date: Mon Jan 11 17:19:26 2010 +0100
-
- Codeml: added significance testing for a few model combinations
-
- lib/bio/appl/paml/codeml/report.rb | 57 +++++++++++++++++++++++++++++++++++-
- 1 files changed, 56 insertions(+), 1 deletions(-)
-
-commit 0e11af19450faca3568f89b23d5bd764688f75c0
-Author: Pjotr Prins <pjotr.public01@thebird.nl>
-Date: Mon Jan 11 16:24:51 2010 +0100
-
- Codeml: raise error instead of a 'nil' error when buffer is incomplete
-
- lib/bio/appl/paml/codeml/report.rb | 1 +
- 1 files changed, 1 insertions(+), 0 deletions(-)
-
-commit 1cb2aaaa701a1613812dd479201d27c1d7dcf016
-Author: Pjotr Prins <pjotr.public01@thebird.nl>
-Date: Mon Jan 11 14:37:52 2010 +0100
-
- Bio::PAML::Codeml::PositiveSites#graph_to_s gets fill character
-
- * Bio::PAML::Codeml::PositiveSites#graph_to_s gets fill character
- as an argument.
- (Part of commit d67259c9f203dc92c68ad04b4112329a7093a259.
- Original commit message is:
- HtmlPaml: show colors for probabilities of positive selection)
-
- lib/bio/appl/paml/codeml/report.rb | 15 +++++++++------
- 1 files changed, 9 insertions(+), 6 deletions(-)
-
-commit ae5b9cf9ee697cc237c77335b12b57709a0e7a46
-Author: Pjotr Prins <pjotr.public01@thebird.nl>
-Date: Mon Jan 11 13:37:52 2010 +0100
-
- Codeml: return correct buffer
-
- lib/bio/appl/paml/codeml/report.rb | 10 +++++-----
- 1 files changed, 5 insertions(+), 5 deletions(-)
-
-commit 44f2e28c3e0d382505b067ec3c7aa55cbb9f0a38
-Author: Pjotr Prins <pjotr.public01@thebird.nl>
-Date: Mon Jan 11 13:10:40 2010 +0100
-
- Improvement of Bio::PAML::Codeml::PositiveSites#initialize, etc
-
- * Improved target analysis location detection in
- Bio::PAML::Codeml::PositiveSites#initialize.
- * Changed description inside Bio::PAML::Codeml::Report#nb_sites
- and sites methods.
- * This is part of commit e88ff474748b3295a8a4089356d3086638200d64.
- (Original commit message: HtmlPaml: improved output)
-
- lib/bio/appl/paml/codeml/report.rb | 20 ++++++++++++--------
- 1 files changed, 12 insertions(+), 8 deletions(-)
-
-commit ee8973696d0434c591ceaffc580f1aa30fd036f9
-Author: Pjotr Prins <pjotr.public01@thebird.nl>
-Date: Mon Jan 11 12:54:40 2010 +0100
-
- Codeml: fixed doctests
-
- lib/bio/appl/paml/codeml/report.rb | 6 +++---
- 1 files changed, 3 insertions(+), 3 deletions(-)
-
-commit f7bbb0859e28cb51137d0a8f8d962821eb67db91
-Author: Pjotr Prins <pjotr.public01@thebird.nl>
-Date: Mon Jan 11 12:51:25 2010 +0100
-
- New method Bio::PAML::Codeml::PositiveSites#to_s
-
- * New method Bio::PAML::Codeml::PositiveSites#to_s
- (part of the commit 82e933fd1961a2b31873bc37cbf3205adbf0a6de,
- original commit message: HtmlPaml: add facility for color output)
-
- lib/bio/appl/paml/codeml/report.rb | 6 ++++++
- 1 files changed, 6 insertions(+), 0 deletions(-)
-
-commit d4f3dbaf78f623d870a1a76ab1353d786e0fb73b
-Author: Pjotr Prins <pjotr.public01@thebird.nl>
-Date: Mon Jan 11 12:34:59 2010 +0100
-
- Codeml: HtmlPaml: minor tweaks
-
- lib/bio/appl/paml/codeml/report.rb | 7 ++-----
- 1 files changed, 2 insertions(+), 5 deletions(-)
-
-commit 7d41b6acb41c5913622fde127a030f940a432cc5
-Author: Pjotr Prins <pjotr.public01@thebird.nl>
-Date: Mon Jan 11 12:19:15 2010 +0100
-
- Codeml: add short description to positive sites line
-
- lib/bio/appl/paml/codeml/report.rb | 13 +++++++++++++
- 1 files changed, 13 insertions(+), 0 deletions(-)
-
-commit a9d6765b3a5d23be7e8cf59954d67cd2354e5878
-Author: Pjotr Prins <pjotr.public01@thebird.nl>
-Date: Mon Jan 11 12:13:55 2010 +0100
-
- Codeml: fixed bug in graph output
-
- lib/bio/appl/paml/codeml/report.rb | 2 +-
- 1 files changed, 1 insertions(+), 1 deletions(-)
-
-commit af124dcaa2adb446e273456f8dd0b84aff9b00db
-Author: Pjotr Prins <pjotr.public01@thebird.nl>
-Date: Mon Jan 11 12:11:00 2010 +0100
-
- Codeml: added graph_seq, which shows the AA of the first sequence at positive sites
-
- lib/bio/appl/paml/codeml/report.rb | 11 +++++++++--
- 1 files changed, 9 insertions(+), 2 deletions(-)
-
-commit 1924dcd951a9e655726bc1af72626526ed223258
-Author: Pjotr Prins <pjotr.public01@thebird.nl>
-Date: Fri Jan 8 10:13:37 2010 +0100
-
- Codeml: added :stopdoc: directive for rdoc
-
- lib/bio/appl/paml/codeml/report.rb | 21 ++++++++++++---------
- 1 files changed, 12 insertions(+), 9 deletions(-)
-
-commit 7b68fd9d785723935f90144f67999fcf74bcc7c0
-Author: Pjotr Prins <pjotr.public01@thebird.nl>
-Date: Fri Jan 8 10:01:49 2010 +0100
-
- Codeml: fixed the doctests and added some info.
- all tests pass &
-
- lib/bio/appl/paml/codeml/report.rb | 43 ++++++++++++++++++++++++-----------
- 1 files changed, 29 insertions(+), 14 deletions(-)
-
-commit ce212c507e9e81120e7ad12be6df955e90d0ad33
-Author: Pjotr Prins <pjotr.public01@thebird.nl>
-Date: Fri Jan 8 09:46:05 2010 +0100
-
- Codeml: exclude TestFile class from RDoc generated documentation
-
- lib/bio/appl/paml/codeml/report.rb | 9 ++++++---
- 1 files changed, 6 insertions(+), 3 deletions(-)
-
-commit 9d64a70b628cb3cda9cc1576b9966dae242e5230
-Author: Pjotr Prins <pjotr.public01@thebird.nl>
-Date: Fri Jan 8 09:39:02 2010 +0100
-
- Codeml: added many comments
-
- lib/bio/appl/paml/codeml/report.rb | 87 +++++++++++++++++++++++++++++------
- 1 files changed, 72 insertions(+), 15 deletions(-)
-
-commit 2b92df64016865a2ab40c93650409cfd67a2a98e
-Author: Pjotr Prins <pjotr.public01@thebird.nl>
-Date: Mon Jan 4 17:57:32 2010 +0100
-
- codeml: Added parser for full Bayesian sites
- all tests pass &
-
- lib/bio/appl/paml/codeml/report.rb | 52 ++++++++++++++++++++++++++++++-----
- 1 files changed, 44 insertions(+), 8 deletions(-)
-
-commit 198f0c014f7993fbe22825d0be67e9b1aa19d2de
-Author: Pjotr Prins <pjotr.public01@thebird.nl>
-Date: Mon Jan 4 17:37:15 2010 +0100
-
- codeml: show graph
-
- lib/bio/appl/paml/codeml/report.rb | 46 ++++++++++++++++++++++++++++++++++-
- 1 files changed, 44 insertions(+), 2 deletions(-)
-
-commit 0843bb4d79dc4d94a22d79a797a39dc2866222c5
-Author: Pjotr Prins <pjotr.public01@thebird.nl>
-Date: Mon Jan 4 17:09:27 2010 +0100
-
- Codeml: added full support for positive selection sites
- doctests + unit tests pass &
-
- lib/bio/appl/paml/codeml/report.rb | 150 ++++++++++++++++++++++++++++--------
- 1 files changed, 118 insertions(+), 32 deletions(-)
-
-commit 1610c5d86cddd53f7f0300d0f7a137daaa61ef94
-Author: Pjotr Prins <pjotr.public01@thebird.nl>
-Date: Mon Jan 4 12:33:20 2010 +0100
-
- codeml: added M3 classes
-
- lib/bio/appl/paml/codeml/report.rb | 28 +++++++++++++++++++++++++---
- 1 files changed, 25 insertions(+), 3 deletions(-)
-
-commit efc939fbd300ceb371b342172382cdec9fcc74b7
-Author: Pjotr Prins <pjotr.public01@thebird.nl>
-Date: Mon Jan 4 12:02:47 2010 +0100
-
- codeml: adding compatibility layer for single model (old type)
- unit tests pass &
-
- lib/bio/appl/paml/codeml/report.rb | 44 +++++++++++++++++++++++++++++++-----
- 1 files changed, 38 insertions(+), 6 deletions(-)
-
-commit b89990daa3ea26a9f9195ec16044fb2070bcdd1a
-Author: Pjotr Prins <pjotr.public01@thebird.nl>
-Date: Sun Jan 3 12:34:53 2010 +0100
-
- Implementation parsing one model - doctests for M0 pass
-
- lib/bio/appl/paml/codeml/report.rb | 90 ++++++++++++++++++++++++++++++++----
- 1 files changed, 81 insertions(+), 9 deletions(-)
-
-commit dce447d3e81e738323e6fb6b2d28324e1fa62e7d
-Author: Pjotr Prins <pjotr.public01@thebird.nl>
-Date: Sun Jan 3 11:27:54 2010 +0100
-
- Codeml: use BioTestFile for locating test data in the doctest
-
- lib/bio/appl/paml/codeml/report.rb | 9 ++++++++-
- 1 files changed, 8 insertions(+), 1 deletions(-)
-
-commit 27a7b558d60b7ec127df2c351542433c321704ac
-Author: Pjotr Prins <pjotr.public01@thebird.nl>
-Date: Sat Jan 2 23:36:47 2010 +0100
-
- Codeml: split new type report and old type report
-
- lib/bio/appl/paml/codeml/report.rb | 19 +++++++++++++++----
- 1 files changed, 15 insertions(+), 4 deletions(-)
-
-commit 027808e4723ca77af3e15b461ddcc09faf692732
-Author: Pjotr Prins <pjotr.public01@thebird.nl>
-Date: Sat Jan 2 23:25:22 2010 +0100
-
- Added example files for PAML codeml dual model runs
-
- test/data/paml/codeml/models/aa.aln | 26 ++
- test/data/paml/codeml/models/aa.dnd | 13 +
- test/data/paml/codeml/models/aa.ph | 13 +
- test/data/paml/codeml/models/alignment.phy | 49 ++++
- test/data/paml/codeml/models/results0-3.txt | 312 ++++++++++++++++++++++++
- test/data/paml/codeml/models/results7-8.txt | 340 +++++++++++++++++++++++++++
- 6 files changed, 753 insertions(+), 0 deletions(-)
- create mode 100644 test/data/paml/codeml/models/aa.aln
- create mode 100644 test/data/paml/codeml/models/aa.dnd
- create mode 100644 test/data/paml/codeml/models/aa.ph
- create mode 100644 test/data/paml/codeml/models/alignment.phy
- create mode 100644 test/data/paml/codeml/models/results0-3.txt
- create mode 100644 test/data/paml/codeml/models/results7-8.txt
-
-commit 1d35e616ce411bf643ab6dcb7126a6e1aca1e186
-Author: Pjotr Prins <pjotr.public01@thebird.nl>
-Date: Sat Jan 2 17:04:56 2010 +0100
-
- Codeml::Report Added new description and reference
-
- lib/bio/appl/paml/codeml/report.rb | 113 ++++++++++++++++++++++++++++++------
- 1 files changed, 96 insertions(+), 17 deletions(-)
-
-commit d21b26044e776fab44dbc95f181afd04b67abe28
+commit d5c054265af4f80318cbfa5a5bbdee6125219de2
Author: Naohisa Goto <ng@bioruby.org>
-Date: Mon Feb 1 22:31:21 2010 +0900
+Date: Thu Jun 28 18:10:05 2012 +0900
- Bug fix and Ruby 1.9 support: Bio::Command.call_command_fork etc.
-
- * Bug fix: In Bio::Command.call_command_fork, thread switching is
- disabled in the child process. Thanks to Andrew Grimm who
- reports the bug ([BioRuby] Thread-safety of alignment).
- Note that call_command_fork no longer works in Ruby 1.9 because
- it is changed to use Thread.critical which is removed in Ruby 1.9.
- * Ruby 1.9 support: In Ruby 1.9, Bio::Command.call_command_popen
- bypasses shell execution by passing command-line as an Array,
- which is a new feature added in Ruby 1.9. Now, call_command_popen
- is safe and robust enough with Ruby 1.9.
- * Ruby 1.9 support: In Ruby 1.9, Bio::Command.call_command and
- query_command use call_command_popen and query_command_popen,
- respectively.
- * RDoc for the above and related methods are modified.
+ .travis.yml: .gemspec is needed to install local gem
- lib/bio/command.rb | 80 +++++++++++++++++++++++++++++++----
- test/functional/bio/test_command.rb | 4 ++
- 2 files changed, 76 insertions(+), 8 deletions(-)
+ .travis.yml | 1 +
+ gemfiles/prepare-gemspec.rb | 25 +++++++++++++++++++++++++
+ 2 files changed, 26 insertions(+), 0 deletions(-)
+ create mode 100644 gemfiles/prepare-gemspec.rb
-commit 981dc1c89049bf00e56a9e83ef352cb4c4b45d6a
+commit 05b6172123f42a1d8d46668d8a3d5f698c371704
Author: Naohisa Goto <ng@bioruby.org>
-Date: Tue Feb 2 22:47:36 2010 +0900
+Date: Thu Jun 28 17:51:43 2012 +0900
- Bug fix: Bio::FastaNumericFormat#to_biosequence bug fix
+ remove 1.9.2; add tar/gem integration tests
- * Bug fix: New method Bio::FastaNumericFormat#to_biosequence is
- defined to avoid NomethodError occurred in the superclass'es
- method. For the purpose, a new module
- Bio::Sequence::Adapter::FastaNumericFormat is added.
- Thanks to Hiroyuki MISHIMA who reports the bug ([BioRuby] trouble
- on the FASTA.QUAL format (Bio::FastaNumericFormat)).
- * Newly added unit test for Bio::FastaNumericFormat#to_biosequence.
+ * Remove ruby version 1.9.2 from matrix for reducing builds
+ * Add tar/gem integration tests
+ * Add a new helper script gemfiles/modify-Gemfile.rb,
+ modifying gemfile when running gem integration test.
+ * Remove jruby version comments
- lib/bio/db/fasta/qual.rb | 24 ++++++++++++++++++++++++
- lib/bio/db/fasta/qual_to_biosequence.rb | 29 +++++++++++++++++++++++++++++
- lib/bio/sequence/adapter.rb | 1 +
- test/unit/bio/db/test_qual.rb | 11 +++++++++--
- 4 files changed, 63 insertions(+), 2 deletions(-)
- create mode 100644 lib/bio/db/fasta/qual_to_biosequence.rb
+ .travis.yml | 26 +++++++++++++++++---------
+ gemfiles/modify-Gemfile.rb | 28 ++++++++++++++++++++++++++++
+ 2 files changed, 45 insertions(+), 9 deletions(-)
+ create mode 100644 gemfiles/modify-Gemfile.rb
-commit 29ed6870e453f54aac2ce9dcb7891186eb01c40d
-Author: Ben J Woodcroft <ben@reefedge.sols.uq.edu.au>
-Date: Wed Jan 13 14:38:13 2010 +1000
-
- Bug fix: fixed uniprot GN parsing issue
-
- lib/bio/db/embl/sptr.rb | 2 +-
- 1 files changed, 1 insertions(+), 1 deletions(-)
-
-commit a3002a79ec012559f5847ba8ebe4faf6e7fa609e
+commit 6813f91893e7ddc3000047357c9ed2dafb32a722
Author: Naohisa Goto <ng@bioruby.org>
-Date: Fri Jan 8 22:14:15 2010 +0900
+Date: Thu Jun 28 17:06:28 2012 +0900
- Tutorial.rd.html is regenerated.
+ descriptions are modified for danger operations
- doc/Tutorial.rd.html | 29 ++++++++++++++---------------
- 1 files changed, 14 insertions(+), 15 deletions(-)
-
-commit 9238c3cb0e8f1156d23a5dfb3ce4e299a91b9f23
-Author: Pjotr Prins <pjotr.public01@thebird.nl>
-Date: Fri Jan 8 09:04:23 2010 +0100
-
- Tutorial: removed bad links
-
- doc/Tutorial.rd | 10 +---------
- 1 files changed, 1 insertions(+), 9 deletions(-)
-
-commit 60542fd9863c5fc1240a15cc76f8fa90644a15c8
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Wed Jan 6 20:38:25 2010 +0900
-
- Changed header and the depth of loading helper due to the rename.
-
- test/unit/bio/appl/clustalw/test_report.rb | 4 ++--
+ Rakefile | 4 ++--
1 files changed, 2 insertions(+), 2 deletions(-)
-commit 68924e736df76fe3c77d9fe132b6df01fc0621fe
+commit a209688952c922d9ba45c227874990bccd3da7c0
Author: Naohisa Goto <ng@bioruby.org>
-Date: Wed Jan 6 20:34:10 2010 +0900
+Date: Mon Jun 25 23:25:51 2012 +0900
- Renamed test/unit/bio/db/test_clustalw.rb to test/unit/bio/appl/clustalw/test_report.rb.
+ regenerate bioruby.gemspec with rake regemspec
- test/unit/bio/appl/clustalw/test_report.rb | 61 ++++++++++++++++++++++++++++
- test/unit/bio/db/test_clustalw.rb | 61 ----------------------------
- 2 files changed, 61 insertions(+), 61 deletions(-)
- create mode 100644 test/unit/bio/appl/clustalw/test_report.rb
- delete mode 100644 test/unit/bio/db/test_clustalw.rb
-
-commit 8368eee50de51f6218ffc7b1bf1aad332702c4ba
-Author: Pjotr Prins <pjotr.public01@thebird.nl>
-Date: Tue Jan 5 12:54:43 2010 +0100
-
- Clustal: unit tests according to Naohisa
-
- lib/bio/appl/clustalw/report.rb | 6 +++---
- test/unit/bio/db/test_clustalw.rb | 10 +++++-----
- 2 files changed, 8 insertions(+), 8 deletions(-)
-
-commit ad525a01fa17052e9b7e9b7f30639c48596552ba
-Author: Pjotr Prins <pjotr.public01@thebird.nl>
-Date: Tue Jan 5 12:50:17 2010 +0100
-
- Clustal: unit test uses File.read
-
- test/unit/bio/db/test_clustalw.rb | 4 ++--
- 1 files changed, 2 insertions(+), 2 deletions(-)
-
-commit 7ab517e05cc470b9ca57273092599adb8c00dc11
-Author: Pjotr Prins <pjotr.public01@thebird.nl>
-Date: Tue Jan 5 12:49:21 2010 +0100
-
- Clustal: unit test, changed class name and copyright header
-
- test/unit/bio/db/test_clustalw.rb | 4 ++--
- 1 files changed, 2 insertions(+), 2 deletions(-)
-
-commit 0829ee91a97976eb6671a2feec7edfc524f44b2c
-Author: Pjotr Prins <pjotr.public01@thebird.nl>
-Date: Tue Jan 5 12:46:37 2010 +0100
-
- Clustal: Changed [] to get_sequence, with method description
-
- * Clustal: Added copyright.
- * Changed [] to get_sequence, with method description.
-
- lib/bio/appl/clustalw/report.rb | 12 ++++++++++--
- 1 files changed, 10 insertions(+), 2 deletions(-)
-
-commit 3b8968a6b7b98e0f03b0822849594262a8f4ac99
-Author: Pjotr Prins <pjotr.public01@thebird.nl>
-Date: Sun Dec 27 16:44:30 2009 +0100
-
- ClustalW: Added [] method to reach sequence + definition
-
- lib/bio/appl/clustalw/report.rb | 9 +++++++++
- test/unit/bio/db/test_clustalw.rb | 6 ++----
- 2 files changed, 11 insertions(+), 4 deletions(-)
-
-commit 3926fabbcc0636c6e4ed08233af3d647c620cd5b
-Author: Pjotr Prins <pjotr.public01@thebird.nl>
-Date: Sun Dec 27 16:22:38 2009 +0100
-
- ClustalW: Add ALN parser unit test
-
- test/data/clustalw/example1.aln | 58 ++++++++++++++++++++++++++++++++++
- test/unit/bio/db/test_clustalw.rb | 63 +++++++++++++++++++++++++++++++++++++
- 2 files changed, 121 insertions(+), 0 deletions(-)
- create mode 100644 test/data/clustalw/example1.aln
- create mode 100644 test/unit/bio/db/test_clustalw.rb
-
-commit 2ef97f945b122dc279eb0ec0a34a2adb0c5f0cff
-Author: Pjotr Prins <pjotr.public01@thebird.nl>
-Date: Sat Jan 2 13:24:33 2010 +0100
-
- Tutorial: Fixed URLs
-
- doc/Tutorial.rd | 10 +++++-----
- 1 files changed, 5 insertions(+), 5 deletions(-)
-
-commit 567ca8b010e15cbea9398ee74c78eae01fc6671d
-Author: Pjotr Prins <pjotr.public01@thebird.nl>
-Date: Fri Jan 1 12:08:50 2010 +0100
-
- Tutorial: Added info on gem install
-
- doc/Tutorial.rd | 9 +++++++--
- 1 files changed, 7 insertions(+), 2 deletions(-)
-
-commit 21070ab4928d9c7446d58f3003d43ee6235046aa
-Author: Pjotr Prins <pjotr.public01@thebird.nl>
-Date: Thu Dec 31 11:41:54 2009 +0100
-
- Tutorial.rd: Added Naohisa's Ruby replacement for sed conversion
-
- doc/Tutorial.rd | 6 +++++-
- 1 files changed, 5 insertions(+), 1 deletions(-)
-
-commit ebded2364f716fa03b0fdbec9887f807836eb789
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Wed Jan 6 10:59:39 2010 +0900
-
- Bio::BIORUBY_EXTRA_VERSION is changed to ".5000".
-
- bioruby.gemspec | 2 +-
- lib/bio/version.rb | 2 +-
- 2 files changed, 2 insertions(+), 2 deletions(-)
-
-commit a1bda9088662edec55af0106b4292c39e51c8b7b
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Mon Dec 28 21:56:33 2009 +0900
-
- BioRuby 1.4.0 is released.
-
- ChangeLog | 32 ++++++++++++++++++++++++++++++++
- bioruby.gemspec | 3 ++-
- 2 files changed, 34 insertions(+), 1 deletions(-)
-
-commit 5c88896357e1eff0686ceb06cbec0a7837f85050
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Mon Dec 28 21:55:41 2009 +0900
-
- Preparation for bioruby-1.4.0 release.
-
- lib/bio/version.rb | 2 +-
- 1 files changed, 1 insertions(+), 1 deletions(-)
-
-commit 11f56d3d8efc2cf5d9408da865af044fa099b925
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Mon Dec 28 21:52:25 2009 +0900
-
- Added about ChangeLog which is replaced by git-log.
-
- RELEASE_NOTES.rdoc | 5 +++++
+ bioruby.gemspec | 5 +++++
1 files changed, 5 insertions(+), 0 deletions(-)
-commit 17d5b1825b6c73d710d72903d8710caa9996353a
+commit 8f6459497be0e9ca7dc3eb2eb9606e42d97ad60c
Author: Naohisa Goto <ng@bioruby.org>
-Date: Mon Dec 28 20:11:49 2009 +0900
+Date: Mon Jun 25 21:01:06 2012 +0900
- ChangeLog is autogenerated from git log.
+ rake tasks added and default task is changed
- * ChangeLog is autogenerated from git log with the following command:
- % git log --stat --summary \
- 3d1dfcc0e13ad582b9c70c7fdde3a89d0bacdc80..HEAD > ChangeLog
+ * New tasks:
+ * gem-install: build gem and install it
+ * gem-install-nodoc: build gem and install it with --no-ri --no-rdoc.
+ * gem-test: test installed bioruby gem installed with gem-install
+ (or gem-install-nodoc)
+ * gem-integration-test: build gem, install and run test (with --no-ri
+ --no-rdoc)
+ * tar-install: DANGER: build tar and install by using setup.rb
+ * installed-test: test installed bioruby
+ * tar-integration-test: DANGER: build tar, install and run test
+ * see-env: see BIORUBY_RAKE_DEFAULT_TASK environment variable and
+ invoke the specified task. If the variable did not exist, it
+ invokes "test" which is previously the default task. It is added
+ for selecting task on Travis-ci. It is not recommended to invoke
+ the task explicitly by hand.
+ * Default task is changed from "test" to "see-env".
- ChangeLog | 2306 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- 1 files changed, 2306 insertions(+), 0 deletions(-)
- create mode 100644 ChangeLog
+ Rakefile | 110 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++--
+ 1 files changed, 107 insertions(+), 3 deletions(-)
-commit 02bf77af589ea62df81e9634df6fe949df2fd3ef
+commit 3b400042cd361e1ab6d0fb0d8c8cce14a6c2ae10
Author: Naohisa Goto <ng@bioruby.org>
-Date: Mon Dec 28 19:25:39 2009 +0900
+Date: Mon Jun 25 20:58:13 2012 +0900
- test_output_size is disabled because it depends on html decorations
-
- test/functional/bio/appl/test_pts1.rb | 6 +++---
- 1 files changed, 3 insertions(+), 3 deletions(-)
-
-commit 5781fb402e85e73fd47948b4466c8129355b714b
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Mon Dec 28 19:21:21 2009 +0900
-
- The PTS1 Predictor's URL had been changed.
+ BIORUBY_TEST_LIB is always added on the top of $LOAD_PATH
- * The PTS1 Predictor's URL had been changed.
- * Changed to use @uri instead of @host and @cgi_path.
+ * When BIORUBY_TEST_LIB is specified, the specified directory name
+ is always added on the top of $LOAD_PATH even if it is already
+ included in the middle of $LOAD_PATH.
- lib/bio/appl/pts1.rb | 6 ++----
- 1 files changed, 2 insertions(+), 4 deletions(-)
+ test/bioruby_test_helper.rb | 4 ++--
+ 1 files changed, 2 insertions(+), 2 deletions(-)
-commit a4e691d913e1ae51eadb1a871efc2c8718ef5587
+commit 848304b6f90310f8fa15c80ba06655ae5cae5053
Author: Naohisa Goto <ng@bioruby.org>
-Date: Mon Dec 28 18:33:00 2009 +0900
+Date: Mon Jun 25 20:42:07 2012 +0900
- Preparation of ChangeLog autogeneration: old ChangeLog is moved to doc/ChangeLog-before-1.3.1.
-
- ChangeLog | 3961 --------------------------------------------
- doc/ChangeLog-before-1.3.1 | 3961 ++++++++++++++++++++++++++++++++++++++++++++
- 2 files changed, 3961 insertions(+), 3961 deletions(-)
- delete mode 100644 ChangeLog
- create mode 100644 doc/ChangeLog-before-1.3.1
-
-commit c011604766baa3cdf5ca2f4a776aa67c56460d29
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Mon Dec 28 17:53:51 2009 +0900
-
- Tutorial.rd.html is regenerated.
-
- doc/Tutorial.rd.html | 70 +++++++++++++------------------------------------
- 1 files changed, 19 insertions(+), 51 deletions(-)
-
-commit 6e2cdd13d61970aa4704475bfb5aefb70719c2e1
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Mon Dec 28 17:42:25 2009 +0900
-
- Added Bio::NCBI.default_email= in the example, and examples using deprecated Bio::PubMed methods are temporarily commented out.
-
- doc/Tutorial.rd | 8 ++++++++
- 1 files changed, 8 insertions(+), 0 deletions(-)
-
-commit 8e6d5e9baf98be7e58f4dda8b5d043a42149874b
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Mon Dec 28 17:15:09 2009 +0900
-
- Reinserted "==>" for Blast example, and removed duplicated Ruby Ensembl API example.
-
- doc/Tutorial.rd | 25 ++-----------------------
- 1 files changed, 2 insertions(+), 23 deletions(-)
-
-commit 849edd7e8c5b26923cab47e7f5542948fab2b1fb
-Author: Pjotr Prins <pjotr.public01@thebird.nl>
-Date: Sun Dec 27 09:49:14 2009 +0100
-
- Tutorial: Added info on how to run rubydoctest
- Removed bioruby> prefix for one failing BLAST test
-
- doc/Tutorial.rd | 69 ++++++++++++++++++++++++++++++++++++++----------------
- 1 files changed, 48 insertions(+), 21 deletions(-)
-
-commit a39fcf0ca1a5265789110f42cc616fc5d3c16414
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Fri Dec 25 12:30:18 2009 +0900
-
- Modified for release notes and fixed typo.
-
- RELEASE_NOTES.rdoc | 29 +++++++++++++++--------------
- 1 files changed, 15 insertions(+), 14 deletions(-)
-
-commit 3fa8b68f19fc2b6aaf8f54eb10517cc761b2193b
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Fri Dec 25 12:10:34 2009 +0900
-
- Changes following the rename to RELEASE_NOTES.rdoc.
-
- README.rdoc | 2 +-
- bioruby.gemspec | 6 +++---
- bioruby.gemspec.erb | 2 +-
- 3 files changed, 5 insertions(+), 5 deletions(-)
-
-commit fd692a1165d368b9bdbe068ea6bf63fd91c9925c
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Fri Dec 25 12:03:41 2009 +0900
-
- Renamed doc/Changes-1.4.rdoc to RELEASE_NOTES.rdoc.
-
- RELEASE_NOTES.rdoc | 160 ++++++++++++++++++++++++++++++++++++++++++++++++++
- doc/Changes-1.4.rdoc | 160 --------------------------------------------------
- 2 files changed, 160 insertions(+), 160 deletions(-)
- create mode 100644 RELEASE_NOTES.rdoc
- delete mode 100644 doc/Changes-1.4.rdoc
-
-commit 0e37f04dd8d34517693fdd4bc27f8bdada7c2f13
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Thu Dec 24 21:48:52 2009 +0900
-
- Changed Bio::PhyloXML::Parser.new to open, and regenerated html.
-
- doc/Tutorial.rd | 10 ++--
- doc/Tutorial.rd.html | 125 ++++++++++++++++++++++++++++++++++++++++++-------
- 2 files changed, 112 insertions(+), 23 deletions(-)
-
-commit aeacbbd425c2e88369c171bd92c60bf8e520a9e5
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Thu Dec 24 19:26:49 2009 +0900
-
- bioruby.gemspec is regenerated
-
- bioruby.gemspec | 8 +++++++-
- 1 files changed, 7 insertions(+), 1 deletions(-)
-
-commit 1034205c199a638c359780922293f8b39c467356
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Thu Dec 24 19:24:56 2009 +0900
-
- Version number changed to 1.4.0-rc1
-
- lib/bio/version.rb | 2 +-
- 1 files changed, 1 insertions(+), 1 deletions(-)
-
-commit 04bf2da43f78fbb702b67323f3be1fe3bd2d0351
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Thu Dec 24 19:22:41 2009 +0900
-
- Issues added and modified.
-
- KNOWN_ISSUES.rdoc | 35 +++++++++++++++++++++++++++++++++--
- 1 files changed, 33 insertions(+), 2 deletions(-)
-
-commit f1a76157b009fb0ca94d9a0e0f8a85522c383b19
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Thu Dec 24 19:22:19 2009 +0900
-
- Added news and incompatible changes.
-
- doc/Changes-1.4.rdoc | 102 ++++++++++++++++++++++++++++++++++++++++++++++++--
- 1 files changed, 98 insertions(+), 4 deletions(-)
-
-commit 9c8ef18a20c49f17d5b89aa1db5819b2c8ee9b1d
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Thu Dec 24 19:10:02 2009 +0900
-
- Email address for NCBI Entrez is given with Bio::NCBI.default_email=.
-
- bin/bioruby | 5 ++++-
- sample/demo_ncbi_rest.rb | 2 ++
- sample/demo_pubmed.rb | 2 ++
- sample/pmfetch.rb | 2 ++
- sample/pmsearch.rb | 2 ++
- test/functional/bio/io/test_pubmed.rb | 4 ++++
- 6 files changed, 16 insertions(+), 1 deletions(-)
-
-commit 7a7179665694da35ab0970909bfbda9ad1b057da
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Thu Dec 24 19:09:09 2009 +0900
-
- Changed autoload hierarchy of Bio::NCBI.
-
- lib/bio.rb | 10 ++++++----
- lib/bio/io/ncbisoap.rb | 3 ++-
- 2 files changed, 8 insertions(+), 5 deletions(-)
-
-commit f8dc0268d9edf699fd3f0cf18dd55a2b10ec3bcc
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Thu Dec 24 18:58:18 2009 +0900
-
- New singleton methods Bio::NCBI.default_email=, default_tool=, etc.
+ New env BIORUBY_TEST_GEM and BIORUBY_TEST_LIB behavior changed
- * New singleton methods Bio::NCBI.default_email=, default_email,
- default_tools=, default_tools, etc., because email and tool
- parameters will be mandatory in Entrez eUtils.
- * Changed to raise error when email or tool is empty. Note that
- default email is nil and library users should always set their
- email address.
- * Default tool name is changed to include $0 and bioruby version ID.
- * Added multi-thread support for Bio::NCBI::REST#ncbi_access_wait.
+ * New environment variable BIORUBY_TEST_GEM for testing installed
+ bio-X.X.X gem. Version number can be specified.
+ Example with version number:
+ % env BIORUBY_TEST_GEM=1.4.2.5000 ruby test/runner.rb
+ Example without version number:
+ % env BIORUBY_TEST_GEM="" ruby test/runner.rb
+ * When BIORUBY_TEST_LIB is empty, it no longer add an empty string to
+ $LOAD_PATH. Moreover, when BIORUBY_TEST_GEM is set, the variable is
+ ignored.
- lib/bio/io/ncbirest.rb | 161 ++++++++++++++++++++++++++++++++++++++---------
- 1 files changed, 130 insertions(+), 31 deletions(-)
+ test/bioruby_test_helper.rb | 49 ++++++++++++++++++++++++++++++++----------
+ 1 files changed, 37 insertions(+), 12 deletions(-)
-commit 2e311dc44290ef6bda48f0bcba09a3c22bf32d9a
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Mon Dec 21 22:24:52 2009 +0900
+commit 9453a6773c24f866698370195fd8e767443a38b9
+Author: Tomoaki NISHIYAMA <tomoakin@kenroku.kanazawa-u.ac.jp>
+Date: Fri Jun 1 18:06:40 2012 +0900
- Description about the incompatible change of Bio::KEGG::REACTION#rpairs.
-
- doc/Changes-1.4.rdoc | 6 +++---
- 1 files changed, 3 insertions(+), 3 deletions(-)
-
-commit d57ace3a89077caae3c681743da4b92d16b90af8
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Mon Dec 21 22:17:46 2009 +0900
-
- Bio::KEGG::R#ACTION#rpairs is changed to return a hash.
-
- lib/bio/db/kegg/reaction.rb | 65 ++++++++++++++++++++++++--------
- test/unit/bio/db/kegg/test_reaction.rb | 27 ++++++++++++-
- 2 files changed, 74 insertions(+), 18 deletions(-)
-
-commit 60e4c77d184ee81c51668b446518cfbc9256be50
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Mon Dec 21 22:15:44 2009 +0900
-
- Document bug fix: return value mistake.
-
- lib/bio/db/kegg/genes.rb | 2 +-
- 1 files changed, 1 insertions(+), 1 deletions(-)
-
-commit 6376dd55aa4995769746e556ca719d37f02975d6
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Sun Dec 20 17:32:52 2009 +0900
-
- Added README.txt for FASTQ example data.
-
- test/data/fastq/README.txt | 109 ++++++++++++++++++++++++++++++++++++++++++++
- 1 files changed, 109 insertions(+), 0 deletions(-)
- create mode 100644 test/data/fastq/README.txt
-
-commit 8dec18794c846726733d66c5a22170f5b2c4bb1a
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Tue Dec 15 13:51:13 2009 +0900
-
- Newly added unit tests for Bio::KEGG::GLYCAN with test data.
-
- test/data/KEGG/G00024.glycan | 47 ++++++
- test/data/KEGG/G01366.glycan | 18 +++
- test/unit/bio/db/kegg/test_glycan.rb | 260 ++++++++++++++++++++++++++++++++++
- 3 files changed, 325 insertions(+), 0 deletions(-)
- create mode 100644 test/data/KEGG/G00024.glycan
- create mode 100644 test/data/KEGG/G01366.glycan
- create mode 100644 test/unit/bio/db/kegg/test_glycan.rb
-
-commit 90b97bfbcfb3f7e3d5c28b195bdb9b9c058df887
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Tue Dec 15 11:42:39 2009 +0900
-
- Newly added unit test for Bio::KEGG::DRUG with test data.
-
- test/data/KEGG/D00063.drug | 104 +++++++++++++++++++
- test/unit/bio/db/kegg/test_drug.rb | 194 ++++++++++++++++++++++++++++++++++++
- 2 files changed, 298 insertions(+), 0 deletions(-)
- create mode 100644 test/data/KEGG/D00063.drug
- create mode 100644 test/unit/bio/db/kegg/test_drug.rb
-
-commit 443f778795b82a7f572cb8b85d2a8a8b3cea1334
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Tue Dec 15 11:38:59 2009 +0900
-
- New method Bio::KEGG::DRUG#products
+ broader FASTQ file recognition
- * New method Bio::KEGG::DRUG#products.
- * Improved RDoc.
+ * Because PacBio RS sequencer may produce kilobases long reads and
+ read buffer size (default 31 lines) for file format detection
+ may not be sufficient to find the second id line starting with "+",
+ the regular expression for FASTQ is truncated only to check the
+ first id line starting with "@".
+ * Test code is added.
- lib/bio/db/kegg/drug.rb | 50 +++++++++++++++++++++++++++++++++++++---------
- 1 files changed, 40 insertions(+), 10 deletions(-)
+ lib/bio/io/flatfile/autodetection.rb | 2 +-
+ test/unit/bio/io/flatfile/test_autodetection.rb | 6 ++++++
+ 2 files changed, 7 insertions(+), 1 deletions(-)
-commit 48184d96b989f909ac0effb759cbc4b1ddc98dd1
+commit 120e780c023cba06b83899c2f8a17c8fc1de4faa
Author: Naohisa Goto <ng@bioruby.org>
-Date: Fri Dec 11 01:36:54 2009 +0900
+Date: Fri Jun 8 15:36:29 2012 +0900
- Methods in Bio::KEGG::Common::* are changed to cache return values in instance variables.
-
- lib/bio/db/kegg/common.rb | 62 ++++++++++++++++++++++++++------------------
- 1 files changed, 37 insertions(+), 25 deletions(-)
-
-commit f364ea609f1e01ca5270a5bd7404e0bbf752bc89
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Fri Dec 11 01:23:42 2009 +0900
-
- Version is changed to 1.4.0-alpha1, and bioruby.gemspec is regenerated.
-
- bioruby.gemspec | 142 ++++++++++++++++++++++++++++++++++++++++++++++++++-
- bioruby.gemspec.erb | 4 +-
- lib/bio/version.rb | 4 +-
- 3 files changed, 145 insertions(+), 5 deletions(-)
-
-commit 096b5fbf6b7ff906203aabf93eb9a0bd56ae9ba2
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Fri Dec 11 01:22:59 2009 +0900
-
- Added documents about Bio::KEGG incompatible changes.
-
- doc/Changes-1.4.rdoc | 48 ++++++++++++++++++++++++++++++++++++++++++------
- 1 files changed, 42 insertions(+), 6 deletions(-)
-
-commit 72ed277fe30bb1033cbc16d462f137510afb84e6
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Fri Dec 11 01:21:26 2009 +0900
-
- Newly added unit tests for Bio::KEGG::ENZYME with test data.
-
- test/data/KEGG/1.1.1.1.enzyme | 935 ++++++++++++++++++++++++++++++++++
- test/unit/bio/db/kegg/test_enzyme.rb | 241 +++++++++
- 2 files changed, 1176 insertions(+), 0 deletions(-)
- create mode 100644 test/data/KEGG/1.1.1.1.enzyme
- create mode 100644 test/unit/bio/db/kegg/test_enzyme.rb
-
-commit b99fcb39f7c5d2857cbb65283d85ea868ae8561d
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Fri Dec 11 01:09:03 2009 +0900
-
- Changed Bio::KEGG::*#dblinks, pathways, orthologs, genes methods.
+ Retry sequence randomize test up to 10 times when fails
- * In Bio::KEGG::COMPOUND, DRUG, ENZYME, GLYCAN and ORTHOLOGY, the
- method dblinks is changed to return a Hash. The old methods are
- renamed to dblinks_as_strings.
- * In Bio::KEGG::COMPOUND, DRUG, ENZYME, GENES, GLYCAN and REACTION,
- the method pathways is changed to return a Hash. The old methods
- are renamed to pathways_as_strings except for GENES.
- * In Bio::KEGG::ENZYME, GENES, GLYCAN and REACTION, the method
- orthologs is changed to return a Hash. The old methods are renamed
- to orthologs_as_strings.
- * Bio::KEGG::ENZYME#genes and Bio::KEGG::ORTHOLOGY#genes is changed
- to return a Hash. The old methods are renamed to genes_as_strings.
- * Added Bio::KEGG::REACTION#rpairs_as_tokens, older behavior of rpairs.
- * Modules in lib/bio/db/kegg/common.rb are moved uner Bio::KEGG::Common
- namespace.
- * Refactoring.
- * Added documents.
- * Tests modified.
+ * To suppress rare failure of chi-square equiprobability tests for
+ Bio::Sequence::Common#randomize, test code changed to retry
+ up to 10 times if the chi-square test fails. The assertion fails
+ if the chi-square test fails 10 consecutive times, and this
+ strongly suggests bugs in codes or in the random number generator.
+ * The chi-square equiprobability tests are separated into a new
+ test class.
- lib/bio/db/kegg/common.rb | 40 +++++++++++++++++++++++++------
- lib/bio/db/kegg/compound.rb | 10 ++++---
- lib/bio/db/kegg/drug.rb | 27 +++++++++++++++------
- lib/bio/db/kegg/enzyme.rb | 31 ++++++++++++++++++++----
- lib/bio/db/kegg/genes.rb | 39 +++++++++++++++++++------------
- lib/bio/db/kegg/glycan.rb | 22 +++++++++++++++--
- lib/bio/db/kegg/orthology.rb | 25 +++++++------------
- lib/bio/db/kegg/reaction.rb | 16 +++++++++---
- test/unit/bio/db/kegg/test_compound.rb | 27 ++++++++++++--------
- test/unit/bio/db/kegg/test_reaction.rb | 13 +++++----
- 10 files changed, 170 insertions(+), 80 deletions(-)
+ test/unit/bio/sequence/test_common.rb | 40 +++++++++++++++++++++++++++++---
+ 1 files changed, 36 insertions(+), 4 deletions(-)
-commit 2cc9d4e2f28f6b2bbcb8f714f9e2eb144c594fbf
+commit 20dde52f7da784d4d9ac551957700cd96e842ef6
Author: Naohisa Goto <ng@bioruby.org>
-Date: Thu Dec 10 16:02:54 2009 +0900
+Date: Sat May 19 18:14:19 2012 +0900
- Bio::KEGG::GENES#structure no more adds PDB: prefix.
-
- * Bio::KEGG::GENES#structure no more adds PDB: prefix.
- * Added Bio::KEGG::GENES#structures as an alias of structure.
+ libxml-ruby is disabled because of build error on Travis-ci
- lib/bio/db/kegg/genes.rb | 7 +++----
- test/unit/bio/db/kegg/test_genes.rb | 7 ++++---
- 2 files changed, 7 insertions(+), 7 deletions(-)
+ gemfiles/Gemfile.travis-jruby1.8 | 3 ++-
+ gemfiles/Gemfile.travis-jruby1.9 | 3 ++-
+ 2 files changed, 4 insertions(+), 2 deletions(-)
-commit a8ceb23bdf19d6649aa4d879cba76a9e3f91d1d4
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Thu Dec 10 15:28:33 2009 +0900
+commit 3c5c1cc277d30737815c7e44a2abbb308f5324b0
+Author: Clayton Wheeler <cswh@umich.edu>
+Date: Mon May 14 21:48:41 2012 -0400
- Refactoring of Bio::KEGG::Orthology#dblinks and genes.
+ Use libxml-ruby instead of libxml-jruby to fix JRuby test failures.
- * Refactoring of Bio::KEGG::Orthology#dblinks and genes: no need
- to treat @data because lines_fetch internally does so.
-
- lib/bio/db/kegg/orthology.rb | 10 ++--------
- 1 files changed, 2 insertions(+), 8 deletions(-)
-
-commit 720e0bccdfdc6fac6222cac1a9f05d6e2419896c
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Wed Dec 9 16:39:03 2009 +0900
-
- Changed dummy lines for RDoc.
-
- lib/bio/db/kegg/compound.rb | 4 ++--
- lib/bio/db/kegg/orthology.rb | 2 +-
- lib/bio/db/kegg/reaction.rb | 4 ++--
- 3 files changed, 5 insertions(+), 5 deletions(-)
-
-commit 20f8c03af92e5cfedcb49e8ed9fc6fda2b86e9c9
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Wed Dec 9 15:17:39 2009 +0900
-
- Refactoring of Bio::KEGG::REACTION#orthologs.
+ The travis-ci Gemfiles currently call for libxml-jruby; this appears
+ not to support the same API as libxml-ruby, resulting in several tests
+ in test/unit/bio/db/test_phyloxml.rb failing with "NameError:
+ uninitialized constant LibXMLJRuby::XML::Parser::Options". Switching
+ to the C libxml-ruby library allows these tests to pass under JRuby in
+ 1.8 mode.
- * Refactoring of Bio::KEGG::REACTION#orthologs: no need to treat
- @data because lines_fetch internally does so.
+ JRuby in 1.9 mode still fails a few PhyloXML tests due to
+ https://jira.codehaus.org/browse/JRUBY-6662.
- lib/bio/db/kegg/reaction.rb | 5 +----
- 1 files changed, 1 insertions(+), 4 deletions(-)
+ gemfiles/Gemfile.travis-jruby1.8 | 2 +-
+ gemfiles/Gemfile.travis-jruby1.9 | 2 +-
+ 2 files changed, 2 insertions(+), 2 deletions(-)
-commit b924601bacd643f66b37dd991913e6862df704a9
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Sun Dec 6 15:51:03 2009 +0900
+commit 01a618242d67f0d00fe681dfd85e68bb393513fc
+Author: Clayton Wheeler <cswh@umich.edu>
+Date: Thu May 10 23:13:56 2012 -0400
- Bio::KEGG::GENES#pathways is changed to return raw lines as an Array of strings.
-
- * Bio::KEGG::GENES#pathways is changed to return raw lines as an
- Array of strings.
- * RDoc is added for Bio::KEGG::GENES.
+ test_tree.rb: to use %f instead of %g to prevent odd behavior.
- lib/bio/db/kegg/genes.rb | 99 ++++++++++++++++++++++++++++++++++++++++++++-
- 1 files changed, 96 insertions(+), 3 deletions(-)
+ test/unit/bio/test_tree.rb | 22 +++++++++++-----------
+ 1 files changed, 11 insertions(+), 11 deletions(-)
-commit 4c840dc6a539db1d854b23991269b3e6515f637e
-Author: Kozo Nishida <kozo-ni@cg05.naist.jp>
-Date: Wed Dec 2 17:02:00 2009 +0900
+commit 5e80e4394bf2a5e4ee472fe84ab76239b293e1b5
+Author: Clayton Wheeler <cswh@umich.edu>
+Date: Thu May 10 23:04:55 2012 -0400
- Added test methods.
+ Fixed spurious JRuby failures in test_tree.rb due to floating point differences.
- test/unit/bio/db/kegg/test_compound.rb | 47 ++++++++++++++++++++++++++++++++
- 1 files changed, 47 insertions(+), 0 deletions(-)
+ test/unit/bio/test_tree.rb | 14 +++++++-------
+ 1 files changed, 7 insertions(+), 7 deletions(-)
-commit 105efa1ecd1bc99a54aac32710a97df15035119d
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Wed Dec 2 23:31:07 2009 +0900
+commit 459d4da894e9a9b9db0d793e3711dc45bae2089b
+Author: Artem Tarasov <lomereiter@gmail.com>
+Date: Thu May 10 16:23:13 2012 +0400
- Refactoring: to use lib/bio/db/kegg/common.rb for dblinks_as_hash method.
-
- lib/bio/db/kegg/orthology.rb | 16 +++++-----------
- 1 files changed, 5 insertions(+), 11 deletions(-)
-
-commit c394ead051c3a13ceb534f93816af7ad35be932a
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Wed Dec 2 23:07:23 2009 +0900
-
- Bio::KEGG::REACTION#orthologies is renamed to orthologs_as_hash with changing its return value to a hash.
+ Test bug fix: order of hash keys are not guaranteed
- * Bio::KEGG::REACTION#orthologies is renamed to orthologs_as_hash
- with changing its return value to a hash.
- * The code of the orthologs_as_hash method is moved to
- lib/bio/db/kegg/common.rb.
- * Added new method Bio::KEGG::REACTION#orthologs, copied from
- lib/bio/db/kegg/glycan.rb.
+ * Test bug fix: Bio::TestSOFT#test_dataset: order of hash keys are
+ not guaranteed.
- lib/bio/db/kegg/common.rb | 18 +++++++++++++++++-
- lib/bio/db/kegg/reaction.rb | 14 ++++++--------
- sample/demo_kegg_reaction.rb | 6 ++++--
- test/unit/bio/db/kegg/test_reaction.rb | 12 ++++++++++--
- 4 files changed, 37 insertions(+), 13 deletions(-)
-
-commit 4e01fda27166faf066104ab9897904fd46f57123
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Wed Dec 2 22:48:06 2009 +0900
-
- Added Bio::KEGG::REACTION#pathways_as_hash and reverted pathways method.
-
- * New method Bio::KEGG::REACTION#pathways_as_hash, using a module
- in lib/bio/db/kegg/common.rb.
- * Bio::KEGG::REACTION#pathways is reverted to return an array of
- string.
-
- lib/bio/db/kegg/reaction.rb | 18 +++++++++++-------
- test/unit/bio/db/kegg/test_reaction.rb | 8 +++++++-
- 2 files changed, 18 insertions(+), 8 deletions(-)
-
-commit 0c2ce4b8462792d496ab3f58206fdbd47143e280
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Wed Dec 2 22:35:21 2009 +0900
-
- New methods Bio::KEGG::COMPOUND#dblinks_as_hash and pathways_as_hash, using modules in lib/bio/db/kegg/common.rb.
-
- lib/bio/db/kegg/compound.rb | 14 +++++++++++
- test/unit/bio/db/kegg/test_compound.rb | 38 ++++++++++++++++++++++++++++++++
- 2 files changed, 52 insertions(+), 0 deletions(-)
-
-commit 63df07e030120eb43de22555277529822b072270
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Wed Dec 2 22:25:20 2009 +0900
-
- Methods commonly used from Bio::KEGG::* classes.
-
- * Modules containing methods commonly used from Bio::KEGG::* classes.
- The "dblinks_as_hash" method is copied from
- lib/bio/db/kegg/orthology.rb. The "pathways_as_hash" method is
- derived from the dblinks_as_hash and Bio::KEGG::REACTION#pathways
- methods.
-
- lib/bio/db/kegg/common.rb | 60 +++++++++++++++++++++++++++++++++++++++++++++
- 1 files changed, 60 insertions(+), 0 deletions(-)
- create mode 100644 lib/bio/db/kegg/common.rb
-
-commit 0e55c6701b09a52356ac55300181ee656773826f
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Wed Dec 2 21:39:06 2009 +0900
-
- Bio::KEGG::COMPOUND#dblinks is reverted to return an array of string.
-
- lib/bio/db/kegg/compound.rb | 11 ++---------
- test/unit/bio/db/kegg/test_compound.rb | 8 +++++++-
- 2 files changed, 9 insertions(+), 10 deletions(-)
-
-commit a05adcddf6c7ed67c042f31ecd86848af1ba8a22
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Wed Dec 2 21:13:39 2009 +0900
-
- Bug fix: fixed a copy-and-paste mistake.
-
- lib/bio/db/kegg/drug.rb | 2 +-
+ test/unit/bio/db/test_soft.rb | 2 +-
1 files changed, 1 insertions(+), 1 deletions(-)
-commit 86925f3c80730e3ea3377a23a70cadb3876258c4
+commit 7e730691d6ec597a610dc0d4665db3598fcfde59
Author: Naohisa Goto <ng@bioruby.org>
-Date: Tue Dec 1 21:31:40 2009 +0900
+Date: Thu May 10 00:06:19 2012 +0900
- Bio::KEGG::ORTHOLOGY#dblinks_as_hash should preserve database names.
+ removed potential circular require about Bio::Sequence::Format
- doc/Changes-1.4.rdoc | 4 ++++
- lib/bio/db/kegg/orthology.rb | 2 +-
- test/unit/bio/db/kegg/test_orthology.rb | 2 +-
- 3 files changed, 6 insertions(+), 2 deletions(-)
+ lib/bio/db/embl/format_embl.rb | 4 ----
+ lib/bio/db/fasta/format_fasta.rb | 4 ----
+ lib/bio/db/fasta/format_qual.rb | 5 -----
+ lib/bio/db/fastq/format_fastq.rb | 1 -
+ lib/bio/db/genbank/format_genbank.rb | 4 ----
+ lib/bio/sequence/format_raw.rb | 4 ----
+ 6 files changed, 0 insertions(+), 22 deletions(-)
-commit 60847cd2d0701fa38a499578649cb216c93993a2
+commit f1c398fdc3488bd18bd13ac864920ce6db4dab9e
Author: Naohisa Goto <ng@bioruby.org>
-Date: Tue Dec 1 20:41:51 2009 +0900
+Date: Wed May 9 15:54:20 2012 +0900
- Test class names are changed to avoid potential class name conflict.
-
- test/unit/bio/db/kegg/test_compound.rb | 2 +-
- test/unit/bio/db/kegg/test_genes.rb | 4 ++--
- test/unit/bio/db/kegg/test_orthology.rb | 2 +-
- test/unit/bio/db/kegg/test_reaction.rb | 2 +-
- 4 files changed, 5 insertions(+), 5 deletions(-)
-
-commit 2bda62af7a020c22379dd9ec3a42496d2a5b94cb
-Author: Kozo Nishida <kozo-ni@cg05.naist.jp>
-Date: Tue Dec 1 04:38:27 2009 +0900
-
- Added unit tests for Bio::KEGG::ORTHOLOGY.
-
- test/data/KEGG/K02338.orthology | 902 +++++++++++++++++++++++++++++++
- test/unit/bio/db/kegg/test_orthology.rb | 50 ++
- 2 files changed, 952 insertions(+), 0 deletions(-)
- create mode 100644 test/data/KEGG/K02338.orthology
- create mode 100644 test/unit/bio/db/kegg/test_orthology.rb
-
-commit acad9497caf5d737394568e911691fdad11ca091
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Mon Nov 30 21:39:32 2009 +0900
-
- Changed to use BioRubyTestDataPath instead of __FILE__.
-
- test/unit/bio/db/kegg/test_compound.rb | 3 +--
- test/unit/bio/db/kegg/test_reaction.rb | 3 +--
- 2 files changed, 2 insertions(+), 4 deletions(-)
-
-commit 8e95f3fb60cd61b2bfad8e66caf03d3ff02a6dca
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Sun Nov 29 16:37:21 2009 +0900
-
- Bio::Fastq::QualityScore is renamed to Bio::Sequence::QualityScore.
+ .travis.yml: comment out apt-get lines
- * Bio::Fastq::QualityScore is renamed to Bio::Sequence::QualityScore.
- * Changes of filenames due to the previous file move.
+ * .travis.yml: comment out apt-get lines because libxml2-dev
+ and libexpat1-dev are already installed.
- lib/bio/db/fasta/format_qual.rb | 18 ++++++++--------
- lib/bio/db/fastq.rb | 7 ++---
- lib/bio/sequence.rb | 3 +-
- lib/bio/sequence/quality_score.rb | 25 +++++++++++------------
- test/unit/bio/sequence/test_quality_score.rb | 28 +++++++++++++-------------
- 5 files changed, 40 insertions(+), 41 deletions(-)
+ .travis.yml | 6 +++---
+ 1 files changed, 3 insertions(+), 3 deletions(-)
-commit 2b29654c1d7e927e445e7acdd525835a873c2a2a
+commit bc5ef4959e51f4a199d9f740b07812e9b8216255
Author: Naohisa Goto <ng@bioruby.org>
-Date: Sun Nov 29 16:15:42 2009 +0900
+Date: Wed May 9 15:47:11 2012 +0900
- lib/bio/db/fastq/quality_score.rb is moved to lib/bio/sequence/. The unit test is also moved.
+ travis-ci: comment out soap4r-ruby1.9 in Gemfile because of error
- * lib/bio/db/fastq/quality_score.rb is moved to lib/bio/sequence/.
- * test/unit/bio/db/fastq/test_quality_score.rb is moved to
- test/unit/bio/sequence/.
- * The file contents will be modified with the following commit.
+ * travis-ci: soap4r-ruby1.9 gem in Gemfile.travis-ruby1.9 and
+ Gemfile.travis-jruby1.9 is commented out because of an error
+ "uninitialized constant XML::SaxParser".
- lib/bio/db/fastq/quality_score.rb | 206 ----------------
- lib/bio/sequence/quality_score.rb | 206 ++++++++++++++++
- test/unit/bio/db/fastq/test_quality_score.rb | 330 --------------------------
- test/unit/bio/sequence/test_quality_score.rb | 330 ++++++++++++++++++++++++++
- 4 files changed, 536 insertions(+), 536 deletions(-)
- delete mode 100644 lib/bio/db/fastq/quality_score.rb
- create mode 100644 lib/bio/sequence/quality_score.rb
- delete mode 100644 test/unit/bio/db/fastq/test_quality_score.rb
- create mode 100644 test/unit/bio/sequence/test_quality_score.rb
+ gemfiles/Gemfile.travis-jruby1.9 | 4 +++-
+ gemfiles/Gemfile.travis-ruby1.9 | 4 +++-
+ 2 files changed, 6 insertions(+), 2 deletions(-)
-commit aa8d49bf31f90dd2796c18ee0aa6291979284ec2
+commit 7e8153c09660c31d6286c1924680b8c5073a10b6
Author: Naohisa Goto <ng@bioruby.org>
-Date: Sun Nov 29 15:20:36 2009 +0900
+Date: Tue May 1 18:11:09 2012 +0900
- Demo codes in the "if __FILE__ == $0" are moved to sample/demo_gff1.rb.
+ config files for Travis CI continuous integration service
- lib/bio/db/gff.rb | 17 -----------------
- sample/demo_gff1.rb | 49 +++++++++++++++++++++++++++++++++++++++++++++++++
- 2 files changed, 49 insertions(+), 17 deletions(-)
- create mode 100644 sample/demo_gff1.rb
+ .travis.yml | 73 ++++++++++++++++++++++++++++++++++++++
+ gemfiles/Gemfile.travis-jruby1.8 | 6 +++
+ gemfiles/Gemfile.travis-jruby1.9 | 7 ++++
+ gemfiles/Gemfile.travis-ruby1.8 | 7 ++++
+ gemfiles/Gemfile.travis-ruby1.9 | 8 ++++
+ 5 files changed, 101 insertions(+), 0 deletions(-)
+ create mode 100644 .travis.yml
+ create mode 100644 gemfiles/Gemfile.travis-jruby1.8
+ create mode 100644 gemfiles/Gemfile.travis-jruby1.9
+ create mode 100644 gemfiles/Gemfile.travis-ruby1.8
+ create mode 100644 gemfiles/Gemfile.travis-ruby1.9
-commit 76fffd2d2429346478fb3d8c88cdcd878a1047b1
+commit f1ecae7763648cb735a885ddb6c46d71c59b0694
Author: Naohisa Goto <ng@bioruby.org>
-Date: Sun Nov 29 15:06:41 2009 +0900
+Date: Fri Mar 23 01:36:59 2012 +0900
- Demo codes in the "if __FILE__ == $0" are moved to sample/demo_tmhmm_report.rb.
+ Test bug fix: tests affected by the bug of Bio::NucleicAcid.to_re("s")
- lib/bio/appl/tmhmm/report.rb | 36 ----------------------
- sample/demo_tmhmm_report.rb | 68 ++++++++++++++++++++++++++++++++++++++++++
- 2 files changed, 68 insertions(+), 36 deletions(-)
- create mode 100644 sample/demo_tmhmm_report.rb
+ test/unit/bio/data/test_na.rb | 2 +-
+ test/unit/bio/sequence/test_na.rb | 2 +-
+ test/unit/bio/test_sequence.rb | 4 ++--
+ 3 files changed, 4 insertions(+), 4 deletions(-)
-commit dfafb0a2bcec4c0b4cd3640374e151e2039056dc
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Sun Nov 29 14:59:27 2009 +0900
+commit 3fd9384b1b59140a929c81dcc4b07cb3c2e47525
+Author: Trevor Wennblom <trevor@well.com>
+Date: Sat Feb 25 15:26:27 2012 -0600
- Demo codes in the "if __FILE__ == $0" are moved to sample/demo_targetp_report.rb.
+ Bug fix: Bio::NucleicAcid.to_re("s") typo
- lib/bio/appl/targetp/report.rb | 105 +------------------------------
- sample/demo_targetp_report.rb | 135 ++++++++++++++++++++++++++++++++++++++++
- 2 files changed, 136 insertions(+), 104 deletions(-)
- create mode 100644 sample/demo_targetp_report.rb
-
-commit 75f7c8527546f8ea3079f53b90a9b4d8260b4de0
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Sun Nov 29 14:33:28 2009 +0900
-
- Follow-up of the SOSUI server URL change.
-
- lib/bio/appl/sosui/report.rb | 6 ++++--
- 1 files changed, 4 insertions(+), 2 deletions(-)
-
-commit 8022696295dc296462f73b40cc74ad5259bee387
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Sun Nov 29 14:32:11 2009 +0900
-
- Demo codes in the "if __FILE__ == $0" are moved to sample/demo_sosui_report.rb.
-
- lib/bio/appl/sosui/report.rb | 53 +------------------------
- sample/demo_sosui_report.rb | 89 ++++++++++++++++++++++++++++++++++++++++++
- 2 files changed, 90 insertions(+), 52 deletions(-)
- create mode 100644 sample/demo_sosui_report.rb
-
-commit 4acfe7f565039b34a036682912a75f55da808b45
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Sun Nov 29 14:02:32 2009 +0900
-
- Demo codes in the "if __FILE__ == $0" are moved to sample/demo_hmmer_report.rb.
-
- lib/bio/appl/hmmer/report.rb | 100 ----------------------------
- sample/demo_hmmer_report.rb | 149 ++++++++++++++++++++++++++++++++++++++++++
- 2 files changed, 149 insertions(+), 100 deletions(-)
- create mode 100644 sample/demo_hmmer_report.rb
-
-commit 4f7bd1b7628d90661d8b557ca854b14cc44fb99c
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Thu Nov 26 15:49:21 2009 +0900
-
- Demo codes in the "if __FILE__ == $0" are removed because they are very short.
-
- lib/bio/appl/fasta/format10.rb | 14 --------------
- lib/bio/appl/hmmer.rb | 16 +---------------
- lib/bio/io/flatfile.rb | 8 +-------
- 3 files changed, 2 insertions(+), 36 deletions(-)
-
-commit c2a72d195189755532e7e206af34d152ab6332d8
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Thu Nov 26 15:20:28 2009 +0900
-
- Bug fix: Failure of Bio::Fasta.remote due to the remote site changes.
-
- lib/bio/appl/fasta.rb | 5 ++++-
- 1 files changed, 4 insertions(+), 1 deletions(-)
-
-commit 549112fb4dfb5f6b2fe3491fb161887a9f5262ac
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Thu Nov 26 15:13:10 2009 +0900
-
- Demo codes in the "if __FILE__ == $0" are moved to sample/demo_fasta_remote.rb.
-
- lib/bio/appl/fasta.rb | 18 ---------------
- sample/demo_fasta_remote.rb | 51 +++++++++++++++++++++++++++++++++++++++++++
- 2 files changed, 51 insertions(+), 18 deletions(-)
- create mode 100644 sample/demo_fasta_remote.rb
-
-commit 0e4ca0db83692fdbbe93e90272a07bcbac89192c
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Thu Nov 26 10:17:47 2009 +0900
-
- Text indents for some comment lines are changed.
-
- sample/demo_blast_report.rb | 4 ++--
- sample/demo_kegg_compound.rb | 4 ++--
- sample/demo_prosite.rb | 4 ++--
- sample/demo_sirna.rb | 4 ++--
- 4 files changed, 8 insertions(+), 8 deletions(-)
-
-commit c0cf91fe2a9247bc3705b20515f9d4fa14288d5a
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Thu Nov 26 10:13:26 2009 +0900
-
- Demo codes in the "if __FILE__ == $0" are moved to sample/demo_keggapi.rb.
-
- * Demo codes in the "if __FILE__ == $0" are moved to
- sample/demo_keggapi.rb.
- * Commented out demonstrations of deprecated methods:
- get_neighbors_by_gene, get_similarity_between_genes,
- get_ko_members, get_oc_members_by_gene, get_pc_members_by_gene.
- * Commented out demonstrations of methods internally using
- the deprecated methods: get_all_neighbors_by_gene,
- get_all_oc_members_by_gene, get_all_pc_members_by_gene.
-
- lib/bio/io/keggapi.rb | 442 ------------------------------------------
- sample/demo_keggapi.rb | 502 ++++++++++++++++++++++++++++++++++++++++++++++++
- 2 files changed, 502 insertions(+), 442 deletions(-)
- create mode 100644 sample/demo_keggapi.rb
-
-commit 8b8206c1d8ee699185fdd19d3329311c85ee003c
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Thu Nov 26 01:50:06 2009 +0900
-
- Fixed the license line.
-
- lib/bio/db/prosite.rb | 2 +-
+ lib/bio/data/na.rb | 2 +-
1 files changed, 1 insertions(+), 1 deletions(-)
-commit ebfeec8243abd4e2f65335fda1ead18efff66897
+commit c552aa3a6773139b14ae95e79e0fb43a2f91c6fb
Author: Naohisa Goto <ng@bioruby.org>
-Date: Thu Nov 26 01:41:58 2009 +0900
+Date: Thu Jan 12 22:24:37 2012 +0900
- Demo codes in the "if __FILE__ == $0" are moved to sample/demo_ncbi_rest.rb.
-
- lib/bio/io/ncbirest.rb | 101 ------------------------------------
- sample/demo_ncbi_rest.rb | 128 ++++++++++++++++++++++++++++++++++++++++++++++
- 2 files changed, 128 insertions(+), 101 deletions(-)
- create mode 100644 sample/demo_ncbi_rest.rb
-
-commit 5a0f8379a374650d12fc88fbbd5b28c38ae96395
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Thu Nov 26 01:33:07 2009 +0900
-
- Demo codes in the "if __FILE__ == $0" are moved to sample/demo_prosite.rb.
-
- lib/bio/db/prosite.rb | 95 +-------------------------------------
- sample/demo_prosite.rb | 120 ++++++++++++++++++++++++++++++++++++++++++++++++
- 2 files changed, 121 insertions(+), 94 deletions(-)
- create mode 100644 sample/demo_prosite.rb
-
-commit c560a5d0ba9d4919dbcca156ea620056dcb8f725
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Thu Nov 26 01:14:37 2009 +0900
-
- Demo codes in the "if __FILE__ == $0" are moved to sample/demo_psort.rb.
-
- lib/bio/appl/psort.rb | 111 ---------------------------------------
- sample/demo_psort.rb | 138 +++++++++++++++++++++++++++++++++++++++++++++++++
- 2 files changed, 138 insertions(+), 111 deletions(-)
- create mode 100644 sample/demo_psort.rb
-
-commit 1299a55d214784a536ae3cd8bfabdfd61fe1da86
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Thu Nov 26 01:04:29 2009 +0900
-
- Demo codes in the "if __FILE__ == $0" are moved to sample/demo_psort_report.rb.
+ Bug fix: GenomeNet BLAST server URI changed.
- * Demo codes in the "if __FILE__ == $0" are moved to
- sample/demo_psort_report.rb, without any checks.
+ * Bug fix: GenomeNet BLAST server URI changed.
+ Reported by joaocardoso via GitHub.
+ ( https://github.com/bioruby/bioruby/issues/44 )
- lib/bio/appl/psort/report.rb | 46 +---------------------------
- sample/demo_psort_report.rb | 70 ++++++++++++++++++++++++++++++++++++++++++
- 2 files changed, 71 insertions(+), 45 deletions(-)
- create mode 100644 sample/demo_psort_report.rb
-
-commit a2686fe3c5a93947c94d4602514a62a808c182d5
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Thu Nov 26 00:53:54 2009 +0900
-
- Demo codes in the "if __FILE__ == $0" are moved to sample/demo_genscan_report.rb.
-
- lib/bio/appl/genscan/report.rb | 176 ----------------------------------
- sample/demo_genscan_report.rb | 202 ++++++++++++++++++++++++++++++++++++++++
- 2 files changed, 202 insertions(+), 176 deletions(-)
- create mode 100644 sample/demo_genscan_report.rb
-
-commit 22f662ba69dd2d4a2273562dd7ea921f5cdd84bd
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Thu Nov 26 00:28:01 2009 +0900
-
- Demo codes in the "if __FILE__ == $0" are moved to sample/demo_ddbjxml.rb.
-
- lib/bio/io/ddbjxml.rb | 182 +-----------------------------------------
- sample/demo_ddbjxml.rb | 212 ++++++++++++++++++++++++++++++++++++++++++++++++
- 2 files changed, 213 insertions(+), 181 deletions(-)
- create mode 100644 sample/demo_ddbjxml.rb
-
-commit ed3b34b6598f632c7b9b3f1a17b42406c19ca32d
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Thu Nov 26 00:12:33 2009 +0900
-
- Demo codes in the "if __FILE__ == $0" are moved to sample/demo_pubmed.rb.
-
- * Demo codes in the "if __FILE__ == $0" are moved to
- sample/demo_pubmed.rb.
- * Codes using Entrez CGI are disabled in the demo.
-
- lib/bio/io/pubmed.rb | 88 -------------------------------------
- sample/demo_pubmed.rb | 116 +++++++++++++++++++++++++++++++++++++++++++++++++
- 2 files changed, 116 insertions(+), 88 deletions(-)
- create mode 100644 sample/demo_pubmed.rb
-
-commit 9e6d720f383e88e247eacab6f0e43f38140a62f2
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Wed Nov 25 23:59:10 2009 +0900
-
- Demo codes in the "if __FILE__ == $0" are removed.
-
- * Demo codes in the "if __FILE__ == $0" are removed because their
- function have already been moved to sample/demo_blast_report.rb.
-
- lib/bio/appl/blast/format0.rb | 193 --------------------------------------
- lib/bio/appl/blast/report.rb | 149 +-----------------------------
- lib/bio/appl/blast/wublast.rb | 208 -----------------------------------------
- 3 files changed, 2 insertions(+), 548 deletions(-)
-
-commit bbba2812fa9131d01fc655eb174d84f06facd8b8
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Wed Nov 25 23:49:36 2009 +0900
-
- New demo code of BLAST parser based on codes in "if __FILE__ ==$0"
-
- * Newly added sample/demo_blast_report.rb, demonstration of
- BLAST parsers Bio::Blast::Report, Bio::Blast::Default::Report,
- and Bio::Blast::WU::Report. It is based on the demonstration codes
- in the "if __FILE__ == $0" in lib/bio/appl/blast/report.rb,
- lib/bio/appl/blast/format0.rb, and lib/bio/appl/blast/wublast.rb.
-
- sample/demo_blast_report.rb | 285 +++++++++++++++++++++++++++++++++++++++++++
- 1 files changed, 285 insertions(+), 0 deletions(-)
- create mode 100644 sample/demo_blast_report.rb
-
-commit 5235ed15db8d3ba3e59d8dc3bbbcf1b5b9c58281
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Wed Nov 25 21:57:08 2009 +0900
-
- Demo codes in the "if __FILE__ == $0" are moved to sample/demo_das.rb.
-
- * Demo codes in the "if __FILE__ == $0" are moved to
- sample/demo_das.rb.
- * Demo codes using UCSC DAS server is added.
- * Demo using the WormBase DAS server is temporarily disabled because
- it does not work well possibly because of the server trouble.
-
- lib/bio/io/das.rb | 44 ----------------------
- sample/demo_das.rb | 105 ++++++++++++++++++++++++++++++++++++++++++++++++++++
- 2 files changed, 105 insertions(+), 44 deletions(-)
- create mode 100644 sample/demo_das.rb
-
-commit b7b0f7bef0505b9678673e54bb863d4ff7897dd5
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Wed Nov 25 20:58:35 2009 +0900
-
- Demo codes in the "if __FILE__ == $0" are moved to sample/demo_kegg_taxonomy.rb, although it does not work correctly now.
-
- lib/bio/db/kegg/taxonomy.rb | 53 +-----------------------
- sample/demo_kegg_taxonomy.rb | 92 ++++++++++++++++++++++++++++++++++++++++++
- 2 files changed, 93 insertions(+), 52 deletions(-)
- create mode 100644 sample/demo_kegg_taxonomy.rb
-
-commit 23da98ca19fce1f0b487e1f955ef4cd896839590
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Wed Nov 25 20:11:12 2009 +0900
-
- Demo codes in the "if __FILE__ == $0" are moved to sample/demo_kegg_reaction.rb.
-
- lib/bio/db/kegg/reaction.rb | 16 +----------
- sample/demo_kegg_reaction.rb | 64 ++++++++++++++++++++++++++++++++++++++++++
- 2 files changed, 65 insertions(+), 15 deletions(-)
- create mode 100644 sample/demo_kegg_reaction.rb
-
-commit 9c0bfb857a6b41d8e6a42ff2cbf7b06ca1d38d78
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Wed Nov 25 19:12:00 2009 +0900
-
- Demo codes in the "if __FILE__ == $0" are moved to sample/demo_kegg_orthology.rb.
-
- lib/bio/db/kegg/orthology.rb | 23 +--------------
- sample/demo_kegg_orthology.rb | 62 +++++++++++++++++++++++++++++++++++++++++
- 2 files changed, 63 insertions(+), 22 deletions(-)
- create mode 100644 sample/demo_kegg_orthology.rb
-
-commit 6f6f1eb3d87dea588ea333708c4d4486ac7136b6
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Wed Nov 25 12:19:26 2009 +0900
-
- Commented out demo for nonexistent method "bindings".
-
- sample/demo_kegg_glycan.rb | 4 ++--
- 1 files changed, 2 insertions(+), 2 deletions(-)
-
-commit 98a6d904058b5af4808f16bcb710d73bd97c9764
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Wed Nov 25 12:18:31 2009 +0900
-
- Demo codes in the "if __FILE__ == $0" are moved to sample/demo_kegg_glycan.rb.
-
- lib/bio/db/kegg/glycan.rb | 21 -------------
- sample/demo_kegg_glycan.rb | 72 ++++++++++++++++++++++++++++++++++++++++++++
- 2 files changed, 72 insertions(+), 21 deletions(-)
- create mode 100644 sample/demo_kegg_glycan.rb
-
-commit d26e835ca9def2287f1050f1b048892e3cafdaa0
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Wed Nov 25 11:49:05 2009 +0900
-
- Added references.
-
- lib/bio/db/kegg/genome.rb | 2 ++
- 1 files changed, 2 insertions(+), 0 deletions(-)
-
-commit c3c460462481b5b8d6e9441216bcf6370b4890ef
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Wed Nov 25 11:45:31 2009 +0900
-
- Demo codes in the "if __FILE__ == $0" are moved to sample/demo_kegg_genome.rb.
-
- lib/bio/db/kegg/genome.rb | 42 +------------------------
- sample/demo_kegg_genome.rb | 74 ++++++++++++++++++++++++++++++++++++++++++++
- 2 files changed, 75 insertions(+), 41 deletions(-)
- create mode 100644 sample/demo_kegg_genome.rb
-
-commit 0d8e709b66bf18ead5944c27a50eb6cf2c47862f
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Wed Nov 25 11:43:24 2009 +0900
-
- Added document about downloading sample data.
-
- sample/demo_kegg_drug.rb | 13 ++++++++++++-
- 1 files changed, 12 insertions(+), 1 deletions(-)
-
-commit 0608893198e9bc88521b6c013069d8c7a13bb0e5
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Wed Nov 25 00:10:48 2009 +0900
-
- Added documents.
-
- lib/bio/db/kegg/drug.rb | 15 +++++++++++++++
- 1 files changed, 15 insertions(+), 0 deletions(-)
-
-commit 0ecdc1ee0460f16dba1e4cd5ab575c92e1c6b1ac
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Wed Nov 25 00:06:02 2009 +0900
-
- Demo codes in the "if __FILE__ == $0" are moved to sample/demo_kegg_drug.rb.
-
- lib/bio/db/kegg/drug.rb | 18 +--------------
- sample/demo_kegg_drug.rb | 54 ++++++++++++++++++++++++++++++++++++++++++++++
- 2 files changed, 55 insertions(+), 17 deletions(-)
- create mode 100644 sample/demo_kegg_drug.rb
-
-commit b0c349103f01a26f4741999bd696bf5b1c032e06
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Tue Nov 24 23:51:13 2009 +0900
-
- Added documents.
-
- lib/bio/db/kegg/compound.rb | 10 ++++++++++
- 1 files changed, 10 insertions(+), 0 deletions(-)
-
-commit e965b454c553ed9670bc83962a2a9d7c5de49929
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Tue Nov 24 23:45:15 2009 +0900
-
- Demo codes in the "if __FILE__ == $0" are moved to sample/demo_kegg_compound.rb.
-
- lib/bio/db/kegg/compound.rb | 19 +-------------
- sample/demo_kegg_compound.rb | 57 ++++++++++++++++++++++++++++++++++++++++++
- 2 files changed, 58 insertions(+), 18 deletions(-)
- create mode 100644 sample/demo_kegg_compound.rb
-
-commit 7454db7c8b8ef7202736d311356d4ca350af336f
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Tue Nov 24 23:06:21 2009 +0900
-
- Demo codes in the "if __FILE__ == $0" are moved to sample/demo_litdb.rb.
-
- lib/bio/db/litdb.rb | 17 +----------------
- sample/demo_litdb.rb | 42 ++++++++++++++++++++++++++++++++++++++++++
- 2 files changed, 43 insertions(+), 16 deletions(-)
- create mode 100644 sample/demo_litdb.rb
-
-commit fde284248e013e44184ee2ba7da85e5b83155a69
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Tue Nov 24 22:57:01 2009 +0900
-
- Ruby 1.9 support: String#each_line instead of String#each
-
- lib/bio/db/go.rb | 6 +++---
- 1 files changed, 3 insertions(+), 3 deletions(-)
-
-commit 8b60099615790fe372b4fde27a391dedc767aab2
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Tue Nov 24 22:53:12 2009 +0900
-
- Sample code bug fix: fixed method names, and workaround for Zlib error.
-
- * Sample code bug fix: Following method name changes.
- * Workaround for Zlib::DataError.
-
- sample/demo_go.rb | 13 +++++++++----
- 1 files changed, 9 insertions(+), 4 deletions(-)
-
-commit 737fec3db555811d127d2356e5ceef63b0413fb8
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Tue Nov 24 19:47:14 2009 +0900
-
- Demo codes in the "if __FILE__ == $0" are moved to sample/demo_go.rb.
-
- lib/bio/db/go.rb | 70 +---------------------------------------
- sample/demo_go.rb | 93 +++++++++++++++++++++++++++++++++++++++++++++++++++++
- 2 files changed, 94 insertions(+), 69 deletions(-)
- create mode 100644 sample/demo_go.rb
-
-commit 8264b15690132d9e766f16d0829bb12cd122b900
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Tue Nov 24 19:20:52 2009 +0900
-
- Document bug fix: Changed Bio::Bl2seq to Bio::Blast::Bl2seq in the RDoc.
-
- * Document bug fix: Changed Bio::Bl2seq to Bio::Blast::Bl2seq
- in the RDoc.
- * Modified copyright line.
-
- lib/bio/appl/bl2seq/report.rb | 18 +++++++++---------
- 1 files changed, 9 insertions(+), 9 deletions(-)
-
-commit c572ff022fee43505355608f0a0e3ba2181e87e2
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Tue Nov 24 19:17:04 2009 +0900
-
- Bug fix: Failed to read Bio::Blast::Bl2seq::Report data by using Bio::FlatFile.
-
- lib/bio/appl/bl2seq/report.rb | 1 +
- 1 files changed, 1 insertions(+), 0 deletions(-)
-
-commit 4f6b080623442dfcc5864e2aefde7e53ace068e8
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Tue Nov 24 19:15:11 2009 +0900
-
- Demo codes in the "if __FILE__ == $0" are moved to sample/demo_bl2seq_report.rb.
-
- lib/bio/appl/bl2seq/report.rb | 194 +------------------------------------
- sample/demo_bl2seq_report.rb | 220 +++++++++++++++++++++++++++++++++++++++++
- 2 files changed, 221 insertions(+), 193 deletions(-)
- create mode 100644 sample/demo_bl2seq_report.rb
-
-commit 2f03e8757383e0d1a26c0f6942c74a30f3b26d90
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Tue Nov 24 18:24:43 2009 +0900
-
- Demo codes in the "if __FILE__ == $0" are moved to sample/demo_genbank.rb.
-
- * Demo codes in the "if __FILE__ == $0" are moved to
- sample/demo_genbank.rb, and modified as below.
- * To get sequences from the NCBI web service.
- * By default, arguments are sequence IDs (accession numbers).
- * New option "--files" (or "-files", "--file", or "-file") to
- read sequences from file(s).
-
- lib/bio/db/genbank/genbank.rb | 87 +--------------------------
- sample/demo_genbank.rb | 132 +++++++++++++++++++++++++++++++++++++++++
- 2 files changed, 133 insertions(+), 86 deletions(-)
- create mode 100644 sample/demo_genbank.rb
-
-commit a2981c28fdb629a655c71c920f6588f8b80aff06
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Tue Nov 24 15:06:50 2009 +0900
-
- Demo codes in the "if __FILE__ == $0" are moved to sample/demo_aaindex.rb.
-
- lib/bio/db/aaindex.rb | 39 +---------------------------
- sample/demo_aaindex.rb | 67 ++++++++++++++++++++++++++++++++++++++++++++++++
- 2 files changed, 68 insertions(+), 38 deletions(-)
- create mode 100644 sample/demo_aaindex.rb
-
-commit b741d17ec5c5ac234bab35b8716fee072635de1a
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Tue Nov 24 12:45:43 2009 +0900
-
- Demo codes in the "if __FILE__ == $0" are moved to sample/demo_sirna.rb
-
- * Demo codes in the "if __FILE__ == $0" are moved to
- sample/demo_sirna.rb, and modified for reading normal sequence
- files instead of a raw sequence.
-
- lib/bio/util/sirna.rb | 24 +------------------
- sample/demo_sirna.rb | 63 +++++++++++++++++++++++++++++++++++++++++++++++++
- 2 files changed, 64 insertions(+), 23 deletions(-)
- create mode 100644 sample/demo_sirna.rb
-
-commit 7cc778e78bc63ef73796ee15d6f0db8d6967aefe
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Mon Nov 23 23:00:42 2009 +0900
-
- Demo codes in the "if __FILE__ == $0" are moved to sample/demo_pathway.rb.
-
- lib/bio/pathway.rb | 171 -----------------------------------------
- sample/demo_pathway.rb | 196 ++++++++++++++++++++++++++++++++++++++++++++++++
- 2 files changed, 196 insertions(+), 171 deletions(-)
- create mode 100644 sample/demo_pathway.rb
-
-commit 7e5510587abc0b50b6851f005a3236bf9dc79d08
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Mon Nov 23 22:49:13 2009 +0900
-
- Demo codes in the "if __FILE__ == $0" are moved to sample/demo_locations.rb.
-
- lib/bio/location.rb | 73 ----------------------------------
- sample/demo_locations.rb | 99 ++++++++++++++++++++++++++++++++++++++++++++++
- 2 files changed, 99 insertions(+), 73 deletions(-)
- create mode 100644 sample/demo_locations.rb
-
-commit f1c02666f4b11d5cf208d6beb592d8ac962ce2da
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Mon Nov 23 22:35:50 2009 +0900
-
- Demo codes in the "if __FILE__ == $0" are moved to sample/demo_codontable.rb.
-
- lib/bio/data/codontable.rb | 96 +-----------------------------------
- sample/demo_codontable.rb | 119 ++++++++++++++++++++++++++++++++++++++++++++
- 2 files changed, 120 insertions(+), 95 deletions(-)
- create mode 100644 sample/demo_codontable.rb
-
-commit c11a7793f85faf3d66d630833c38358ffa34a698
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Mon Nov 23 16:35:16 2009 +0900
-
- Demo codes in the "if __FILE__ == $0" are moved to sample/demo_nucleicacid.rb.
-
- lib/bio/data/na.rb | 27 +-----------------------
- sample/demo_nucleicacid.rb | 49 ++++++++++++++++++++++++++++++++++++++++++++
- 2 files changed, 50 insertions(+), 26 deletions(-)
- create mode 100644 sample/demo_nucleicacid.rb
-
-commit de41b67c3f65baa0f122689b2e9f479d8a247934
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Mon Nov 23 16:25:05 2009 +0900
-
- Demo codes in the "if __FILE__ == $0" are moved to sample/demo_aminoacid.rb.
-
- lib/bio/data/aa.rb | 78 +-----------------------------------
- sample/demo_aminoacid.rb | 101 ++++++++++++++++++++++++++++++++++++++++++++++
- 2 files changed, 102 insertions(+), 77 deletions(-)
- create mode 100644 sample/demo_aminoacid.rb
-
-commit e652dd44ecb6b6dad652e33a398f92bb8373e7dd
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Mon Nov 23 16:12:48 2009 +0900
-
- Added an error message about encoding in Ruby 1.9.1
-
- KNOWN_ISSUES.rdoc | 3 ++-
+ lib/bio/appl/blast/genomenet.rb | 3 ++-
1 files changed, 2 insertions(+), 1 deletions(-)
-commit 003133b0d4e2234c27927c9d10b75185c354102e
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Mon Nov 23 15:52:21 2009 +0900
+commit f33abf9bbd90c3c1e320f06447fdb54ffd094c5d
+Author: peterjc <p.j.a.cock@googlemail.com>
+Date: Fri Nov 25 11:20:08 2011 +0000
- changed recommended Ruby version
+ Mark echoarg2.bat and echoarg2.sh as world executable
- README.rdoc | 4 ++--
- 1 files changed, 2 insertions(+), 2 deletions(-)
+ 0 files changed, 0 insertions(+), 0 deletions(-)
+ mode change 100644 => 100755 test/data/command/echoarg2.bat
+ mode change 100644 => 100755 test/data/command/echoarg2.sh
-commit 408483d36b713678361cecf6c77ff7a2098f71fc
+commit d2d66f833d0b20647e8d761d2a240b99b206eaa8
Author: Naohisa Goto <ng@bioruby.org>
-Date: Sun Nov 22 17:07:37 2009 +0900
+Date: Thu Nov 24 13:32:37 2011 +0900
- added information about doc/Changes-1.4.rdoc
+ Bug fix: rake aborted without git
- README.rdoc | 1 +
- 1 files changed, 1 insertions(+), 0 deletions(-)
-
-commit ef342933839e8c6cef9883045fcaf468aff5da23
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Sun Nov 22 16:50:55 2009 +0900
-
- In PhyloXML support, added a link to GNOME Libxml2 and fixed RDoc syntax.
-
- README.rdoc | 6 ++++--
- 1 files changed, 4 insertions(+), 2 deletions(-)
-
-commit 0237ef42d60c7a76cadf8ea78f4251bcfe89c95f
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Thu Nov 19 09:43:15 2009 +0900
-
- Ruby 1.9 support: String#each_line instead of String#each
-
- lib/bio/appl/meme/mast/report.rb | 2 +-
+ bioruby.gemspec.erb | 2 +-
1 files changed, 1 insertions(+), 1 deletions(-)
-commit ec935ea9b19415bf3325bcc0763fbc22f3c71a3d
+commit c2139739988ef731d61bf1a8cdba2dc5c48393bd
Author: Naohisa Goto <ng@bioruby.org>
-Date: Thu Nov 19 09:40:49 2009 +0900
+Date: Thu Nov 24 13:07:10 2011 +0900
- The "libpath magic" is replaced by loading helper routine.
+ regenerate bioruby.gemspec with rake regemspec.
- test/unit/bio/appl/meme/mast/test_report.rb | 11 ++++++-----
- test/unit/bio/appl/meme/test_mast.rb | 11 ++++++-----
- test/unit/bio/appl/meme/test_motif.rb | 8 +++++---
- 3 files changed, 17 insertions(+), 13 deletions(-)
+ bioruby.gemspec | 18 ++++++++++--------
+ 1 files changed, 10 insertions(+), 8 deletions(-)
-commit 3f65eeb503f3b2ef866cab4c73d2d700ca572835
-Author: Adam Kraut <adamnkraut@gmail.com>
-Date: Tue Mar 17 19:41:31 2009 -0400
-
- Added basic support for MEME/MAST applications
-
- lib/bio/appl/meme/mast.rb | 156 +++++++++++++++++++++++++++
- lib/bio/appl/meme/mast/report.rb | 91 ++++++++++++++++
- lib/bio/appl/meme/motif.rb | 48 ++++++++
- test/data/meme/mast.out | 13 +++
- test/data/meme/meme.out | 3 +
- test/unit/bio/appl/meme/mast/test_report.rb | 45 ++++++++
- test/unit/bio/appl/meme/test_mast.rb | 102 +++++++++++++++++
- test/unit/bio/appl/meme/test_motif.rb | 36 ++++++
- 8 files changed, 494 insertions(+), 0 deletions(-)
- create mode 100644 lib/bio/appl/meme/mast.rb
- create mode 100644 lib/bio/appl/meme/mast/report.rb
- create mode 100644 lib/bio/appl/meme/motif.rb
- create mode 100644 test/data/meme/db
- create mode 100644 test/data/meme/mast
- create mode 100644 test/data/meme/mast.out
- create mode 100644 test/data/meme/meme.out
- create mode 100644 test/unit/bio/appl/meme/mast/test_report.rb
- create mode 100644 test/unit/bio/appl/meme/test_mast.rb
- create mode 100644 test/unit/bio/appl/meme/test_motif.rb
-
-commit 3862f54fda0caec2a07e563a1f8a11913baca2e3
+commit 6213b45d28bfea2cc8c838813b524d48c369266b
Author: Naohisa Goto <ng@bioruby.org>
-Date: Wed Nov 18 20:29:56 2009 +0900
+Date: Thu Nov 24 13:05:07 2011 +0900
- New version of PhyloXML schema, version 1.10.
-
- * Upgraded to New version of PhyloXML schema, version 1.10,
- developed by Christian M Zmasek.
+ Added workaround for changes of a module name and file names to require.
- lib/bio/db/phyloxml/phyloxml.xsd | 1155 +++++++++++++++++++-------------------
- 1 files changed, 582 insertions(+), 573 deletions(-)
+ Rakefile | 21 +++++++++++++++++++--
+ 1 files changed, 19 insertions(+), 2 deletions(-)
-commit 45ffd9228d513b3dbf29e1011c6a6689a8bd1b08
+commit 39f847cf8d453476275361078b831da43d400816
Author: Naohisa Goto <ng@bioruby.org>
-Date: Wed Nov 18 00:26:44 2009 +0900
+Date: Thu Nov 24 12:08:47 2011 +0900
- Newly added sample script to test big PhyloXML data
-
- * Newly added a sample script to test big PhyloXML data based on
- Diana Jaunzeikare's work.
- (http://github.com/latvianlinuxgirl/bioruby/blob/
- 20627fc5a443d6c2e3dc73ed50e9c578ffcbc330/
- test/unit/bio/db/test_phyloxml_big.rb).
+ Use binary mode to open files.
- sample/test_phyloxml_big.rb | 205 +++++++++++++++++++++++++++++++++++++++++++
- 1 files changed, 205 insertions(+), 0 deletions(-)
- create mode 100644 sample/test_phyloxml_big.rb
+ Rakefile | 6 ++++--
+ 1 files changed, 4 insertions(+), 2 deletions(-)
-commit 828a8971e057919b80508cf29fd9518828b74a2f
+commit 688779e71a27e861fb01e07f816384561b8cfe45
Author: Naohisa Goto <ng@bioruby.org>
-Date: Tue Nov 17 23:54:37 2009 +0900
+Date: Thu Nov 24 11:49:30 2011 +0900
- Speed up of Bio::Tree#children and parent: caching node's parent.
+ Rakefile: new tasks: test-all to run all tests, etc.
- * For speed up of Bio::Tree#children and parent, internal cache of
- the parent for each node is added. The cache is automatically
- cleared when the tree is modified. Note that the cache can only
- be accessed from inside Bio::Tree.
- * Bio::Tree#parent is changed to directly raise IndexError when
- both of the root specified in the argument and preset in the
- tree are nil (previously, the same error is raised in the path
- method which is internally called from the parent method).
- * Bio::Tree#path is changed not to call bfs_shortest_path if the
- node1 and node2 are adjacent.
+ * Rakefile: new tasks: test-all to run all tests, and test-network
+ to run tests in test/network.
- lib/bio/tree.rb | 75 +++++++++++++++++++++++++++++++++++++++++++++++++++---
- 1 files changed, 70 insertions(+), 5 deletions(-)
-
-commit 75862212e6bb807a570338e39e19d527219b6f13
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Mon Nov 16 22:11:15 2009 +0900
-
- Documented incompatible changes of Bio::KEGG::COMPOUND and Bio::KEGG:REACTION.
-
- doc/Changes-1.4.rdoc | 10 ++++++++++
+ Rakefile | 10 ++++++++++
1 files changed, 10 insertions(+), 0 deletions(-)
-commit c74cfabd6414c8b50db0251739f967accd90773f
+commit 53719535defcb0fefb3cf8bebe3fad6716bf7de2
Author: Naohisa Goto <ng@bioruby.org>
-Date: Mon Nov 16 21:20:42 2009 +0900
+Date: Thu Nov 24 11:28:38 2011 +0900
- Ruby compatibility issue: Enumerable#each_slice(4).each does not work in Ruby 1.8.5.
+ test/runner.rb: Run tests only in test/unit and test/functional.
- lib/bio/db/kegg/reaction.rb | 2 +-
- 1 files changed, 1 insertions(+), 1 deletions(-)
+ test/runner.rb | 22 ++++++++++++++++------
+ 1 files changed, 16 insertions(+), 6 deletions(-)
-commit e6a920e401a2b06c355174ccdc9b993a38f9d7ec
-Author: Mitsuteru Nakao <mitsuteru.nakao@gmail.com>
-Date: Wed Jul 22 22:50:22 2009 +0900
-
- Added new method Bio::KEGG::GENES#structure with the unit tests.
-
- lib/bio/db/kegg/genes.rb | 12 ++++++++++++
- test/unit/bio/db/kegg/test_genes.rb | 25 +++++++++++++++++++++++++
- 2 files changed, 37 insertions(+), 0 deletions(-)
-
-commit 9fee0c133d069348857014410983f682e468c1c7
+commit fb9ee403db6b447aee73ebb7f12ff5a5b73d6c52
Author: Naohisa Goto <ng@bioruby.org>
-Date: Mon Nov 16 21:04:02 2009 +0900
+Date: Wed Nov 23 20:36:36 2011 +0900
- The "libpath magic" is replaced by loading helper routine.
+ A test class using network connection is moved under test/network/.
- test/unit/bio/db/kegg/test_compound.rb | 6 ++++--
- test/unit/bio/db/kegg/test_reaction.rb | 6 ++++--
- 2 files changed, 8 insertions(+), 4 deletions(-)
+ test/functional/bio/test_command.rb | 16 ----------------
+ test/network/bio/test_command.rb | 35 +++++++++++++++++++++++++++++++++++
+ 2 files changed, 35 insertions(+), 16 deletions(-)
+ create mode 100644 test/network/bio/test_command.rb
-commit 1199330eab95b8434303e92c5f792818e96db814
-Author: Kozo Nishida <kozo-ni@cg05.naist.jp>
-Date: Sat Nov 14 09:03:50 2009 +0900
-
- Newly added unit tests for Bio::KEGG::COMPOUND and Bio::KEGG::REACTION
-
- * Newly added unit tests for Bio::KEGG::COMPOUND and
- Bio::KEGG::REACTION with test data. (Note that this is a
- combination of several commits made by Kozo Nishida,
- merged from git://github.com/kozo2/bioruby.git ).
-
- test/data/KEGG/C00025.compound | 102 ++++++++++++++++++++++++++++++++
- test/data/KEGG/R00006.reaction | 14 ++++
- test/unit/bio/db/kegg/test_compound.rb | 49 +++++++++++++++
- test/unit/bio/db/kegg/test_reaction.rb | 57 ++++++++++++++++++
- 4 files changed, 222 insertions(+), 0 deletions(-)
- create mode 100644 test/data/KEGG/C00025.compound
- create mode 100644 test/data/KEGG/R00006.reaction
- create mode 100644 test/unit/bio/db/kegg/test_compound.rb
- create mode 100644 test/unit/bio/db/kegg/test_reaction.rb
-
-commit 1b47640665d4332bafd9e9709628ee9722f1f3f4
-Author: Kozo Nishida <kozo-ni@cg05.naist.jp>
-Date: Sat Nov 14 09:03:50 2009 +0900
-
- Bio::KEGG::COMPOUND#dblinks changed to return hash list
-
- * Bio::KEGG::COMPOUND#dblinks is changed to return hash list (array
- containing hashes).
-
- lib/bio/db/kegg/compound.rb | 11 +++++++++--
- 1 files changed, 9 insertions(+), 2 deletions(-)
-
-commit 2aa43a0aa765ee4502923c2102e352826a9a7abd
-Author: Kozo Nishida <kozo-ni@cg05.naist.jp>
-Date: Sat Nov 14 07:29:19 2009 +0900
-
- Bio::KEGG:REACTION#rpair and pathways changed to return hash list, and added orthologies method.
-
- * New method: Bio::KEGG:REACTION#orthologies
- * Bio::KEGG:REACTION#rpair and pathways are changed to return hash
- list (array containing hashes).
-
- lib/bio/db/kegg/reaction.rb | 33 ++++++++++++++++++++++++++++++---
- 1 files changed, 30 insertions(+), 3 deletions(-)
-
-commit a82f5d228370beeeb397be07e07394652fd7837e
+commit a6dda2215aa686a9ca4af7484aa190f726d51e69
Author: Naohisa Goto <ng@bioruby.org>
-Date: Mon Nov 16 20:03:19 2009 +0900
+Date: Wed Nov 23 20:28:58 2011 +0900
- Changed not to modify given argument
-
- lib/bio/util/restriction_enzyme/single_strand.rb | 2 +-
- 1 files changed, 1 insertions(+), 1 deletions(-)
-
-commit ff10d5540759a5e7eaaa71da020d95170b98e007
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Mon Nov 16 19:50:08 2009 +0900
-
- Newly added a document for incompatible and/or important changes of the new release version.
+ Tests using network connections are moved to test/network/
- * Newly added a document for incompatible and/or important changes
- of the new release version.
- * Added description about Bio::RestrictionEnzyme validation is
- disabled (although very small change).
+ * Tests using network connections are moved to test/network/.
+ * renamed: test/functional/bio/appl -> test/network/bio/appl
+ * renamed: test/functional/bio/io -> test/network/bio/io
- doc/Changes-1.4.rdoc | 16 ++++++++++++++++
- 1 files changed, 16 insertions(+), 0 deletions(-)
- create mode 100644 doc/Changes-1.4.rdoc
+ test/functional/bio/appl/blast/test_remote.rb | 93 ---------
+ test/functional/bio/appl/test_blast.rb | 61 ------
+ test/functional/bio/appl/test_pts1.rb | 117 -----------
+ test/functional/bio/io/test_ddbjrest.rb | 47 -----
+ test/functional/bio/io/test_ensembl.rb | 230 ---------------------
+ test/functional/bio/io/test_pubmed.rb | 135 -------------
+ test/functional/bio/io/test_soapwsdl.rb | 53 -----
+ test/functional/bio/io/test_togows.rb | 268 -------------------------
+ test/network/bio/appl/blast/test_remote.rb | 93 +++++++++
+ test/network/bio/appl/test_blast.rb | 61 ++++++
+ test/network/bio/appl/test_pts1.rb | 117 +++++++++++
+ test/network/bio/io/test_ddbjrest.rb | 47 +++++
+ test/network/bio/io/test_ensembl.rb | 230 +++++++++++++++++++++
+ test/network/bio/io/test_pubmed.rb | 135 +++++++++++++
+ test/network/bio/io/test_soapwsdl.rb | 53 +++++
+ test/network/bio/io/test_togows.rb | 268 +++++++++++++++++++++++++
+ 16 files changed, 1004 insertions(+), 1004 deletions(-)
+ delete mode 100644 test/functional/bio/appl/blast/test_remote.rb
+ delete mode 100644 test/functional/bio/appl/test_blast.rb
+ delete mode 100644 test/functional/bio/appl/test_pts1.rb
+ delete mode 100644 test/functional/bio/io/test_ddbjrest.rb
+ delete mode 100644 test/functional/bio/io/test_ensembl.rb
+ delete mode 100644 test/functional/bio/io/test_pubmed.rb
+ delete mode 100644 test/functional/bio/io/test_soapwsdl.rb
+ delete mode 100644 test/functional/bio/io/test_togows.rb
+ create mode 100644 test/network/bio/appl/blast/test_remote.rb
+ create mode 100644 test/network/bio/appl/test_blast.rb
+ create mode 100644 test/network/bio/appl/test_pts1.rb
+ create mode 100644 test/network/bio/io/test_ddbjrest.rb
+ create mode 100644 test/network/bio/io/test_ensembl.rb
+ create mode 100644 test/network/bio/io/test_pubmed.rb
+ create mode 100644 test/network/bio/io/test_soapwsdl.rb
+ create mode 100644 test/network/bio/io/test_togows.rb
-commit 629e537f90e0825fadeec2e0207f8caddfbed59a
-Author: trevor <>
-Date: Sat Sep 19 11:03:23 2009 -0500
-
- speed-up serial calls to RestrictionEnzyme
-
- lib/bio/db/rebase.rb | 2 +-
- lib/bio/util/restriction_enzyme/single_strand.rb | 3 +-
- .../util/restriction_enzyme/test_single_strand.rb | 24 ++++++++++---------
- .../test_single_strand_complement.rb | 24 ++++++++++---------
- 4 files changed, 29 insertions(+), 24 deletions(-)
-
-commit 9b55a92d5300294bef7b624d0f9aa3edd3e8d7fc
-Author: trevor <>
-Date: Sat Sep 19 10:46:21 2009 -0500
-
- speed-up rebase library
-
- lib/bio/db/rebase.rb | 9 ++++-----
- 1 files changed, 4 insertions(+), 5 deletions(-)
-
-commit 4aaa24b3fc3cf2d1f7cf8b6d974d2115958b5a1b
+commit ec747aa33d06e08a6469dfd330360161d1b0f8e2
Author: Naohisa Goto <ng@bioruby.org>
-Date: Mon Nov 16 15:08:31 2009 +0900
+Date: Wed Nov 23 15:03:08 2011 +0900
- Ruby 1.9 support: Array#to_s is changed to join('')
+ Test bug fix: use binmode to disable CR/LF conversion (fail on Windows)
- lib/bio/db/sanger_chromatogram/scf.rb | 2 +-
- 1 files changed, 1 insertions(+), 1 deletions(-)
+ test/unit/bio/appl/blast/test_rpsblast.rb | 1 +
+ test/unit/bio/io/flatfile/test_buffer.rb | 1 +
+ 2 files changed, 2 insertions(+), 0 deletions(-)
-commit 1cf924b81150545e807169144aeaca6a75f9731c
+commit 07ce32da009baa2c4e81f6d96f45e3dac49da183
Author: Naohisa Goto <ng@bioruby.org>
-Date: Mon Nov 16 12:59:10 2009 +0900
+Date: Wed Nov 23 14:47:33 2011 +0900
- Ruby 1.9 support: Array#nitems (counts the number of non-nil elements) is removed in 1.9.
+ Test bug fix: Read Sanger chromatogram files with binary mode
- * Ruby 1.9 support: Array#nitems (counts the number of non-nil
- elements) is removed in Ruby 1.9. In scf.rb, it seems that
- nil would never be included in the array, and simply replaced
- by Array#size.
+ * Test bug fix: Read Sanger chromatogram files with binary mode.
+ Fix error/failure on Windows due to default text mode reading.
- lib/bio/db/sanger_chromatogram/scf.rb | 8 ++++----
- 1 files changed, 4 insertions(+), 4 deletions(-)
+ test/unit/bio/db/sanger_chromatogram/test_abif.rb | 3 ++-
+ test/unit/bio/db/sanger_chromatogram/test_scf.rb | 6 ++++--
+ 2 files changed, 6 insertions(+), 3 deletions(-)
-commit a95994d9cfbf4fc89fa716358ac5b92d42a1307b
+commit 20d9068643214e3482d18c36028e50b3c9109755
Author: Naohisa Goto <ng@bioruby.org>
-Date: Sun Nov 15 19:23:12 2009 +0900
+Date: Wed Nov 23 14:17:25 2011 +0900
- Bug fix: error when quality_scores are larger than the sequence length, and added a require line.
+ Incompatible change: Bio::FlatFile.open and auto use binary mode
- * Bug fix: error when sequence.quality_scores are larger than
- the sequence length.
- * Added a require line.
+ * Incompatible change: Bio::FlatFile.open and auto use binary mode
+ (binmode) unless text mode option is explicitly given.
- lib/bio/db/fasta/format_qual.rb | 5 ++++-
- 1 files changed, 4 insertions(+), 1 deletions(-)
+ RELEASE_NOTES.rdoc | 7 ++
+ lib/bio/io/flatfile/buffer.rb | 84 ++++++++++++++++++
+ test/unit/bio/io/flatfile/test_buffer.rb | 139 ++++++++++++++++++++++++++++++
+ 3 files changed, 230 insertions(+), 0 deletions(-)
-commit c5aafca19b58b1651080e81699b7020cd3fd3f47
+commit 48bd150a6180d59879872bd85dd95c7ddf1a19c0
Author: Naohisa Goto <ng@bioruby.org>
-Date: Sun Nov 15 19:21:49 2009 +0900
+Date: Tue Nov 22 17:32:23 2011 +0900
- Newly added unit tests for Bio::Sequence::Format::Formatter::Fasta_numeric and Qual.
+ Test bug fix: fixed incomplete Windows platform detection.
- test/unit/bio/db/fasta/test_format_qual.rb | 346 ++++++++++++++++++++++++++++
- 1 files changed, 346 insertions(+), 0 deletions(-)
- create mode 100644 test/unit/bio/db/fasta/test_format_qual.rb
+ test/unit/bio/test_command.rb | 13 +++++++++----
+ 1 files changed, 9 insertions(+), 4 deletions(-)
-commit 6e24170e29d2576ff69b18eaadc94e9769b8612a
+commit d499bcee7956b1a0a4c04aeb106e50a0839167b0
Author: Naohisa Goto <ng@bioruby.org>
-Date: Sat Nov 14 02:41:13 2009 +0900
+Date: Tue Nov 22 16:15:05 2011 +0900
- Newly added Bio::Sequence::Format::Formatter::Qual and Fasta_numeric, formatter for Qual format and FastaNumericFormat.
-
- lib/bio/db/fasta/format_qual.rb | 201 +++++++++++++++++++++++++++++++++++++++
- lib/bio/sequence/format.rb | 7 ++
- 2 files changed, 208 insertions(+), 0 deletions(-)
- create mode 100644 lib/bio/db/fasta/format_qual.rb
-
-commit 6959fd359040b6ca9570111d515118dc2d472029
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Sat Nov 14 02:19:17 2009 +0900
-
- Split quality score methods in Bio::Fastq::FormatData into separete modules
+ FuncTestCommandCall is changed to test various command-lines.
- * Quality score calculation methods in Bio::Fastq::FormatData in
- lib/bio/db/fastq.rb is splitted into separate modules
- Bio::Fastq::QualityScore::Converter, Phred, and Solexa
- in lib/bio/db/fastq/quality_score.rb.
- * Unit tests for Bio::Fastq::QualityScore::* are newly added
- in test/unit/bio/db/fastq/test_quality_score.rb.
- * Possible bug fix: probability should be 0 <= p <= 1.
+ * New file test/data/command/echoarg2.sh shell script, which acts
+ like echoarg2.bat for Windows.
+ * FuncTestCommandCall is changed to test various command-lines.
- lib/bio/db/fastq.rb | 112 +--------
- lib/bio/db/fastq/quality_score.rb | 206 ++++++++++++++++
- test/unit/bio/db/fastq/test_quality_score.rb | 330 ++++++++++++++++++++++++++
- 3 files changed, 544 insertions(+), 104 deletions(-)
- create mode 100644 lib/bio/db/fastq/quality_score.rb
- create mode 100644 test/unit/bio/db/fastq/test_quality_score.rb
+ test/data/command/echoarg2.sh | 4 ++
+ test/functional/bio/test_command.rb | 70 +++++++++++++++++++++++++++++------
+ 2 files changed, 62 insertions(+), 12 deletions(-)
+ create mode 100644 test/data/command/echoarg2.sh
-commit 98f7703c28f0c2c34e4fe1631de227e20b9666c3
+commit d45e311c09ad2f4116770dd903f81e652a63ca2a
Author: Naohisa Goto <ng@bioruby.org>
-Date: Fri Nov 13 23:48:19 2009 +0900
+Date: Tue Nov 22 14:21:34 2011 +0900
- When no error_probabilities in the sequence and quality_score_type is nil, Fastq formatter implicitly assumes that the quality_score_type is :phred.
+ Test bug fix: Opened files should be closed.
- * When no error_probabilities in the sequence and
- quality_score_type is nil, Fastq formatter implicitly assumes
- that the quality_score_type is :phred.
- * Bug fix: fixed typo in lib/bio/db/fastq/format_fastq.rb.
+ * Test bug fix: Opened files should be closed. When finalizing writer
+ tests, temporary files are not properly closed after verify reading,
+ and removing the temporary files raise erro on Windows.
- lib/bio/db/fastq/format_fastq.rb | 5 ++++-
- lib/bio/sequence.rb | 3 +++
- 2 files changed, 7 insertions(+), 1 deletions(-)
+ test/unit/bio/db/test_phyloxml_writer.rb | 24 +++++++++++++++---------
+ 1 files changed, 15 insertions(+), 9 deletions(-)
-commit f85a6aee9827bc573dcb735f4a1a1827926cc66c
+commit a9022c61b98746e98a83f1cfd902e0e6b11c7bbb
Author: Naohisa Goto <ng@bioruby.org>
-Date: Fri Nov 13 23:29:19 2009 +0900
+Date: Tue Nov 22 13:55:15 2011 +0900
- Bug fix: fixed typo for Bio::Sequence#quality_score_type.
-
- lib/bio/sequence.rb | 2 +-
- 1 files changed, 1 insertions(+), 1 deletions(-)
-
-commit d81a611d7c7c46a789b86e99cebe064ba559e3e0
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Fri Nov 13 20:42:12 2009 +0900
-
- Splitting lib/bio/db/fasta.rb: FastaNumericFormat is moved to a new file, etc.
+ New method Bio::PhyloXML::Parser#closed?, and Bio::PhyloXML::Parser.open with block.
- * Splitting lib/bio/db/fasta.rb as follows:
- * Bio::FastaNumericFormat is moved to lib/bio/db/fasta/qual.rb.
- * Demo codes in the "if __FILE__ == $0" are moved to
- sample/demo_fastaformat.rb.
- * Unit tests for Bio::FastaNumericFormat are moved from
- test/unit/bio/db/test_fasta.rb to test/unit/bio/db/test_qual.rb.
- * lib/bio.rb is also modified for the autoload.
- * Bug fix: fixed incorrect autoload path for Bio::FastaDefline.
+ * New method Bio::PhyloXML::Parser#closed? to check if it is closed
+ or not.
+ * Bio::PhyloXML::Parser.open and open_uri now can get a block.
+ When a block is given, a Bio::PhyloXML::Parser object is passed
+ to the block as an argument. When the block terminates, the object
+ is closed.
+ * Added tests about the above changes.
- lib/bio.rb | 4 +-
- lib/bio/db/fasta.rb | 135 +---------------------------------------
- lib/bio/db/fasta/qual.rb | 102 ++++++++++++++++++++++++++++++
- sample/demo_fastaformat.rb | 105 +++++++++++++++++++++++++++++++
- test/unit/bio/db/test_fasta.rb | 43 -------------
- test/unit/bio/db/test_qual.rb | 63 +++++++++++++++++++
- 6 files changed, 273 insertions(+), 179 deletions(-)
- create mode 100644 lib/bio/db/fasta/qual.rb
- create mode 100644 sample/demo_fastaformat.rb
- create mode 100644 test/unit/bio/db/test_qual.rb
+ lib/bio/db/phyloxml/phyloxml_parser.rb | 57 +++++++++++++++++++++++++++++---
+ test/unit/bio/db/test_phyloxml.rb | 56 ++++++++++++++++++++++++++++++-
+ 2 files changed, 106 insertions(+), 7 deletions(-)
-commit c70bed5c3f828c94084fdeabe255fbb3930097d0
-Author: Andrew Grimm <andrew.j.grimm@gmail.com>
-Date: Sun Aug 16 19:49:38 2009 +1000
-
- Removed use of uninitialized variable in FastaNumericFormat.
-
- lib/bio/db/fasta.rb | 2 +-
- 1 files changed, 1 insertions(+), 1 deletions(-)
-
-commit ce6dcc344a3d7beec544d7164308dd97bafa8a19
+commit 893cbe6ca993eca08427074059c2ba03621ea889
Author: Naohisa Goto <ng@bioruby.org>
-Date: Fri Nov 13 13:04:11 2009 +0900
+Date: Sat Nov 5 00:49:10 2011 +0900
- User data type should be stored as is, even if unknown data type.
+ Ruby 1.9 should be fully supported, and optional requirements are revised.
- lib/bio/db/sanger_chromatogram/abif.rb | 3 ++-
- 1 files changed, 2 insertions(+), 1 deletions(-)
+ README.rdoc | 48 +++++++++++++++++++++++++++++++++---------------
+ 1 files changed, 33 insertions(+), 15 deletions(-)
-commit ca96e59f151c2e10b5cd8c0690b8297979e52036
+commit 38b1715c2d6bad39560e0846781ca903b1c16eda
Author: Naohisa Goto <ng@bioruby.org>
-Date: Fri Nov 13 12:50:59 2009 +0900
+Date: Fri Nov 4 22:12:38 2011 +0900
- Removed Bio::Abif#method_missing and added alternative method
-
- * Removed Bio::Abif#method_missing, because method_missing can
- hide many errors related to method calls e.g. method name typo,
- and it is not suitable for only getting data.
- * New method Bio::Abif#data is added to get data (alternative of
- the method_missing).
+ Added REFERENCE.
- lib/bio/db/sanger_chromatogram/abif.rb | 19 ++++++++++++-------
- 1 files changed, 12 insertions(+), 7 deletions(-)
+ README.rdoc | 12 ++++++++++++
+ 1 files changed, 12 insertions(+), 0 deletions(-)
-commit 8b0da27523998cb9a9df07f5e907cda6e3cef0dc
+commit 9a766cd17236bbe1e28d6972001dd5e3ed596123
Author: Naohisa Goto <ng@bioruby.org>
-Date: Fri Nov 13 12:04:41 2009 +0900
+Date: Fri Nov 4 21:39:20 2011 +0900
- removed a non-ascii character in comment
+ Removed "setup.rb test" and added about running tests.
- lib/bio/db/sanger_chromatogram/chromatogram.rb | 2 +-
- 1 files changed, 1 insertions(+), 1 deletions(-)
+ README.rdoc | 39 ++++++++++++++++++++++++++++++++++-----
+ 1 files changed, 34 insertions(+), 5 deletions(-)
-commit 55c1a180fec97338bae8e3c5b5d5ceec64aed0f6
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Fri Nov 13 12:02:53 2009 +0900
+commit 39737179b06366e1d5acf2e5ac930e41b3a4ee38
+Author: Pjotr Prins <pjotr.public01@thebird.nl>
+Date: Fri Oct 14 08:58:01 2011 +0200
- Bug fix: Bio::SangerChromatogram#complement fails when the object is frozen.
+ Tutorial: added info on biogems
- lib/bio/db/sanger_chromatogram/chromatogram.rb | 2 +-
- 1 files changed, 1 insertions(+), 1 deletions(-)
+ doc/Tutorial.rd | 16 ++++++++++++++++
+ doc/Tutorial.rd.html | 23 +++++++++++++++--------
+ 2 files changed, 31 insertions(+), 8 deletions(-)
-commit 4e7d8b0ba304d1ff01364fad68035f7ec9463fb9
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Thu Nov 12 22:23:47 2009 +0900
+commit e84400c5e9e94d95d6a8d3c4b72388b94d204766
+Author: Pjotr Prins <pjotr.public01@thebird.nl>
+Date: Fri Oct 14 08:49:41 2011 +0200
- fixed a typo in a copyright line
+ Tutorial: small updates
- test/unit/bio/util/test_sirna.rb | 2 +-
- 1 files changed, 1 insertions(+), 1 deletions(-)
+ doc/Tutorial.rd | 8 +++++---
+ doc/Tutorial.rd.html | 9 +++++----
+ 2 files changed, 10 insertions(+), 7 deletions(-)
-commit f376124112d23ba9b0491dbd427d328edc81d872
+commit 9fe07345b3b7be890d5baad9a51f0752af5e0ac4
Author: Naohisa Goto <ng@bioruby.org>
-Date: Thu Nov 12 22:05:37 2009 +0900
+Date: Tue Sep 13 23:05:39 2011 +0900
- The "libpath magic" in tests are replaced by the load of helper routine.
+ README_DEV.rdoc: added git tips and policies, etc.
- * In all unit tests, the "libpath magic" are replaced by the load
- of helper routine.
- * Changed to use a constant BioRubyTestDataPath for generating test
- data file path.
- * Some "require" lines are modified.
- * "File.open(...).read" in some tests are replaced by "File.read(...)".
- * Header comment lines of some tests with wrong filename and/or
- class/module name information are fixed.
+ * Added Git tips about sending a patch or a pull request.
+ * Added Git management policies for the blessed repository.
+ * Added some coding styles.
+ * Added descriptions about Ruby versions and OS.
- test/functional/bio/appl/test_pts1.rb | 6 ++++--
- test/functional/bio/io/test_ensembl.rb | 7 ++++---
- test/functional/bio/io/test_pubmed.rb | 8 +++++---
- test/functional/bio/io/test_soapwsdl.rb | 9 +++++----
- test/functional/bio/io/test_togows.rb | 9 +++++----
- test/functional/bio/sequence/test_output_embl.rb | 10 ++++++----
- test/functional/bio/test_command.rb | 10 +++++-----
- test/runner.rb | 8 +++++---
- test/unit/bio/appl/bl2seq/test_report.rb | 9 +++++----
- test/unit/bio/appl/blast/test_ncbioptions.rb | 6 ++++--
- test/unit/bio/appl/blast/test_report.rb | 9 +++++----
- test/unit/bio/appl/blast/test_rpsblast.rb | 9 +++++----
- test/unit/bio/appl/gcg/test_msf.rb | 10 +++++-----
- test/unit/bio/appl/genscan/test_report.rb | 17 ++++++++---------
- test/unit/bio/appl/hmmer/test_report.rb | 9 +++++----
- test/unit/bio/appl/iprscan/test_report.rb | 11 ++++++-----
- test/unit/bio/appl/mafft/test_report.rb | 11 ++++++-----
- test/unit/bio/appl/paml/codeml/test_rates.rb | 9 +++++----
- test/unit/bio/appl/paml/codeml/test_report.rb | 9 +++++----
- test/unit/bio/appl/paml/test_codeml.rb | 9 +++++----
- test/unit/bio/appl/sim4/test_report.rb | 9 +++++----
- test/unit/bio/appl/sosui/test_report.rb | 11 ++++++-----
- test/unit/bio/appl/targetp/test_report.rb | 8 +++++---
- test/unit/bio/appl/test_blast.rb | 9 +++++----
- test/unit/bio/appl/test_fasta.rb | 6 ++++--
- test/unit/bio/appl/test_pts1.rb | 6 ++++--
- test/unit/bio/appl/tmhmm/test_report.rb | 11 ++++++-----
- test/unit/bio/data/test_aa.rb | 8 +++++---
- test/unit/bio/data/test_codontable.rb | 9 +++++----
- test/unit/bio/data/test_na.rb | 8 +++++---
- test/unit/bio/db/biosql/tc_biosql.rb | 6 +++++-
- test/unit/bio/db/embl/test_common.rb | 6 ++++--
- test/unit/bio/db/embl/test_embl.rb | 12 ++++++------
- test/unit/bio/db/embl/test_embl_rel89.rb | 12 ++++++------
- test/unit/bio/db/embl/test_embl_to_bioseq.rb | 15 +++++++--------
- test/unit/bio/db/embl/test_sptr.rb | 14 ++++++--------
- test/unit/bio/db/embl/test_uniprot.rb | 11 ++++++-----
- test/unit/bio/db/kegg/test_genes.rb | 8 +++++---
- test/unit/bio/db/pdb/test_pdb.rb | 6 ++++--
- test/unit/bio/db/sanger_chromatogram/test_abif.rb | 3 ++-
- test/unit/bio/db/sanger_chromatogram/test_scf.rb | 3 ++-
- test/unit/bio/db/test_aaindex.rb | 12 ++++++------
- test/unit/bio/db/test_fasta.rb | 8 +++++---
- test/unit/bio/db/test_fastq.rb | 10 +++++-----
- test/unit/bio/db/test_gff.rb | 6 ++++--
- test/unit/bio/db/test_lasergene.rb | 12 +++++++-----
- test/unit/bio/db/test_medline.rb | 6 ++++--
- test/unit/bio/db/test_newick.rb | 12 ++++++------
- test/unit/bio/db/test_nexus.rb | 6 ++++--
- test/unit/bio/db/test_phyloxml.rb | 14 +++++++-------
- test/unit/bio/db/test_phyloxml_writer.rb | 15 +++++++--------
- test/unit/bio/db/test_prosite.rb | 11 ++++++-----
- test/unit/bio/db/test_rebase.rb | 8 +++++---
- test/unit/bio/db/test_soft.rb | 13 +++++++------
- test/unit/bio/io/flatfile/test_autodetection.rb | 13 ++++++-------
- test/unit/bio/io/flatfile/test_buffer.rb | 11 ++++++-----
- test/unit/bio/io/flatfile/test_splitter.rb | 8 ++++----
- test/unit/bio/io/test_ddbjxml.rb | 7 ++++---
- test/unit/bio/io/test_ensembl.rb | 8 +++++---
- test/unit/bio/io/test_fastacmd.rb | 7 ++++---
- test/unit/bio/io/test_flatfile.rb | 11 ++++++-----
- test/unit/bio/io/test_soapwsdl.rb | 7 ++++---
- test/unit/bio/io/test_togows.rb | 6 ++++--
- test/unit/bio/sequence/test_aa.rb | 8 +++++---
- test/unit/bio/sequence/test_common.rb | 6 ++++--
- test/unit/bio/sequence/test_compat.rb | 6 ++++--
- test/unit/bio/sequence/test_dblink.rb | 8 +++++---
- test/unit/bio/sequence/test_na.rb | 6 ++++--
- test/unit/bio/shell/plugin/test_seq.rb | 8 +++++---
- test/unit/bio/test_alignment.rb | 8 +++++---
- test/unit/bio/test_command.rb | 7 ++++---
- test/unit/bio/test_db.rb | 8 +++++---
- test/unit/bio/test_feature.rb | 6 ++++--
- test/unit/bio/test_location.rb | 6 ++++--
- test/unit/bio/test_map.rb | 8 +++++---
- test/unit/bio/test_pathway.rb | 6 ++++--
- test/unit/bio/test_reference.rb | 6 ++++--
- test/unit/bio/test_sequence.rb | 8 +++++---
- test/unit/bio/test_shell.rb | 8 +++++---
- test/unit/bio/test_tree.rb | 12 ++++++------
- .../analysis/test_calculated_cuts.rb | 6 ++++--
- .../restriction_enzyme/analysis/test_cut_ranges.rb | 6 ++++--
- .../analysis/test_sequence_range.rb | 6 ++++--
- .../double_stranded/test_aligned_strands.rb | 6 ++++--
- .../double_stranded/test_cut_location_pair.rb | 6 ++++--
- .../test_cut_location_pair_in_enzyme_notation.rb | 6 ++++--
- .../double_stranded/test_cut_locations.rb | 6 ++++--
- .../test_cut_locations_in_enzyme_notation.rb | 6 ++++--
- .../test_cut_locations_in_enzyme_notation.rb | 6 ++++--
- .../bio/util/restriction_enzyme/test_analysis.rb | 6 ++++--
- .../bio/util/restriction_enzyme/test_cut_symbol.rb | 6 ++++--
- .../restriction_enzyme/test_double_stranded.rb | 6 ++++--
- .../util/restriction_enzyme/test_single_strand.rb | 6 ++++--
- .../test_single_strand_complement.rb | 6 ++++--
- .../restriction_enzyme/test_string_formatting.rb | 6 ++++--
- test/unit/bio/util/test_color_scheme.rb | 8 +++++---
- test/unit/bio/util/test_contingency_table.rb | 8 +++++---
- test/unit/bio/util/test_restriction_enzyme.rb | 6 ++++--
- test/unit/bio/util/test_sirna.rb | 8 +++++---
- 99 files changed, 479 insertions(+), 343 deletions(-)
+ README_DEV.rdoc | 95 +++++++++++++++++++++++++++++++++++++++++++++++++++++-
+ 1 files changed, 93 insertions(+), 2 deletions(-)
-commit f4fa0a5edc6ff6fc35577d84bda86363014a57a4
+commit 3c952c4a782501b21f36ece5bcab672dab12fc6d
Author: Naohisa Goto <ng@bioruby.org>
-Date: Wed Nov 11 17:04:43 2009 +0900
+Date: Tue Sep 13 13:21:20 2011 +0900
- test_chromatogram.rb is splitted into test_abif.rb and test_scf.rb
+ README.rdoc: for release notes and changelog, about sample files.
- test/unit/bio/db/sanger_chromatogram/test_abif.rb | 75 +++++++++++++++
- .../db/sanger_chromatogram/test_chromatogram.rb | 101 --------------------
- test/unit/bio/db/sanger_chromatogram/test_scf.rb | 97 +++++++++++++++++++
- 3 files changed, 172 insertions(+), 101 deletions(-)
- create mode 100644 test/unit/bio/db/sanger_chromatogram/test_abif.rb
- delete mode 100644 test/unit/bio/db/sanger_chromatogram/test_chromatogram.rb
- create mode 100644 test/unit/bio/db/sanger_chromatogram/test_scf.rb
+ README.rdoc | 10 +++++++++-
+ 1 files changed, 9 insertions(+), 1 deletions(-)
-commit d9cc613273cadc7f9fdfe2bafbd933efb1f403ca
+commit fba9a6c0f1f79dd567ca54ba085b6258ac8efb31
Author: Naohisa Goto <ng@bioruby.org>
-Date: Wed Nov 11 17:01:37 2009 +0900
+Date: Tue Sep 13 13:20:05 2011 +0900
- Newly added unit test helper routine which aims to replace the libpath magic
+ RELEASE_NOTES.rdoc: mentioned about removal of rdoc.zsh.
- test/bioruby_test_helper.rb | 61 +++++++++++++++++++++++++++++++++++++++++++
- 1 files changed, 61 insertions(+), 0 deletions(-)
- create mode 100644 test/bioruby_test_helper.rb
+ RELEASE_NOTES.rdoc | 6 +++++-
+ 1 files changed, 5 insertions(+), 1 deletions(-)
-commit 10e76db2a8ec37bde541157d0735303b4ca8b3b8
+commit 685b6bb7b98083e1b50e73baf4e7fa71bc9a39fa
Author: Naohisa Goto <ng@bioruby.org>
-Date: Tue Nov 10 20:59:01 2009 +0900
+Date: Mon Sep 12 21:23:34 2011 +0900
- Bio::SangerChromatogram#to_s is renamed to sequence_string.
-
- lib/bio/db/sanger_chromatogram/chromatogram.rb | 2 +-
- 1 files changed, 1 insertions(+), 1 deletions(-)
-
-commit 0ec2c2f38c4b4a3e451841dc32540dfa10743bc2
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Fri Oct 30 22:49:19 2009 +0900
-
- Renamed/moved files/directories following the rename of class names.
+ bioruby.gemspec.erb: LEGAL is added to rdoc files
- * renamed: lib/bio/db/chromatogram.rb ->
- lib/bio/db/sanger_chromatogram/chromatogram.rb
- * renamed: lib/bio/db/chromatogram/abi.rb ->
- lib/bio/db/sanger_chromatogram/abif.rb
- * renamed: lib/bio/db/chromatogram/scf.rb ->
- lib/bio/db/sanger_chromatogram/scf.rb
- * renamed: lib/bio/db/chromatogram/chromatogram_to_biosequence.rb ->
- lib/bio/db/sanger_chromatogram/chromatogram_to_biosequence.rb
- * renamed: test/unit/bio/db/test_chromatogram.rb ->
- test/unit/bio/db/sanger_chromatogram/test_chromatogram.rb
- * renamed: test/data/chromatogram/test_chromatogram_abi.ab1 ->
- test/data/sanger_chromatogram/test_chromatogram_abif.ab1
- * renamed: test/data/chromatogram/*.scf ->
- test/data/sanger_chromatogram/*.scf
+ * bioruby.gemspec.erb: LEGAL is added to rdoc files.
+ * bioruby.gemspec is updated by "rake regemspec".
- lib/bio/db/chromatogram.rb | 133 -------------
- lib/bio/db/chromatogram/abi.rb | 114 -----------
- .../db/chromatogram/chromatogram_to_biosequence.rb | 32 ---
- lib/bio/db/chromatogram/scf.rb | 210 --------------------
- lib/bio/db/sanger_chromatogram/abif.rb | 114 +++++++++++
- lib/bio/db/sanger_chromatogram/chromatogram.rb | 133 +++++++++++++
- .../chromatogram_to_biosequence.rb | 32 +++
- lib/bio/db/sanger_chromatogram/scf.rb | 210 ++++++++++++++++++++
- test/data/chromatogram/test_chromatogram_abi.ab1 | Bin 228656 -> 0 bytes
- .../data/chromatogram/test_chromatogram_scf_v2.scf | Bin 47503 -> 0 bytes
- .../data/chromatogram/test_chromatogram_scf_v3.scf | Bin 47503 -> 0 bytes
- .../sanger_chromatogram/test_chromatogram_abif.ab1 | Bin 0 -> 228656 bytes
- .../test_chromatogram_scf_v2.scf | Bin 0 -> 47503 bytes
- .../test_chromatogram_scf_v3.scf | Bin 0 -> 47503 bytes
- .../db/sanger_chromatogram/test_chromatogram.rb | 101 ++++++++++
- test/unit/bio/db/test_chromatogram.rb | 101 ----------
- 16 files changed, 590 insertions(+), 590 deletions(-)
- delete mode 100644 lib/bio/db/chromatogram.rb
- delete mode 100644 lib/bio/db/chromatogram/abi.rb
- delete mode 100644 lib/bio/db/chromatogram/chromatogram_to_biosequence.rb
- delete mode 100644 lib/bio/db/chromatogram/scf.rb
- create mode 100644 lib/bio/db/sanger_chromatogram/abif.rb
- create mode 100644 lib/bio/db/sanger_chromatogram/chromatogram.rb
- create mode 100644 lib/bio/db/sanger_chromatogram/chromatogram_to_biosequence.rb
- create mode 100644 lib/bio/db/sanger_chromatogram/scf.rb
- delete mode 100644 test/data/chromatogram/test_chromatogram_abi.ab1
- delete mode 100644 test/data/chromatogram/test_chromatogram_scf_v2.scf
- delete mode 100644 test/data/chromatogram/test_chromatogram_scf_v3.scf
- create mode 100644 test/data/sanger_chromatogram/test_chromatogram_abif.ab1
- create mode 100644 test/data/sanger_chromatogram/test_chromatogram_scf_v2.scf
- create mode 100644 test/data/sanger_chromatogram/test_chromatogram_scf_v3.scf
- create mode 100644 test/unit/bio/db/sanger_chromatogram/test_chromatogram.rb
- delete mode 100644 test/unit/bio/db/test_chromatogram.rb
+ bioruby.gemspec | 9 ++++++---
+ bioruby.gemspec.erb | 6 +++++-
+ 2 files changed, 11 insertions(+), 4 deletions(-)
-commit 49bfe319e535c8414be32b47c07fe5204a24b398
+commit 414a6331f40fc99f554042e9a031689ea6d76da4
Author: Naohisa Goto <ng@bioruby.org>
-Date: Fri Oct 30 22:02:08 2009 +0900
+Date: Mon Sep 12 20:54:06 2011 +0900
- Renamed Chromatogram to SangerChromatogram and Abi to Abif, and preparation of filename changes.
+ deleted rdoc.zsh which is obsolete and unused
- * Renamed Chromatogram to SangerChromatogram because the word
- "chromatogram" may be used by various experimental methods
- other than the Sanger chromatogram.
- * Renamed Abi to Abif because Applied Biosystems who determined
- the file format says that its name is ABIF.
- * Preparation of changing filenames. However, filenames are
- not really changed now because of recording history of file
- contents modification. The paths shown in the "require" lines
- and test data paths may not be existed now.
+ * Deleted rdoc.zsh which is obsolete and unused.
+ To generate rdoc html, "rake rdoc" or "rake rerdoc".
+ See "rake -T" for more information.
- lib/bio.rb | 6 ++--
- lib/bio/db/chromatogram.rb | 24 +++++++-------
- lib/bio/db/chromatogram/abi.rb | 15 +++++----
- .../db/chromatogram/chromatogram_to_biosequence.rb | 10 +++---
- lib/bio/db/chromatogram/scf.rb | 15 +++++----
- lib/bio/sequence/adapter.rb | 3 +-
- test/unit/bio/db/test_chromatogram.rb | 32 ++++++++++---------
- 7 files changed, 57 insertions(+), 48 deletions(-)
+ rdoc.zsh | 8 --------
+ 1 files changed, 0 insertions(+), 8 deletions(-)
+ delete mode 100644 rdoc.zsh
-commit 6c020440663214014973ae8e5007ce2d31d8d45e
+commit 272d9106cec43b0f219edd92a6f7bd3f9875a761
Author: Naohisa Goto <ng@bioruby.org>
-Date: Sat Oct 24 00:44:47 2009 +0900
+Date: Mon Sep 12 20:35:47 2011 +0900
- New class method Bio::PhyloXML::Parser.open(filename) and API change of new(), etc.
+ Added new ChangeLog, showing changes after 1.4.2 release.
- * New class methods to create parser object from various data
- source are added: Bio::PhyloXML::Parser.open(filename),
- for_io(io), open_uri(uri).
- * API change of Bio::PhyloXML::Parser.new(). Now, new(filename)
- is deprecated and it can only take a XML-formatted string.
- * Tests are added and modified to reflect the above changes.
- * test/unit/bio/db/test_phyloxml_writer.rb: avoid using WeakRef
- for temporary directory maintenance.
+ * Added new ChangeLog, showing changes after 1.4.2 release.
+ For the changes before 1.4.2, see doc/ChangeLog-before-1.4.2.
+ For the changes before 1.3.1, see doc/ChangeLog-before-1.3.1.
- lib/bio/db/phyloxml/phyloxml_parser.rb | 224 +++++++++++++++++++++++++++---
- lib/bio/db/phyloxml/phyloxml_writer.rb | 4 +-
- test/unit/bio/db/test_phyloxml.rb | 178 ++++++++++++++++++++++--
- test/unit/bio/db/test_phyloxml_writer.rb | 70 +++++-----
- 4 files changed, 408 insertions(+), 68 deletions(-)
+ ChangeLog | 64 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ 1 files changed, 64 insertions(+), 0 deletions(-)
+ create mode 100644 ChangeLog
-commit fca5e800fc051a38ac6d25652c684fdd4f9bff14
+commit 941493378f9884978c81d5f63ee4ed5c175d4bea
Author: Naohisa Goto <ng@bioruby.org>
-Date: Fri Oct 23 15:13:25 2009 +0900
+Date: Mon Sep 12 20:28:28 2011 +0900
- Rearrangement of require and autoload so as to correctly load PhyloXML classes
-
- lib/bio.rb | 11 +++++++----
- lib/bio/db/phyloxml/phyloxml_elements.rb | 16 +++++++++++++++-
- lib/bio/db/phyloxml/phyloxml_parser.rb | 11 ++++++-----
- lib/bio/db/phyloxml/phyloxml_writer.rb | 5 ++++-
- test/unit/bio/db/test_phyloxml.rb | 5 -----
- test/unit/bio/db/test_phyloxml_writer.rb | 3 ---
- 6 files changed, 32 insertions(+), 19 deletions(-)
-
-commit a291af62ef262ee04f3a0e1b6415d4e256c56a94
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Fri Oct 23 00:08:44 2009 +0900
-
- Fixed argument order of assert_equal(expected, actual), etc.
+ Rakefile: add new task :rechangelog to update ChangeLog using git log.
- * Test bug fix: Argument order of assert_equal must be
- assert_equal(expected, actual).
- * assert_instance_of() instead of assert_equal() in
- TestPhyloXML1#test_init.
- * Removed some commented-out tests which may not be needed.
+ * Rakefile: add new task :rechangelog to update ChangeLog using
+ git log. Note that the tag name (currently 1.4.2) is hardcoded
+ in Rakefile.
- test/unit/bio/db/test_phyloxml.rb | 295 +++++++++++++++---------------
- test/unit/bio/db/test_phyloxml_writer.rb | 8 +-
- 2 files changed, 147 insertions(+), 156 deletions(-)
+ Rakefile | 9 +++++++++
+ 1 files changed, 9 insertions(+), 0 deletions(-)
-commit 152304dc9809102f56a2f1779c59111f84b9cd02
+commit 1c89e6546223c3c05ea79b8ade4b493580851efa
Author: Naohisa Goto <ng@bioruby.org>
-Date: Sat Oct 17 01:40:49 2009 +0900
+Date: Mon Sep 12 20:24:49 2011 +0900
- Improvement of tests for Bio::Fastq and related classes.
+ renamed ChangeLog to doc/ChangeLog-before-1.4.2
- test/unit/bio/db/test_fastq.rb | 372 ++++++++++++++++++++++++++--------------
- 1 files changed, 245 insertions(+), 127 deletions(-)
+ ChangeLog | 5013 --------------------------------------------
+ doc/ChangeLog-before-1.4.2 | 5013 ++++++++++++++++++++++++++++++++++++++++++++
+ 2 files changed, 5013 insertions(+), 5013 deletions(-)
+ delete mode 100644 ChangeLog
+ create mode 100644 doc/ChangeLog-before-1.4.2
-commit 61556223a469a5f8b1bb4f343eca92c88c66cb9a
+commit 2233fbada55034bd16fb5b9c642292b4b6ccca83
Author: Naohisa Goto <ng@bioruby.org>
-Date: Sat Oct 17 01:38:52 2009 +0900
+Date: Mon Sep 12 20:22:49 2011 +0900
- FASTQ output support is added to Bio::Sequence.
+ ChangeLog updated: add log about 1.4.2 release
- lib/bio/db/fastq/format_fastq.rb | 172 ++++++++++++++++++++++++++++++++++++++
- lib/bio/sequence/format.rb | 9 ++
- 2 files changed, 181 insertions(+), 0 deletions(-)
- create mode 100644 lib/bio/db/fastq/format_fastq.rb
+ ChangeLog | 9 +++++++++
+ 1 files changed, 9 insertions(+), 0 deletions(-)
-commit ea4203ebb7ca268a5b6d6c50aeb63ed0eed5a803
+commit 1c02ab0488e4097a2cf5c16180c3179c78e3d572
Author: Naohisa Goto <ng@bioruby.org>
-Date: Sat Oct 17 01:32:50 2009 +0900
+Date: Mon Sep 12 19:40:54 2011 +0900
- New attributes for genome sequencer data are added to Bio::Sequence.
-
- * New attributes for genome sequencer data are added to
- Bio::Sequence class: quality_scores, quality_scores_type,
- error_probabilities.
+ New RELEASE_NOTES.rdoc for next release version.
- lib/bio/sequence.rb | 13 +++++++++++++
- 1 files changed, 13 insertions(+), 0 deletions(-)
+ RELEASE_NOTES.rdoc | 47 +++++++++++++++++++++++++++++++++++++++++++++++
+ 1 files changed, 47 insertions(+), 0 deletions(-)
+ create mode 100644 RELEASE_NOTES.rdoc
-commit fce158b2194519081361e12c170882ec2e87fc5e
+commit 4e63e69e98c0c440ec476ef3407fcc8fd2411056
Author: Naohisa Goto <ng@bioruby.org>
-Date: Sat Oct 17 01:13:27 2009 +0900
+Date: Mon Sep 12 19:32:48 2011 +0900
- New methods Bio::Fastq#to_biosequence, etc. and improvement of tolerance for overflows
-
- * Bio::Fastq#to_biosequence is newly added.
- * New methods: Bio::Fastq#seq, entry_id, quality_score_type.
- * Default behavior of Bio::Fastq::FormatData#scores2str is changed
- not to raise error but to truncate saturated values.
- * Improvement of tolerance for overflows, and preventing to calculate
- log of negative number.
+ renamed RELEASE_NOTES.rdoc to doc/RELEASE_NOTES-1.4.2.rdoc
- lib/bio/db/fastq.rb | 105 ++++++++++++++++++++++++++++--
- lib/bio/db/fastq/fastq_to_biosequence.rb | 40 +++++++++++
- lib/bio/sequence/adapter.rb | 1 +
- 3 files changed, 139 insertions(+), 7 deletions(-)
- create mode 100644 lib/bio/db/fastq/fastq_to_biosequence.rb
+ RELEASE_NOTES.rdoc | 132 ------------------------------------------
+ doc/RELEASE_NOTES-1.4.2.rdoc | 132 ++++++++++++++++++++++++++++++++++++++++++
+ 2 files changed, 132 insertions(+), 132 deletions(-)
+ delete mode 100644 RELEASE_NOTES.rdoc
+ create mode 100644 doc/RELEASE_NOTES-1.4.2.rdoc
-commit 0f189974d2027cecee575b27e969de7f62508309
+commit 9c5c8cafc3ec372ef80aa20d01d13034f94d5af2
Author: Naohisa Goto <ng@bioruby.org>
-Date: Tue Oct 13 21:41:58 2009 +0900
+Date: Fri Sep 2 12:02:41 2011 +0900
- Avoid using Numeric#fdiv because it can only be used in Ruby 1.8.7 or later
+ Bio::BIORUBY_EXTRA_VERSION set to ".5000" (unstable version).
- lib/bio/db/fastq.rb | 6 +++---
- test/unit/bio/db/test_fastq.rb | 10 +++++-----
- 2 files changed, 8 insertions(+), 8 deletions(-)
-
-commit 42999fc6230e52c4f241f411d299db941196f62e
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Tue Oct 13 21:30:25 2009 +0900
-
- Bio::Fastq#qualities is renamed to quality_scores.
-
- * Bio::Fastq#qualities is renamed to Bio::Fastq#quality_scores, and
- the original method name is changed to be an alias of the new name.
-
- lib/bio/db/fastq.rb | 16 +++++++++-------
- test/unit/bio/db/test_fastq.rb | 30 +++++++++++++++---------------
- 2 files changed, 24 insertions(+), 22 deletions(-)
-
-commit cc0ee2169f298046c5e55fcbadfeaac01f6bf704
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Sun Oct 11 19:19:18 2009 +0900
-
- Newly added unit tests for Bio::Fastq with test data
-
- * Newly added unit tests for Bio::Fastq with test data. The test data
- is created by P.J.A. Cock et al., and is also used in Biopython and
- BioPerl.
-
- test/data/fastq/error_diff_ids.fastq | 20 +
- test/data/fastq/error_double_qual.fastq | 22 +
- test/data/fastq/error_double_seq.fastq | 22 +
- test/data/fastq/error_long_qual.fastq | 20 +
- test/data/fastq/error_no_qual.fastq | 20 +
- test/data/fastq/error_qual_del.fastq | 20 +
- test/data/fastq/error_qual_escape.fastq | 20 +
- test/data/fastq/error_qual_null.fastq | Bin 0 -> 610 bytes
- test/data/fastq/error_qual_space.fastq | 21 +
- test/data/fastq/error_qual_tab.fastq | 21 +
- test/data/fastq/error_qual_unit_sep.fastq | 20 +
- test/data/fastq/error_qual_vtab.fastq | 20 +
- test/data/fastq/error_short_qual.fastq | 20 +
- test/data/fastq/error_spaces.fastq | 20 +
- test/data/fastq/error_tabs.fastq | 21 +
- test/data/fastq/error_trunc_at_plus.fastq | 19 +
- test/data/fastq/error_trunc_at_qual.fastq | 19 +
- test/data/fastq/error_trunc_at_seq.fastq | 18 +
- test/data/fastq/error_trunc_in_plus.fastq | 19 +
- test/data/fastq/error_trunc_in_qual.fastq | 20 +
- test/data/fastq/error_trunc_in_seq.fastq | 18 +
- test/data/fastq/error_trunc_in_title.fastq | 17 +
- .../fastq/illumina_full_range_as_illumina.fastq | 8 +
- .../data/fastq/illumina_full_range_as_sanger.fastq | 8 +
- .../data/fastq/illumina_full_range_as_solexa.fastq | 8 +
- .../illumina_full_range_original_illumina.fastq | 8 +
- test/data/fastq/longreads_as_illumina.fastq | 40 ++
- test/data/fastq/longreads_as_sanger.fastq | 40 ++
- test/data/fastq/longreads_as_solexa.fastq | 40 ++
- test/data/fastq/longreads_original_sanger.fastq | 120 ++++
- test/data/fastq/misc_dna_as_illumina.fastq | 16 +
- test/data/fastq/misc_dna_as_sanger.fastq | 16 +
- test/data/fastq/misc_dna_as_solexa.fastq | 16 +
- test/data/fastq/misc_dna_original_sanger.fastq | 16 +
- test/data/fastq/misc_rna_as_illumina.fastq | 16 +
- test/data/fastq/misc_rna_as_sanger.fastq | 16 +
- test/data/fastq/misc_rna_as_solexa.fastq | 16 +
- test/data/fastq/misc_rna_original_sanger.fastq | 16 +
- .../data/fastq/sanger_full_range_as_illumina.fastq | 8 +
- test/data/fastq/sanger_full_range_as_sanger.fastq | 8 +
- test/data/fastq/sanger_full_range_as_solexa.fastq | 8 +
- .../fastq/sanger_full_range_original_sanger.fastq | 8 +
- .../data/fastq/solexa_full_range_as_illumina.fastq | 8 +
- test/data/fastq/solexa_full_range_as_sanger.fastq | 8 +
- test/data/fastq/solexa_full_range_as_solexa.fastq | 8 +
- .../fastq/solexa_full_range_original_solexa.fastq | 8 +
- test/data/fastq/wrapping_as_illumina.fastq | 12 +
- test/data/fastq/wrapping_as_sanger.fastq | 12 +
- test/data/fastq/wrapping_as_solexa.fastq | 12 +
- test/data/fastq/wrapping_original_sanger.fastq | 24 +
- test/unit/bio/db/test_fastq.rb | 711 ++++++++++++++++++++
- 51 files changed, 1652 insertions(+), 0 deletions(-)
- create mode 100644 test/data/fastq/error_diff_ids.fastq
- create mode 100644 test/data/fastq/error_double_qual.fastq
- create mode 100644 test/data/fastq/error_double_seq.fastq
- create mode 100644 test/data/fastq/error_long_qual.fastq
- create mode 100644 test/data/fastq/error_no_qual.fastq
- create mode 100644 test/data/fastq/error_qual_del.fastq
- create mode 100644 test/data/fastq/error_qual_escape.fastq
- create mode 100644 test/data/fastq/error_qual_null.fastq
- create mode 100644 test/data/fastq/error_qual_space.fastq
- create mode 100644 test/data/fastq/error_qual_tab.fastq
- create mode 100644 test/data/fastq/error_qual_unit_sep.fastq
- create mode 100644 test/data/fastq/error_qual_vtab.fastq
- create mode 100644 test/data/fastq/error_short_qual.fastq
- create mode 100644 test/data/fastq/error_spaces.fastq
- create mode 100644 test/data/fastq/error_tabs.fastq
- create mode 100644 test/data/fastq/error_trunc_at_plus.fastq
- create mode 100644 test/data/fastq/error_trunc_at_qual.fastq
- create mode 100644 test/data/fastq/error_trunc_at_seq.fastq
- create mode 100644 test/data/fastq/error_trunc_in_plus.fastq
- create mode 100644 test/data/fastq/error_trunc_in_qual.fastq
- create mode 100644 test/data/fastq/error_trunc_in_seq.fastq
- create mode 100644 test/data/fastq/error_trunc_in_title.fastq
- create mode 100644 test/data/fastq/illumina_full_range_as_illumina.fastq
- create mode 100644 test/data/fastq/illumina_full_range_as_sanger.fastq
- create mode 100644 test/data/fastq/illumina_full_range_as_solexa.fastq
- create mode 100644 test/data/fastq/illumina_full_range_original_illumina.fastq
- create mode 100644 test/data/fastq/longreads_as_illumina.fastq
- create mode 100644 test/data/fastq/longreads_as_sanger.fastq
- create mode 100644 test/data/fastq/longreads_as_solexa.fastq
- create mode 100644 test/data/fastq/longreads_original_sanger.fastq
- create mode 100644 test/data/fastq/misc_dna_as_illumina.fastq
- create mode 100644 test/data/fastq/misc_dna_as_sanger.fastq
- create mode 100644 test/data/fastq/misc_dna_as_solexa.fastq
- create mode 100644 test/data/fastq/misc_dna_original_sanger.fastq
- create mode 100644 test/data/fastq/misc_rna_as_illumina.fastq
- create mode 100644 test/data/fastq/misc_rna_as_sanger.fastq
- create mode 100644 test/data/fastq/misc_rna_as_solexa.fastq
- create mode 100644 test/data/fastq/misc_rna_original_sanger.fastq
- create mode 100644 test/data/fastq/sanger_full_range_as_illumina.fastq
- create mode 100644 test/data/fastq/sanger_full_range_as_sanger.fastq
- create mode 100644 test/data/fastq/sanger_full_range_as_solexa.fastq
- create mode 100644 test/data/fastq/sanger_full_range_original_sanger.fastq
- create mode 100644 test/data/fastq/solexa_full_range_as_illumina.fastq
- create mode 100644 test/data/fastq/solexa_full_range_as_sanger.fastq
- create mode 100644 test/data/fastq/solexa_full_range_as_solexa.fastq
- create mode 100644 test/data/fastq/solexa_full_range_original_solexa.fastq
- create mode 100644 test/data/fastq/wrapping_as_illumina.fastq
- create mode 100644 test/data/fastq/wrapping_as_sanger.fastq
- create mode 100644 test/data/fastq/wrapping_as_solexa.fastq
- create mode 100644 test/data/fastq/wrapping_original_sanger.fastq
- create mode 100644 test/unit/bio/db/test_fastq.rb
-
-commit 951d8f7303a5c28783a2c8b25c9fb347730c1a8f
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Sun Oct 11 19:10:15 2009 +0900
-
- Bio::Fastq API changed.
-
- * Bio::Fastq API changed. Removed methods: phred_quality, solexa_quality.
- New methods: qualities, error_probabilities, format, format=,
- validate_format.
- * New exception classes Bio::Fastq::Error::* for errors.
- * Internal structure is also changed. Internal only classes
- Bio::Fastq::FormatData::* which store parameters for format variants.
-
- lib/bio/db/fastq.rb | 519 +++++++++++++++++++++++++++++++++++++++++++++++++--
- 1 files changed, 501 insertions(+), 18 deletions(-)
-
-commit 9bb7f6ca762c615e50d98c35b60982a4caeea323
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Fri Sep 25 23:36:13 2009 +0900
-
- Bug fix: infinite loop in Bio::Fastq.new. Thanks to Hiroyuki Mishima for reporting the bug.
-
- lib/bio/db/fastq.rb | 16 ++++++++++------
- 1 files changed, 10 insertions(+), 6 deletions(-)
-
-commit fca6aa5333a95db4dc87e8fc814bd028d5720de4
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Fri Mar 20 11:52:33 2009 +0900
-
- Added file format autodetection for Bio::Fastq
-
- lib/bio/io/flatfile/autodetection.rb | 6 ++++++
- 1 files changed, 6 insertions(+), 0 deletions(-)
-
-commit 1ba21545e7d49ae8b775fbed7a4e92b1daa54ac6
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Fri Mar 20 11:48:59 2009 +0900
-
- Added autoload for Bio::Fastq
-
- lib/bio.rb | 1 +
- 1 files changed, 1 insertions(+), 0 deletions(-)
-
-commit 380b99106d4c7955b9d07ee8668b53d384c974f4
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Thu Mar 19 17:07:25 2009 +0900
-
- Newly added FASTQ format parser (still a prototype)
-
- lib/bio/db/fastq.rb | 162 +++++++++++++++++++++++++++++++++++++++++++++++++++
- 1 files changed, 162 insertions(+), 0 deletions(-)
- create mode 100644 lib/bio/db/fastq.rb
-
-commit 2c5df2a5f1b5ae1ea9e61c1dccc8bcd2f496f6ce
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Sun Sep 20 19:08:55 2009 +0900
-
- Removed "require 'rubygems'".
-
- lib/bio/db/phyloxml/phyloxml_parser.rb | 2 --
- 1 files changed, 0 insertions(+), 2 deletions(-)
-
-commit 67818d2550e5d53eeee0f3d710f66f7506fb8127
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Sat Sep 19 17:06:21 2009 +0900
-
- Use Bio::PubMed.esearch and efetch, etc.
-
- * Changed to use Bio::PubMed.esearch and efetch instead of
- deprecated methods.
- * Regular expression for extracting option is changed.
-
- sample/pmfetch.rb | 15 +++++++++++----
- sample/pmsearch.rb | 17 +++++++++++++----
- 2 files changed, 24 insertions(+), 8 deletions(-)
-
-commit 0c95889bf69e3140b5f09ade1203d50136aee014
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Fri Sep 18 17:58:17 2009 +0900
-
- Changed to use temporary directory when writing a file, etc.
-
- * To avoid unexpected file corruption and possibly security risk,
- changed to use temporary directory when writing files. The
- temporary directory is normally removed when all tests end.
- To prevent removing the directory, set environment variable
- BIORUBY_TEST_DEBUG.
- * To avoid test class name conflict, TestPhyloXMLData is renamed
- to TestPhyloXMLWriterData.
- * Added a new test to check existence of libxml-ruby, and removed
- code to raise error when it is not found. The code of the new
- test is completely the same as of in test_phyloxml.rb, but it
- is added for the purpose when test_phyloxml_writer.rb is called
- independently.
-
- test/unit/bio/db/test_phyloxml_writer.rb | 161 +++++++++++++++++++++---------
- 1 files changed, 112 insertions(+), 49 deletions(-)
-
-commit 520d0f5ed535f621aed60b71d8765a99e97306a6
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Sun Sep 20 18:34:19 2009 +0900
-
- Newly added internal-only class Bio::Command::Tmpdir to handle temporary directory
-
- * Newly added internal-only class Bio::Command::Tmpdir to handle
- temporary directory. It is BioRuby library internal use only.
- * Bio::Command.mktmpdir is changed to be completely compatible
- with Ruby 1.9.x's Dir.mktmpdir.
-
- lib/bio/command.rb | 104 +++++++++++++++++++++++++++++++---
- test/functional/bio/test_command.rb | 49 ++++++++++++++++
- 2 files changed, 143 insertions(+), 10 deletions(-)
-
-commit c813b60ae62f44d9688b21d47c84e4b7083547e6
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Fri Sep 18 17:55:14 2009 +0900
-
- Added new test to check existence of libxml-ruby, instead of raising error.
-
- test/unit/bio/db/test_phyloxml.rb | 30 ++++++++++++++++++++----------
- 1 files changed, 20 insertions(+), 10 deletions(-)
-
-commit 1b71dd9624640f3f775baab360eef0be92a86677
-Author: Diana Jaunzeikare <latvianlinuxgirl@gmail.com>
-Date: Fri Sep 18 21:43:18 2009 -0400
-
- Renamed output files generated by phyloxml_writer unit tests.
-
- test/unit/bio/db/test_phyloxml_writer.rb | 13 ++++++++++---
- 1 files changed, 10 insertions(+), 3 deletions(-)
-
-commit f8e138cb9e28996f1024fa9cf7c68c8f08603941
-Author: Diana Jaunzeikare <latvianlinuxgirl@gmail.com>
-Date: Fri Sep 18 21:33:35 2009 -0400
-
- Added ncbi_taxonomy_mollusca_short.xml test file
-
- .../data/phyloxml/ncbi_taxonomy_mollusca_short.xml | 65 ++++++++++++++++++++
- 1 files changed, 65 insertions(+), 0 deletions(-)
- create mode 100644 test/data/phyloxml/ncbi_taxonomy_mollusca_short.xml
-
-commit be1be310b7581928581cde24303fe2e16c04e82f
-Author: Diana Jaunzeikare <latvianlinuxgirl@gmail.com>
-Date: Fri Sep 18 21:29:20 2009 -0400
-
- Made the code compactible with libxml-ruby 1.1.3 (previous was 0.9.4) version.
-
- lib/bio/db/phyloxml/phyloxml_elements.rb | 58 +++++++++++++++---------------
- lib/bio/db/phyloxml/phyloxml_parser.rb | 10 ++++-
- lib/bio/db/phyloxml/phyloxml_writer.rb | 8 +++--
- 3 files changed, 42 insertions(+), 34 deletions(-)
-
-commit a3441afd5650069a5ada64b202a0714e8723e911
-Author: Diana Jaunzeikare <latvianlinuxgirl@gmail.com>
-Date: Tue May 26 00:55:47 2009 -0400
-
- Newly added PhyloXML support written by Diana Jaunzeikare.
-
- * Newly added PhyloXML support written by Diana Jaunzeikare.
- It have been written during the Google Summer of Code 2009
- "Implementing phyloXML support in BioRuby", mentored by
- Christian Zmasek et al. with NESCent. For details of development,
- see git://github.com/latvianlinuxgirl/bioruby.git and BioRuby
- mailing list archives.
- * This is a combination of 119 commits. The last commit date was
- Mon Aug 17 10:30:10 2009 -0400.
-
- README.rdoc | 3 +
- doc/Tutorial.rd | 120 ++-
- lib/bio.rb | 6 +
- lib/bio/db/phyloxml/phyloxml.xsd | 573 ++++++++
- lib/bio/db/phyloxml/phyloxml_elements.rb | 1160 +++++++++++++++++
- lib/bio/db/phyloxml/phyloxml_parser.rb | 767 +++++++++++
- lib/bio/db/phyloxml/phyloxml_writer.rb | 223 ++++
- test/data/phyloxml/apaf.xml | 666 ++++++++++
- test/data/phyloxml/bcl_2.xml | 2097 ++++++++++++++++++++++++++++++
- test/data/phyloxml/made_up.xml | 144 ++
- test/data/phyloxml/phyloxml_examples.xml | 415 ++++++
- test/unit/bio/db/test_phyloxml.rb | 619 +++++++++
- test/unit/bio/db/test_phyloxml_writer.rb | 258 ++++
- 13 files changed, 7050 insertions(+), 1 deletions(-)
- create mode 100644 lib/bio/db/phyloxml/phyloxml.xsd
- create mode 100644 lib/bio/db/phyloxml/phyloxml_elements.rb
- create mode 100644 lib/bio/db/phyloxml/phyloxml_parser.rb
- create mode 100644 lib/bio/db/phyloxml/phyloxml_writer.rb
- create mode 100644 test/data/phyloxml/apaf.xml
- create mode 100644 test/data/phyloxml/bcl_2.xml
- create mode 100644 test/data/phyloxml/made_up.xml
- create mode 100644 test/data/phyloxml/phyloxml_examples.xml
- create mode 100644 test/unit/bio/db/test_phyloxml.rb
- create mode 100644 test/unit/bio/db/test_phyloxml_writer.rb
-
-commit fd8281f03423ddf23f7d409863b4df647f1b1564
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Wed Sep 9 21:08:15 2009 +0900
-
- Newly added Chromatogram classes contributed by Anthony Underwood.
-
- * Newly added Chromatogram classes contributed by Anthony Underwood.
- See git://github.com/aunderwo/bioruby.git for details of development
- before this merge.
-
- lib/bio.rb | 3 +
- lib/bio/db/chromatogram.rb | 133 +++++++++++++
- lib/bio/db/chromatogram/abi.rb | 111 +++++++++++
- .../db/chromatogram/chromatogram_to_biosequence.rb | 32 +++
- lib/bio/db/chromatogram/scf.rb | 207 ++++++++++++++++++++
- lib/bio/sequence/adapter.rb | 1 +
- test/data/chromatogram/test_chromatogram_abi.ab1 | Bin 0 -> 228656 bytes
- .../data/chromatogram/test_chromatogram_scf_v2.scf | Bin 0 -> 47503 bytes
- .../data/chromatogram/test_chromatogram_scf_v3.scf | Bin 0 -> 47503 bytes
- test/unit/bio/db/test_chromatogram.rb | 99 ++++++++++
- 10 files changed, 586 insertions(+), 0 deletions(-)
- create mode 100644 lib/bio/db/chromatogram.rb
- create mode 100644 lib/bio/db/chromatogram/abi.rb
- create mode 100644 lib/bio/db/chromatogram/chromatogram_to_biosequence.rb
- create mode 100644 lib/bio/db/chromatogram/scf.rb
- create mode 100644 test/data/chromatogram/test_chromatogram_abi.ab1
- create mode 100644 test/data/chromatogram/test_chromatogram_scf_v2.scf
- create mode 100644 test/data/chromatogram/test_chromatogram_scf_v3.scf
- create mode 100644 test/unit/bio/db/test_chromatogram.rb
-
-commit 78f9463b764687401ff4a7480c1383c5594e5133
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Thu Sep 10 12:38:25 2009 +0900
-
- Bio::BIORUBY_EXTRA_VERSION is changed to ".5000".
-
- bioruby.gemspec | 2 +-
lib/bio/version.rb | 2 +-
- 2 files changed, 2 insertions(+), 2 deletions(-)
-
-commit e731c6e52bc9a672e4546eeca4f2d2d968bdba09
-Author: Naohisa Goto <ng@bioruby.org>
-Date: Wed Sep 2 15:24:00 2009 +0900
-
- BioRuby 1.3.1 is released.
-
- ChangeLog is modified, and bioruby.gemspec is regenerated.
-
- ChangeLog | 11 +++++++++++
- bioruby.gemspec | 2 +-
- 2 files changed, 12 insertions(+), 1 deletions(-)
+ 1 files changed, 1 insertions(+), 1 deletions(-)