ngoto's Profile

ngoto created tag 1.4.0 at bioruby/bioruby Mon Dec 28 05:22:10 -0800 2009

New tag is at bioruby/bioruby/tree/1.4.0

ngoto pushed to master at bioruby/bioruby Mon Dec 28 05:20:13 -0800 2009

HEAD is a1bda9088662edec55af0106b4292c39e51c8b7b

11 commits »

Naohisa Goto committed a1bda908:

BioRuby 1.4.0 is released.
Naohisa Goto committed 5c888963:

Preparation for bioruby-1.4.0 release.
Naohisa Goto committed 11f56d3d:

Added about ChangeLog which is replaced by git-log.
Naohisa Goto committed 17d5b182:

ChangeLog is autogenerated from git log.
Naohisa Goto committed 02bf77af:

test_output_size is disabled because it depends on html decorations
Naohisa Goto committed 5781fb40:

The PTS1 Predictor's URL had been changed.
Naohisa Goto committed a4e691d9:

Preparation of ChangeLog autogeneration: old ChangeLog is moved to doc/ChangeLog-before-1.3.1.
Naohisa Goto committed c0116047:

Tutorial.rd.html is regenerated.
Naohisa Goto committed 6e2cdd13:

Added Bio::NCBI.default_email= in the example, and examples using deprecated Bio::PubMed methods are temporarily commented out.
Naohisa Goto committed 8e6d5e9b:

Reinserted "==>" for Blast example, and removed duplicated Ruby Ensembl API example.
pjotrp committed 849edd7e:

Tutorial: Added info on how to run rubydoctest

ngoto pushed to master at ngoto/bioruby Mon Dec 28 05:08:55 -0800 2009

HEAD is a1bda9088662edec55af0106b4292c39e51c8b7b

11 commits »

Naohisa Goto committed a1bda908:

BioRuby 1.4.0 is released.
Naohisa Goto committed 5c888963:

Preparation for bioruby-1.4.0 release.
Naohisa Goto committed 11f56d3d:

Added about ChangeLog which is replaced by git-log.
Naohisa Goto committed 17d5b182:

ChangeLog is autogenerated from git log.
Naohisa Goto committed 02bf77af:

test_output_size is disabled because it depends on html decorations
Naohisa Goto committed 5781fb40:

The PTS1 Predictor's URL had been changed.
Naohisa Goto committed a4e691d9:

Preparation of ChangeLog autogeneration: old ChangeLog is moved to doc/ChangeLog-before-1.3.1.
Naohisa Goto committed c0116047:

Tutorial.rd.html is regenerated.
Naohisa Goto committed 6e2cdd13:

Added Bio::NCBI.default_email= in the example, and examples using deprecated Bio::PubMed methods are temporarily commented out.
Naohisa Goto committed 8e6d5e9b:

Reinserted "==>" for Blast example, and removed duplicated Ruby Ensembl API example.
pjotrp committed 849edd7e:

Tutorial: Added info on how to run rubydoctest

ngoto pushed to incoming at ngoto/bioruby Mon Dec 28 05:00:59 -0800 2009

HEAD is a1bda9088662edec55af0106b4292c39e51c8b7b

7 commits »

ngoto pushed to incoming at ngoto/bioruby Mon Dec 28 01:29:06 -0800 2009

HEAD is c011604766baa3cdf5ca2f4a776aa67c56460d29

4 commits »

ngoto pushed to master at bioruby/bioruby Thu Dec 24 22:03:31 -0800 2009

HEAD is a39fcf0ca1a5265789110f42cc616fc5d3c16414

14 commits »

Naohisa Goto committed a39fcf0c:

Modified for release notes and fixed typo.
Naohisa Goto committed 3fa8b68f:

Changes following the rename to RELEASE_NOTES.rdoc.
Naohisa Goto committed fd692a11:

Renamed doc/Changes-1.4.rdoc to RELEASE_NOTES.rdoc.
Naohisa Goto committed 0e37f04d:

Changed Bio::PhyloXML::Parser.new to open, and regenerated html.
Naohisa Goto committed aeacbbd4:

bioruby.gemspec is regenerated
Naohisa Goto committed 1034205c:

Version number changed to 1.4.0-rc1
Naohisa Goto committed 04bf2da4:

Issues added and modified.
Naohisa Goto committed f1a76157:

Added news and incompatible changes.
Naohisa Goto committed 9c8ef18a:

Email address for NCBI Entrez is given with Bio::NCBI.default_email=.
Naohisa Goto committed 7a717966:

Changed autoload hierarchy of Bio::NCBI.
Naohisa Goto committed f8dc0268:

New singleton methods Bio::NCBI.default_email=, default_tool=, etc.
Naohisa Goto committed 2e311dc4:

Description about the incompatible change of Bio::KEGG::REACTION#rpairs.
Naohisa Goto committed d57ace3a:

Bio::KEGG::R#ACTION#rpairs is changed to return a hash.
Naohisa Goto committed 60e4c77d:

Document bug fix: return value mistake.

ngoto pushed to master at ngoto/bioruby Thu Dec 24 21:59:59 -0800 2009

HEAD is a39fcf0ca1a5265789110f42cc616fc5d3c16414

14 commits »

Naohisa Goto committed a39fcf0c:

Modified for release notes and fixed typo.
Naohisa Goto committed 3fa8b68f:

Changes following the rename to RELEASE_NOTES.rdoc.
Naohisa Goto committed fd692a11:

Renamed doc/Changes-1.4.rdoc to RELEASE_NOTES.rdoc.
Naohisa Goto committed 0e37f04d:

Changed Bio::PhyloXML::Parser.new to open, and regenerated html.
Naohisa Goto committed aeacbbd4:

bioruby.gemspec is regenerated
Naohisa Goto committed 1034205c:

Version number changed to 1.4.0-rc1
Naohisa Goto committed 04bf2da4:

Issues added and modified.
Naohisa Goto committed f1a76157:

Added news and incompatible changes.
Naohisa Goto committed 9c8ef18a:

Email address for NCBI Entrez is given with Bio::NCBI.default_email=.
Naohisa Goto committed 7a717966:

Changed autoload hierarchy of Bio::NCBI.
Naohisa Goto committed f8dc0268:

New singleton methods Bio::NCBI.default_email=, default_tool=, etc.
Naohisa Goto committed 2e311dc4:

Description about the incompatible change of Bio::KEGG::REACTION#rpairs.
Naohisa Goto committed d57ace3a:

Bio::KEGG::R#ACTION#rpairs is changed to return a hash.
Naohisa Goto committed 60e4c77d:

Document bug fix: return value mistake.

ngoto pushed to incoming at ngoto/bioruby Thu Dec 24 20:28:40 -0800 2009

HEAD is a39fcf0ca1a5265789110f42cc616fc5d3c16414

3 commits »

ngoto pushed to incoming at ngoto/bioruby Thu Dec 24 04:51:14 -0800 2009

HEAD is 0e37f04dd8d34517693fdd4bc27f8bdada7c2f13

Naohisa Goto committed 0e37f04d:

Changed Bio::PhyloXML::Parser.new to open, and regenerated html.

ngoto pushed to incoming at ngoto/bioruby Thu Dec 24 02:27:50 -0800 2009

HEAD is aeacbbd425c2e88369c171bd92c60bf8e520a9e5

10 commits »

Naohisa Goto committed aeacbbd4:

bioruby.gemspec is regenerated
Naohisa Goto committed 1034205c:

Version number changed to 1.4.0-rc1
Naohisa Goto committed 04bf2da4:

Issues added and modified.
Naohisa Goto committed f1a76157:

Added news and incompatible changes.
Naohisa Goto committed 9c8ef18a:

Email address for NCBI Entrez is given with Bio::NCBI.default_email=.
Naohisa Goto committed 7a717966:

Changed autoload hierarchy of Bio::NCBI.
Naohisa Goto committed f8dc0268:

New singleton methods Bio::NCBI.default_email=, default_tool=, etc.
Naohisa Goto committed 2e311dc4:

Description about the incompatible change of Bio::KEGG::REACTION#rpairs.
Naohisa Goto committed d57ace3a:

Bio::KEGG::R#ACTION#rpairs is changed to return a hash.
Naohisa Goto committed 60e4c77d:

Document bug fix: return value mistake.

ngoto pushed to master at bioruby/bioruby Sun Dec 20 00:58:19 -0800 2009

HEAD is 6376dd55aa4995769746e556ca719d37f02975d6

Naohisa Goto committed 6376dd55:

Added README.txt for FASTQ example data.

ngoto pushed to master at ngoto/bioruby Sun Dec 20 00:56:23 -0800 2009

HEAD is 6376dd55aa4995769746e556ca719d37f02975d6

Naohisa Goto committed 6376dd55:

Added README.txt for FASTQ example data.

ngoto pushed to incoming at ngoto/bioruby Sun Dec 20 00:56:00 -0800 2009

HEAD is 6376dd55aa4995769746e556ca719d37f02975d6

Naohisa Goto committed 6376dd55:

Added README.txt for FASTQ example data.

ngoto pushed to master at bioruby/bioruby Wed Dec 16 09:16:48 -0800 2009

HEAD is 8dec18794c846726733d66c5a22170f5b2c4bb1a

24 commits »

Naohisa Goto committed f364ea60:

Version is changed to 1.4.0-alpha1, and bioruby.gemspec is regenerated.
Naohisa Goto committed 096b5fbf:

Added documents about Bio::KEGG incompatible changes.
Naohisa Goto committed 72ed277f:

Newly added unit tests for Bio::KEGG::ENZYME with test data.
Naohisa Goto committed b99fcb39:

Changed Bio::KEGG::*#dblinks, pathways, orthologs, genes methods.
Naohisa Goto committed 2cc9d4e2:

Bio::KEGG::GENES#structure no more adds PDB: prefix.
Naohisa Goto committed a8ceb23b:

Refactoring of Bio::KEGG::Orthology#dblinks and genes.
Naohisa Goto committed 720e0bcc:

Changed dummy lines for RDoc.
Naohisa Goto committed 20f8c03a:

Refactoring of Bio::KEGG::REACTION#orthologs.
Naohisa Goto committed b924601b:

Bio::KEGG::GENES#pathways is changed to return raw lines as an Array of strings.
Kozo Nishida committed 4c840dc6:

Added test methods.
Naohisa Goto committed 105efa1e:

Refactoring: to use lib/bio/db/kegg/common.rb for dblinks_as_hash method.
Naohisa Goto committed c394ead0:

Bio::KEGG::REACTION#orthologies is renamed to orthologs_as_hash with changing its return value to a hash.
Naohisa Goto committed 4e01fda2:

Added Bio::KEGG::REACTION#pathways_as_hash and reverted pathways method.
Naohisa Goto committed 0c2ce4b8:

New methods Bio::KEGG::COMPOUND#dblinks_as_hash and pathways_as_hash, using modules in lib/bio/db/kegg/common.rb.
Naohisa Goto committed 63df07e0:

Methods commonly used from Bio::KEGG::* classes.
Naohisa Goto committed 0e55c670:

Bio::KEGG::COMPOUND#dblinks is reverted to return an array of string.
Naohisa Goto committed a05adcdd:

Bug fix: fixed a copy-and-paste mistake.
Naohisa Goto committed 86925f3c:

Bio::KEGG::ORTHOLOGY#dblinks_as_hash should preserve database names.
Naohisa Goto committed 60847cd2:

Test class names are changed to avoid potential class name conflict.
Kozo Nishida committed 2bda62af:

Added unit tests for Bio::KEGG::ORTHOLOGY.

And 4 more commits...

ngoto pushed to master at ngoto/bioruby Mon Dec 14 23:40:20 -0800 2009

HEAD is 8dec18794c846726733d66c5a22170f5b2c4bb1a

3 commits »

ngoto pushed to incoming at ngoto/bioruby Mon Dec 14 22:21:09 -0800 2009

HEAD is 8dec18794c846726733d66c5a22170f5b2c4bb1a

2 commits »

ngoto pushed to incoming at ngoto/bioruby Mon Dec 14 20:35:46 -0800 2009

HEAD is 0706fcf7fb7b738c5e82c5c33cf63a3d69edcecb

Naohisa Goto committed 0706fcf7:

Newly added unit test for Bio::KEGG::DRUG with test data.

ngoto pushed to incoming at ngoto/bioruby Mon Dec 14 18:45:57 -0800 2009

HEAD is b7fbc729e6274555ad41237e9944924bf423304d

2 commits »

ngoto pushed to master at ngoto/bioruby Thu Dec 10 08:40:53 -0800 2009

HEAD is 48184d96b989f909ac0effb759cbc4b1ddc98dd1

Naohisa Goto committed 48184d96:

Methods in Bio::KEGG::Common::* are changed to cache return values in instance variables.

ngoto pushed to incoming at ngoto/bioruby Thu Dec 10 08:40:18 -0800 2009

HEAD is 48184d96b989f909ac0effb759cbc4b1ddc98dd1

Naohisa Goto committed 48184d96:

Methods in Bio::KEGG::Common::* are changed to cache return values in instance variables.

ngoto pushed to incoming at ngoto/bioruby Thu Dec 10 08:39:25 -0800 2009

HEAD is 314b37576bf96d6c049961fdfcee08b9991df715

Naohisa Goto committed 314b3757:

Methods in Bio::KEGG::Common are changed to cache return values in instance variables.

ngoto pushed to master at ngoto/bioruby Thu Dec 10 08:26:44 -0800 2009

HEAD is f364ea609f1e01ca5270a5bd7404e0bbf752bc89

20 commits »

Naohisa Goto committed f364ea60:

Version is changed to 1.4.0-alpha1, and bioruby.gemspec is regenerated.
Naohisa Goto committed 096b5fbf:

Added documents about Bio::KEGG incompatible changes.
Naohisa Goto committed 72ed277f:

Newly added unit tests for Bio::KEGG::ENZYME with test data.
Naohisa Goto committed b99fcb39:

Changed Bio::KEGG::*#dblinks, pathways, orthologs, genes methods.
Naohisa Goto committed 2cc9d4e2:

Bio::KEGG::GENES#structure no more adds PDB: prefix.
Naohisa Goto committed a8ceb23b:

Refactoring of Bio::KEGG::Orthology#dblinks and genes.
Naohisa Goto committed 720e0bcc:

Changed dummy lines for RDoc.
Naohisa Goto committed 20f8c03a:

Refactoring of Bio::KEGG::REACTION#orthologs.
Naohisa Goto committed b924601b:

Bio::KEGG::GENES#pathways is changed to return raw lines as an Array of strings.
Kozo Nishida committed 4c840dc6:

Added test methods.
Naohisa Goto committed 105efa1e:

Refactoring: to use lib/bio/db/kegg/common.rb for dblinks_as_hash method.
Naohisa Goto committed c394ead0:

Bio::KEGG::REACTION#orthologies is renamed to orthologs_as_hash with changing its return value to a hash.
Naohisa Goto committed 4e01fda2:

Added Bio::KEGG::REACTION#pathways_as_hash and reverted pathways method.
Naohisa Goto committed 0c2ce4b8:

New methods Bio::KEGG::COMPOUND#dblinks_as_hash and pathways_as_hash, using modules in lib/bio/db/kegg/common.rb.
Naohisa Goto committed 63df07e0:

Methods commonly used from Bio::KEGG::* classes.
Naohisa Goto committed 0e55c670:

Bio::KEGG::COMPOUND#dblinks is reverted to return an array of string.
Naohisa Goto committed a05adcdd:

Bug fix: fixed a copy-and-paste mistake.
Naohisa Goto committed 86925f3c:

Bio::KEGG::ORTHOLOGY#dblinks_as_hash should preserve database names.
Naohisa Goto committed 60847cd2:

Test class names are changed to avoid potential class name conflict.
Kozo Nishida committed 2bda62af:

Added unit tests for Bio::KEGG::ORTHOLOGY.

ngoto pushed to incoming at ngoto/bioruby Thu Dec 10 08:26:10 -0800 2009

HEAD is f364ea609f1e01ca5270a5bd7404e0bbf752bc89

9 commits »

Naohisa Goto committed f364ea60:

Version is changed to 1.4.0-alpha1, and bioruby.gemspec is regenerated.
Naohisa Goto committed 096b5fbf:

Added documents about Bio::KEGG incompatible changes.
Naohisa Goto committed 72ed277f:

Newly added unit tests for Bio::KEGG::ENZYME with test data.
Naohisa Goto committed b99fcb39:

Changed Bio::KEGG::*#dblinks, pathways, orthologs, genes methods.
Naohisa Goto committed 2cc9d4e2:

Bio::KEGG::GENES#structure no more adds PDB: prefix.
Naohisa Goto committed a8ceb23b:

Refactoring of Bio::KEGG::Orthology#dblinks and genes.
Naohisa Goto committed 720e0bcc:

Changed dummy lines for RDoc.
Naohisa Goto committed 20f8c03a:

Refactoring of Bio::KEGG::REACTION#orthologs.
Naohisa Goto committed b924601b:

Bio::KEGG::GENES#pathways is changed to return raw lines as an Array of strings.

ngoto pushed to incoming at ngoto/bioruby Wed Dec 02 06:58:23 -0800 2009

HEAD is 4c840dc6a539db1d854b23991269b3e6515f637e

8 commits »

Kozo Nishida committed 4c840dc6:

Added test methods.
Naohisa Goto committed 105efa1e:

Refactoring: to use lib/bio/db/kegg/common.rb for dblinks_as_hash method.
Naohisa Goto committed c394ead0:

Bio::KEGG::REACTION#orthologies is renamed to orthologs_as_hash with changing its return value to a hash.
Naohisa Goto committed 4e01fda2:

Added Bio::KEGG::REACTION#pathways_as_hash and reverted pathways method.
Naohisa Goto committed 0c2ce4b8:

New methods Bio::KEGG::COMPOUND#dblinks_as_hash and pathways_as_hash, using modules in lib/bio/db/kegg/common.rb.
Naohisa Goto committed 63df07e0:

Methods commonly used from Bio::KEGG::* classes.
Naohisa Goto committed 0e55c670:

Bio::KEGG::COMPOUND#dblinks is reverted to return an array of string.
Naohisa Goto committed a05adcdd:

Bug fix: fixed a copy-and-paste mistake.

ngoto pushed to incoming at ngoto/bioruby Tue Dec 01 04:41:15 -0800 2009

HEAD is 86925f3c80730e3ea3377a23a70cadb3876258c4

Naohisa Goto committed 86925f3c:

Bio::KEGG::ORTHOLOGY#dblinks_as_hash should preserve database names.

ngoto pushed to incoming at ngoto/bioruby Tue Dec 01 03:45:43 -0800 2009

HEAD is 60847cd2d0701fa38a499578649cb216c93993a2

2 commits »

ngoto pushed to master at bioruby/bioruby Tue Dec 01 02:49:10 -0800 2009

HEAD is acad9497caf5d737394568e911691fdad11ca091

Naohisa Goto committed acad9497:

Changed to use BioRubyTestDataPath instead of __FILE__.

ngoto pushed to master at ngoto/bioruby Mon Nov 30 05:31:02 -0800 2009

HEAD is acad9497caf5d737394568e911691fdad11ca091

Naohisa Goto committed acad9497:

Changed to use BioRubyTestDataPath instead of __FILE__.

ngoto pushed to incoming at ngoto/bioruby Mon Nov 30 05:30:39 -0800 2009

HEAD is acad9497caf5d737394568e911691fdad11ca091

Naohisa Goto committed acad9497:

Changed to use BioRubyTestDataPath instead of __FILE__.

ngoto pushed to master at bioruby/bioruby Sat Nov 28 23:53:34 -0800 2009

HEAD is 8e95f3fb60cd61b2bfad8e66caf03d3ff02a6dca

55 commits »

Naohisa Goto committed e965b454:

Demo codes in the "if __FILE__ == $0" are moved to sample/demo_kegg_compound.rb.
Naohisa Goto committed 7454db7c:

Demo codes in the "if __FILE__ == $0" are moved to sample/demo_litdb.rb.
Naohisa Goto committed fde28424:

Ruby 1.9 support: String#each_line instead of String#each
Naohisa Goto committed 8b600996:

Sample code bug fix: fixed method names, and workaround for Zlib error.
Naohisa Goto committed 737fec3d:

Demo codes in the "if __FILE__ == $0" are moved to sample/demo_go.rb.
Naohisa Goto committed 8264b156:

Document bug fix: Changed Bio::Bl2seq to Bio::Blast::Bl2seq in the RDoc.
Naohisa Goto committed c572ff02:

Bug fix: Failed to read Bio::Blast::Bl2seq::Report data by using Bio::FlatFile.
Naohisa Goto committed 4f6b0806:

Demo codes in the "if __FILE__ == $0" are moved to sample/demo_bl2seq_report.rb.
Naohisa Goto committed 2f03e875:

Demo codes in the "if __FILE__ == $0" are moved to sample/demo_genbank.rb.
Naohisa Goto committed a2981c28:

Demo codes in the "if __FILE__ == $0" are moved to sample/demo_aaindex.rb.
Naohisa Goto committed b741d17e:

Demo codes in the "if __FILE__ == $0" are moved to sample/demo_sirna.rb
Naohisa Goto committed 7cc778e7:

Demo codes in the "if __FILE__ == $0" are moved to sample/demo_pathway.rb.
Naohisa Goto committed 7e551058:

Demo codes in the "if __FILE__ == $0" are moved to sample/demo_locations.rb.
Naohisa Goto committed f1c02666:

Demo codes in the "if __FILE__ == $0" are moved to sample/demo_codontable.rb.
Naohisa Goto committed c11a7793:

Demo codes in the "if __FILE__ == $0" are moved to sample/demo_nucleicacid.rb.
Naohisa Goto committed de41b67c:

Demo codes in the "if __FILE__ == $0" are moved to sample/demo_aminoacid.rb.
Naohisa Goto committed e652dd44:

Added an error message about encoding in Ruby 1.9.1
Naohisa Goto committed 003133b0:

changed recommended Ruby version
Naohisa Goto committed 408483d3:

added information about doc/Changes-1.4.rdoc
Naohisa Goto committed ef342933:

In PhyloXML support, added a link to GNOME Libxml2 and fixed RDoc syntax.

And 35 more commits...

ngoto pushed to incoming at ngoto/bioruby Sat Nov 28 23:43:31 -0800 2009

HEAD is 8e95f3fb60cd61b2bfad8e66caf03d3ff02a6dca

2 commits »

ngoto pushed to master at ngoto/bioruby Sat Nov 28 23:43:20 -0800 2009

HEAD is 8e95f3fb60cd61b2bfad8e66caf03d3ff02a6dca

2 commits »

ngoto pushed to master at ngoto/bioruby Sat Nov 28 22:48:09 -0800 2009

HEAD is aa8d49bf31f90dd2796c18ee0aa6291979284ec2

53 commits »

Naohisa Goto committed e965b454:

Demo codes in the "if __FILE__ == $0" are moved to sample/demo_kegg_compound.rb.
Naohisa Goto committed 7454db7c:

Demo codes in the "if __FILE__ == $0" are moved to sample/demo_litdb.rb.
Naohisa Goto committed fde28424:

Ruby 1.9 support: String#each_line instead of String#each
Naohisa Goto committed 8b600996:

Sample code bug fix: fixed method names, and workaround for Zlib error.
Naohisa Goto committed 737fec3d:

Demo codes in the "if __FILE__ == $0" are moved to sample/demo_go.rb.
Naohisa Goto committed 8264b156:

Document bug fix: Changed Bio::Bl2seq to Bio::Blast::Bl2seq in the RDoc.
Naohisa Goto committed c572ff02:

Bug fix: Failed to read Bio::Blast::Bl2seq::Report data by using Bio::FlatFile.
Naohisa Goto committed 4f6b0806:

Demo codes in the "if __FILE__ == $0" are moved to sample/demo_bl2seq_report.rb.
Naohisa Goto committed 2f03e875:

Demo codes in the "if __FILE__ == $0" are moved to sample/demo_genbank.rb.
Naohisa Goto committed a2981c28:

Demo codes in the "if __FILE__ == $0" are moved to sample/demo_aaindex.rb.
Naohisa Goto committed b741d17e:

Demo codes in the "if __FILE__ == $0" are moved to sample/demo_sirna.rb
Naohisa Goto committed 7cc778e7:

Demo codes in the "if __FILE__ == $0" are moved to sample/demo_pathway.rb.
Naohisa Goto committed 7e551058:

Demo codes in the "if __FILE__ == $0" are moved to sample/demo_locations.rb.
Naohisa Goto committed f1c02666:

Demo codes in the "if __FILE__ == $0" are moved to sample/demo_codontable.rb.
Naohisa Goto committed c11a7793:

Demo codes in the "if __FILE__ == $0" are moved to sample/demo_nucleicacid.rb.
Naohisa Goto committed de41b67c:

Demo codes in the "if __FILE__ == $0" are moved to sample/demo_aminoacid.rb.
Naohisa Goto committed e652dd44:

Added an error message about encoding in Ruby 1.9.1
Naohisa Goto committed 003133b0:

changed recommended Ruby version
Naohisa Goto committed 408483d3:

added information about doc/Changes-1.4.rdoc
Naohisa Goto committed ef342933:

In PhyloXML support, added a link to GNOME Libxml2 and fixed RDoc syntax.

And 33 more commits...

ngoto pushed to incoming at ngoto/bioruby Sat Nov 28 22:47:20 -0800 2009

HEAD is aa8d49bf31f90dd2796c18ee0aa6291979284ec2

6 commits »

ngoto pushed to incoming at ngoto/bioruby Wed Nov 25 22:59:52 -0800 2009

HEAD is 4f7bd1b7628d90661d8b557ca854b14cc44fb99c

Naohisa Goto committed 4f7bd1b7:

Demo codes in the "if __FILE__ == $0" are removed because they are very short.

ngoto (Naohisa Goto)

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