ChangeLog in bio-1.4.3 vs ChangeLog in bio-1.4.3.0001

- old
+ new

@@ -1,13 +1,84 @@ +commit 960497899e75c0fe36ef662ec4a0159559c836b1 +Author: Naohisa Goto <ng@bioruby.org> +Date: Sat May 25 03:41:51 2013 +0900 + + regenerate bioruby.gemspec with rake regemspec + + bioruby.gemspec | 4 +--- + 1 file changed, 1 insertion(+), 3 deletions(-) + +commit e8fa160e158970259d915abc6113cb425537b8d6 +Author: Naohisa Goto <ng@bioruby.org> +Date: Sat May 25 03:38:17 2013 +0900 + + Bio::BIORUBY_EXTRA_VERSION set to ".0001" (Release version with patches) + + lib/bio/version.rb | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +commit 9d84d408479aa261b239e3f371f60262782bfb76 +Author: Naohisa Goto <ng@bioruby.org> +Date: Sat May 25 03:37:55 2013 +0900 + + Added release notes for 1.4.3.0001 release + + RELEASE_NOTES.rdoc | 18 ++++++++++++++++++ + 1 file changed, 18 insertions(+) + +commit 1d3530cd1424f2cc0123057424b5c892f45dc93b +Author: Naohisa Goto <ng@bioruby.org> +Date: Sat May 25 02:46:32 2013 +0900 + + Ruby 2.0 support: not to add ChangeLog and LEGAL to rdoc_files + + * Ruby 2.0 support: not to add ChangeLog and LEGAL to rdoc_files. + Because ChangeLog is not rdoc format, rdoc bundled with Ruby 2.0 + raises error during parsing. + + bioruby.gemspec.erb | 4 ++-- + 1 file changed, 2 insertions(+), 2 deletions(-) + +commit be72602cb42e6d09d465b9636257335dccb278a4 +Author: Naohisa Goto <ng@bioruby.org> +Date: Thu Jan 10 01:27:03 2013 +0900 + + Ruby 2.0 support: Set script encoding to US-ASCII for gff.rb. + + lib/bio/db/gff.rb | 1 + + 1 file changed, 1 insertion(+) + +commit 091f6951d23c5ed2418981b2cf94733b1ee7a8b1 +Author: Naohisa Goto <ng@bioruby.org> +Date: Mon Oct 1 21:11:14 2012 +0900 + + Bug fix: parse error when subject sequence contains spaces + + * Bug fix: parse error when subject sequence contains spaces. + Thanks to Edward Rice who reports the bug. (Bug #3385) + (https://redmine.open-bio.org/issues/3385) + + lib/bio/appl/blast/format0.rb | 38 +++++++++++++++++++------------------- + 1 file changed, 19 insertions(+), 19 deletions(-) + +commit ad0d7a1712d8b02358763233d38e67a0fff54917 +Author: Naohisa Goto <ng@bioruby.org> +Date: Wed Aug 22 00:18:14 2012 +0900 + + BioRuby 1.4.3 is re-released + + ChangeLog | 9 +++++++++ + 1 file changed, 9 insertions(+) + commit 51ab2dec144c99a14ca9009c7b589b500f1cad5f Author: Naohisa Goto <ng@bioruby.org> Date: Wed Aug 22 00:12:47 2012 +0900 Preparation to re-release BioRuby 1.4.3 ChangeLog | 22 ++++++++++++++++++++++ - 1 files changed, 22 insertions(+), 0 deletions(-) + 1 file changed, 22 insertions(+) commit 5ff159d12252393ff04afe52b59a315d15c63d18 Author: Naohisa Goto <ng@bioruby.org> Date: Wed Aug 22 00:00:40 2012 +0900 @@ -16,20 +87,20 @@ * Bug fix: bin/bioruby: Failed to save object with error message "can't convert Symbol into String" on Ruby 1.9. RELEASE_NOTES.rdoc | 2 ++ lib/bio/shell/core.rb | 1 + - 2 files changed, 3 insertions(+), 0 deletions(-) + 2 files changed, 3 insertions(+) commit 74c6ce09413e7ddde1431d74e10cc9c4cdbb95ba Author: Naohisa Goto <ng@bioruby.org> Date: Tue Aug 21 22:35:18 2012 +0900 BioRuby 1.4.3 is released. ChangeLog | 21 +++++++++++++++++++++ - 1 files changed, 21 insertions(+), 0 deletions(-) + 1 file changed, 21 insertions(+) commit 61af85b6cfc7bb1f3668ed68232113eb0751e7ea Author: Naohisa Goto <ng@bioruby.org> Date: Tue Aug 21 22:33:30 2012 +0900 @@ -66,20 +137,20 @@ document JRUBY-5678 (resolved) and related issue with the workaround. KNOWN_ISSUES.rdoc | 9 +++++++++ RELEASE_NOTES.rdoc | 9 +++++++++ - 2 files changed, 18 insertions(+), 0 deletions(-) + 2 files changed, 18 insertions(+) commit 2fdd7a3b3555a33dead31181c9526af22f24916f Author: Naohisa Goto <ng@bioruby.org> Date: Mon Aug 20 19:44:39 2012 +0900 update recommended Ruby versions and the year in copyright lines README.rdoc | 7 +++---- - 1 files changed, 3 insertions(+), 4 deletions(-) + 1 file changed, 3 insertions(+), 4 deletions(-) commit b156227749e5ada74330e837c9ce48a16e6a6a2f Author: Naohisa Goto <ng@bioruby.org> Date: Mon Aug 20 19:16:25 2012 +0900 @@ -110,12 +181,12 @@ * 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. - lib/bio/command.rb | 98 ++++++++++++++++++++++++++++++++++++++++++++++----- - 1 files changed, 88 insertions(+), 10 deletions(-) + lib/bio/command.rb | 98 ++++++++++++++++++++++++++++++++++++++++++++++------ + 1 file changed, 88 insertions(+), 10 deletions(-) commit 05f51fa2e871e71c2b20559eb05e456768a4f7d6 Author: Naohisa Goto <ng@bioruby.org> Date: Sat Aug 18 00:32:31 2012 +0900 @@ -123,11 +194,11 @@ * New default etc/bioinformatics/seqdatabase.ini, with currently available services. etc/bioinformatics/seqdatabase.ini | 27 +++++++++++++++++++++++++++ - 1 files changed, 27 insertions(+), 0 deletions(-) + 1 file changed, 27 insertions(+) create mode 100644 etc/bioinformatics/seqdatabase.ini commit a4264cc3667b98289c09efc7ccba9c8e86f6d89c Author: Naohisa Goto <ng@bioruby.org> Date: Sat Aug 18 00:31:10 2012 +0900 @@ -145,11 +216,11 @@ Date: Sat Aug 18 00:30:38 2012 +0900 known issue about http://bioruby.org/cgi-bin/biofetch.rb server down KNOWN_ISSUES.rdoc | 9 +++++++++ - 1 files changed, 9 insertions(+), 0 deletions(-) + 1 file changed, 9 insertions(+) commit 4a8193f7b91ff703c8f3dc6e6a6ae0c981a404e6 Author: Naohisa Goto <ng@bioruby.org> Date: Fri Aug 17 23:45:41 2012 +0900 @@ -178,56 +249,56 @@ Date: Wed Aug 8 09:41:20 2012 +1000 fill in missing piece of documentation in FastaFormat lib/bio/db/fasta.rb | 2 +- - 1 files changed, 1 insertions(+), 1 deletions(-) + 1 file changed, 1 insertion(+), 1 deletion(-) commit 83bf09d4d81803c8d06e0d45ca25e7c09016161c Author: Naohisa Goto <ng@bioruby.org> Date: Wed Aug 8 00:08:26 2012 +0900 RELEASE_NOTE.rdoc modified to reflect recent changes - RELEASE_NOTES.rdoc | 107 ++++++++++++++++++++++++++++++++++++++++++++------- - 1 files changed, 92 insertions(+), 15 deletions(-) + RELEASE_NOTES.rdoc | 107 ++++++++++++++++++++++++++++++++++++++++++++-------- + 1 file changed, 92 insertions(+), 15 deletions(-) commit c3afb1eb98cf8777ee021624c3d2eab92b3543f2 Author: Naohisa Goto <ng@bioruby.org> Date: Wed Aug 8 00:06:09 2012 +0900 Descriptions about JRuby, Rubinius, DDBJ Web API, SOAP4R etc. KNOWN_ISSUES.rdoc | 45 +++++++++++++++++++++++++++++++++++++++++++-- - 1 files changed, 43 insertions(+), 2 deletions(-) + 1 file changed, 43 insertions(+), 2 deletions(-) commit 01da7401a011aa519c43a021f89f6e7f769b4649 Author: Naohisa Goto <ng@bioruby.org> Date: Tue Aug 7 23:55:09 2012 +0900 regenerate bioruby.gemspec with rake regemspec bioruby.gemspec | 3 +-- - 1 files changed, 1 insertions(+), 2 deletions(-) + 1 file changed, 1 insertion(+), 2 deletions(-) commit 9f70c27d9b75408fddae8384a2a09715b959dcb5 Author: Naohisa Goto <ng@bioruby.org> Date: Tue Aug 7 23:51:56 2012 +0900 improve documentation; version changed to 1.4.3-pre1 lib/bio/version.rb | 13 +++++++++++-- - 1 files changed, 11 insertions(+), 2 deletions(-) + 1 file changed, 11 insertions(+), 2 deletions(-) commit c11f12c8aa56b8509cd082f3478e96374210e5d7 Author: Naohisa Goto <ng@bioruby.org> Date: Tue Aug 7 23:31:41 2012 +0900 Remove autorequire which have been deprecated bioruby.gemspec.erb | 1 - - 1 files changed, 0 insertions(+), 1 deletions(-) + 1 file changed, 1 deletion(-) commit 7792b092033d2c819f2bcad0e206f27608481db5 Author: Ben J Woodcroft <donttrustben@gmail.com> Date: Mon Aug 6 09:40:55 2012 +1000 @@ -248,38 +319,38 @@ include lines. * When running jruby, Set TMPDIR to avoid known issue about FileUtils#remove_entry_secure. .travis.yml | 52 ++++++++++++++++++---------------------------------- - 1 files changed, 18 insertions(+), 34 deletions(-) + 1 file changed, 18 insertions(+), 34 deletions(-) commit 553fd102c533c42675f93895557e3e00d36fd3e7 Author: Naohisa Goto <ng@bioruby.org> Date: Fri Aug 3 22:05:39 2012 +0900 Improve tests for BLAST "-m 8" tabular format parser test/unit/bio/appl/blast/test_report.rb | 119 +++++++++++++++++++++++++++++++ - 1 files changed, 119 insertions(+), 0 deletions(-) + 1 file changed, 119 insertions(+) commit 3e1c062dbc168bd558ca8408a6da115aa570f3a7 Author: Naohisa Goto <ng@bioruby.org> Date: Fri Aug 3 22:05:07 2012 +0900 Improve test and suppress warning: assigned but unused variable test/unit/bio/io/flatfile/test_buffer.rb | 1 + - 1 files changed, 1 insertions(+), 0 deletions(-) + 1 file changed, 1 insertion(+) commit 7e29ce1f050e9e5b23299372d8ddfae781447dc3 Author: Naohisa Goto <ng@bioruby.org> Date: Fri Aug 3 22:02:21 2012 +0900 Improve test and suppress warning: assigned but unused variable test/unit/bio/db/test_newick.rb | 2 ++ - 1 files changed, 2 insertions(+), 0 deletions(-) + 1 file changed, 2 insertions(+) commit 1053b62069df74f336934e4ed0f3f217e4ad3312 Author: Naohisa Goto <ng@bioruby.org> Date: Fri Jul 27 13:56:53 2012 +0900 @@ -287,11 +358,11 @@ * Suppress warnings: shadowing outer local variable. Thanks to Andrew Grimm: https://github.com/bioruby/bioruby/pull/64 lib/bio/db/gff.rb | 8 ++++---- - 1 files changed, 4 insertions(+), 4 deletions(-) + 1 file changed, 4 insertions(+), 4 deletions(-) commit e55794f65b3fb45c99e61d45220fe42f718426a3 Author: Naohisa Goto <ng@bioruby.org> Date: Wed Jul 25 23:29:17 2012 +0900 @@ -300,38 +371,38 @@ * 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 lib/bio/alignment.rb | 2 +- - 1 files changed, 1 insertions(+), 1 deletions(-) + 1 file changed, 1 insertion(+), 1 deletion(-) commit 174a38ea8c4ecea70724bf6ec8e72b2e4259853b Author: Naohisa Goto <ng@bioruby.org> Date: Wed Jul 25 23:12:51 2012 +0900 Modified to follow changes of GenomeNet BLAST site lib/bio/appl/blast/genomenet.rb | 6 +++--- - 1 files changed, 3 insertions(+), 3 deletions(-) + 1 file changed, 3 insertions(+), 3 deletions(-) commit 93e24935840dcdec76984313719700134d69daf2 Author: Naohisa Goto <ng@bioruby.org> Date: Wed Jul 25 15:21:32 2012 +0900 suppress warnings: instance variable @comment not initialized lib/bio/db/gff.rb | 6 ++++-- - 1 files changed, 4 insertions(+), 2 deletions(-) + 1 file changed, 4 insertions(+), 2 deletions(-) commit 0ad3818fedb707a26e849877bde1f8dab006b848 Author: Naohisa Goto <ng@bioruby.org> Date: Wed Jul 25 00:54:02 2012 +0900 suppress warnings: URI.escape/URI.unescape is obsolete lib/bio/db/gff.rb | 39 +++++++++++++++++++++++++++++++++------ - 1 files changed, 33 insertions(+), 6 deletions(-) + 1 file changed, 33 insertions(+), 6 deletions(-) commit 1263938742e7eeedb4a877aff7314e304320eca9 Author: Naohisa Goto <ng@bioruby.org> Date: Mon Jul 23 21:15:52 2012 +0900 @@ -340,47 +411,47 @@ * Added link to blastall options reference. Thanks to Gareth Rees who sent a pull request. (https://github.com/bioruby/bioruby/pull/49) lib/bio/appl/blast/genomenet.rb | 5 +++++ - 1 files changed, 5 insertions(+), 0 deletions(-) + 1 file changed, 5 insertions(+) commit 2ec5f4fd5abd0db7ec79ab3a9fd4adde7c9384a8 Author: Naohisa Goto <ng@bioruby.org> Date: Mon Jul 23 17:26:45 2012 +0900 Next bioruby release version will be 1.4.3. RELEASE_NOTES.rdoc | 2 +- - 1 files changed, 1 insertions(+), 1 deletions(-) + 1 file changed, 1 insertion(+), 1 deletion(-) commit 6cf1318507a5d82bb93acdfe33e96723a2e742fc Author: Naohisa Goto <ng@bioruby.org> Date: Mon Jul 23 17:25:35 2012 +0900 fix typo README.rdoc | 2 +- - 1 files changed, 1 insertions(+), 1 deletions(-) + 1 file changed, 1 insertion(+), 1 deletion(-) commit 2fd71cac315affe6e4d90b03dadac782f11553a5 Author: Naohisa Goto <ng@bioruby.org> Date: Mon Jul 23 17:21:57 2012 +0900 Bug fix: Genomenet remote blast: catch up changes of the server lib/bio/appl/blast/genomenet.rb | 33 +++++++++++++++++++++++---------- - 1 files changed, 23 insertions(+), 10 deletions(-) + 1 file changed, 23 insertions(+), 10 deletions(-) commit 69d9717da11b2fe81a8f840bbafcc5fbb0dbe688 Author: Naohisa Goto <ng@bioruby.org> Date: Fri Jul 20 11:24:37 2012 +0900 regenerate bioruby.gemspec with rake regemspec bioruby.gemspec | 2 ++ - 1 files changed, 2 insertions(+), 0 deletions(-) + 1 file changed, 2 insertions(+) commit 9683da186579dbfa5da1bb1a32edc49cfdc026b8 Author: Naohisa Goto <ng@bioruby.org> Date: Wed Jul 18 23:19:33 2012 +0900 @@ -388,11 +459,11 @@ * Incompatible changes in Bio::KEGG::KGML are documented. * Next BioRuby release version will be 1.4.3. RELEASE_NOTES.rdoc | 44 +++++++++++++++++++++++++++++++++++++++++--- - 1 files changed, 41 insertions(+), 3 deletions(-) + 1 file changed, 41 insertions(+), 3 deletions(-) commit 6cab377ae760d1abfda06caafe4a04ecd549e21d Author: Naohisa Goto <ng@bioruby.org> Date: Wed Jul 18 22:56:00 2012 +0900 @@ -403,11 +474,11 @@ 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/kegg/kgml.rb | 48 ++++++++++++++-- + lib/bio/db/kegg/kgml.rb | 48 ++++++++++++++--- test/unit/bio/db/kegg/test_kgml.rb | 104 +++++++++++++++++++++++++++++++++++- 2 files changed, 144 insertions(+), 8 deletions(-) commit 3cb1e09709d3c6b934028e28f9cafed149c9c751 Author: Naohisa Goto <ng@bioruby.org> @@ -417,20 +488,20 @@ * In Bio::KEGG::KGML#parse_* (private methods) new attribute method names should be used instead of deprecated old names. lib/bio/db/kegg/kgml.rb | 18 +++++++++--------- - 1 files changed, 9 insertions(+), 9 deletions(-) + 1 file changed, 9 insertions(+), 9 deletions(-) commit c5ef981db6add98dc6778cd9809aff38a7071593 Author: Naohisa Goto <ng@bioruby.org> Date: Wed Jul 18 22:14:33 2012 +0900 modified documentation for Bio::KEGG::KGML lib/bio/db/kegg/kgml.rb | 73 +++++++++++++++++++++++++++-------------------- - 1 files changed, 42 insertions(+), 31 deletions(-) + 1 file changed, 42 insertions(+), 31 deletions(-) commit 5416b84eaa37b5abf15f905586a5eee65c4026f0 Author: Naohisa Goto <ng@bioruby.org> Date: Wed Jul 18 15:01:58 2012 +0900 @@ -476,29 +547,29 @@ Date: Tue Jul 17 22:23:28 2012 +0900 rdoc documentation for Bio::KEGG::KGML lib/bio/db/kegg/kgml.rb | 166 ++++++++++++++++++++++++++++++++++++++++++++--- - 1 files changed, 157 insertions(+), 9 deletions(-) + 1 file changed, 157 insertions(+), 9 deletions(-) commit 4a97e7034cae835b3bbc8ef918b9c6c48910dec5 Author: Naohisa Goto <ng@bioruby.org> Date: Wed Jul 11 15:16:49 2012 +0900 autoload should not be used for libraries outside bio lib/bio/db/kegg/kgml.rb | 3 +-- - 1 files changed, 1 insertions(+), 2 deletions(-) + 1 file changed, 1 insertion(+), 2 deletions(-) commit 338d4cd9913d70041349c5201f80f7a65e7135a6 Author: Naohisa Goto <ng@bioruby.org> Date: Fri Jul 6 00:50:01 2012 +0900 remove unnecessary require "bio/db" in lib/bio/db/pdb.rb lib/bio/db/pdb.rb | 5 +---- - 1 files changed, 1 insertions(+), 4 deletions(-) + 1 file changed, 1 insertion(+), 4 deletions(-) commit 87c806a480fcacb0fc610c9669de19e4cb661a9c Author: Naohisa Goto <ng@bioruby.org> Date: Fri Jul 6 00:47:20 2012 +0900 @@ -518,11 +589,11 @@ Date: Fri Jul 6 00:24:24 2012 +0900 regenerate bioruby.gemspec with rake regemspec bioruby.gemspec | 1 + - 1 files changed, 1 insertions(+), 0 deletions(-) + 1 file changed, 1 insertion(+) commit 090d4edb5698135f87df450a963ef35a307349c4 Author: Naohisa Goto <ng@bioruby.org> Date: Fri Jul 6 00:19:54 2012 +0900 @@ -559,38 +630,38 @@ Date: Thu Jul 5 23:29:42 2012 +0900 remove old require lines that are commented out lib/bio/appl/blast/format0.rb | 5 ----- - 1 files changed, 0 insertions(+), 5 deletions(-) + 1 file changed, 5 deletions(-) commit c632fbf2d0320860eadfacb196d51d80ed3a2b34 Author: Naohisa Goto <ng@bioruby.org> Date: Thu Jul 5 23:16:49 2012 +0900 Remove old workaround of strscan.so for Ruby 1.7 or earlier lib/bio/appl/blast/format0.rb | 18 +----------------- - 1 files changed, 1 insertions(+), 17 deletions(-) + 1 file changed, 1 insertion(+), 17 deletions(-) commit c81dce87f53d3ea7c7d2335e077fa609f2737779 Author: Naohisa Goto <ng@bioruby.org> Date: Thu Jul 5 23:03:40 2012 +0900 .travis.yml: include ruby 1.9.2 test .travis.yml | 2 ++ - 1 files changed, 2 insertions(+), 0 deletions(-) + 1 file changed, 2 insertions(+) commit 34709d114089c722b5da796028ffb91021761fdd Author: Naohisa Goto <ng@bioruby.org> Date: Thu Jul 5 23:00:37 2012 +0900 Remove old comment lines lib/bio/sequence/format.rb | 6 ------ - 1 files changed, 0 insertions(+), 6 deletions(-) + 1 file changed, 6 deletions(-) commit e0d5ed61e0101e2e72ad024dccd58c8c90def2b9 Author: Naohisa Goto <ng@bioruby.org> Date: Thu Jul 5 22:42:17 2012 +0900 @@ -605,12 +676,12 @@ 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/command.rb | 56 +++++++++++++++++++++++++++------------------------ - 1 files changed, 30 insertions(+), 26 deletions(-) + lib/bio/command.rb | 56 ++++++++++++++++++++++++++++------------------------ + 1 file changed, 30 insertions(+), 26 deletions(-) commit cca98d1378ce66d6db84cc9c1beadd39ed0e0fee Author: Naohisa Goto <ng@bioruby.org> Date: Thu Jul 5 22:21:34 2012 +0900 @@ -645,61 +716,61 @@ * 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/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 +++---- + 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 +++---- + .../restriction_enzyme/double_stranded/aligned_strands.rb | 7 +++---- + .../double_stranded/cut_location_pair.rb | 7 +++---- + .../cut_location_pair_in_enzyme_notation.rb | 7 +++---- + .../restriction_enzyme/double_stranded/cut_locations.rb | 7 +++---- + .../double_stranded/cut_locations_in_enzyme_notation.rb | 7 +++---- + lib/bio/util/restriction_enzyme/range/cut_range.rb | 7 +++---- + lib/bio/util/restriction_enzyme/range/cut_ranges.rb | 7 +++---- + .../util/restriction_enzyme/range/horizontal_cut_range.rb | 7 +++---- + lib/bio/util/restriction_enzyme/range/sequence_range.rb | 7 +++---- + .../range/sequence_range/calculated_cuts.rb | 7 +++---- + .../restriction_enzyme/range/sequence_range/fragment.rb | 7 +++---- + .../restriction_enzyme/range/sequence_range/fragments.rb | 7 +++---- + .../util/restriction_enzyme/range/vertical_cut_range.rb | 7 +++---- + lib/bio/util/restriction_enzyme/single_strand.rb | 6 +++--- + .../single_strand/cut_locations_in_enzyme_notation.rb | 7 +++---- + .../util/restriction_enzyme/single_strand_complement.rb | 7 +++---- + lib/bio/util/restriction_enzyme/sorted_num_array.rb | 3 +++ + lib/bio/util/restriction_enzyme/string_formatting.rb | 7 +++---- 23 files changed, 75 insertions(+), 81 deletions(-) commit 7df4843288ffde6d7132a5651fe978301f8ebd2b Author: Naohisa Goto <ng@bioruby.org> Date: Thu Jul 5 20:18:08 2012 +0900 workaround to avoid JRuby autoload bug lib/bio/util/restriction_enzyme.rb | 4 +--- - 1 files changed, 1 insertions(+), 3 deletions(-) + 1 file changed, 1 insertion(+), 3 deletions(-) commit 97d95f2b400006d4229a7ce69d7d8a5cdce42764 Author: Naohisa Goto <ng@bioruby.org> Date: Wed Jul 4 22:00:27 2012 +0900 changed require to autoload for the workaround of JRuby autoload bug lib/bio/feature.rb | 5 ++--- - 1 files changed, 2 insertions(+), 3 deletions(-) + 1 file changed, 2 insertions(+), 3 deletions(-) commit 530b82a45731c2a71a110826341be425de1271e0 Author: Naohisa Goto <ng@bioruby.org> Date: Wed Jul 4 22:00:06 2012 +0900 workaround to avoid JRuby autoload bug lib/bio/sequence/common.rb | 4 +--- - 1 files changed, 1 insertions(+), 3 deletions(-) + 1 file changed, 1 insertion(+), 3 deletions(-) commit 8614f31b36fb93d6e49d109268d646ff3032cd1a Author: Naohisa Goto <ng@bioruby.org> Date: Wed Jul 4 21:28:52 2012 +0900 @@ -707,56 +778,56 @@ * Workaround to avoid JRuby autoload bug. * Changed to require bio/db.rb because it is always loaded. lib/bio/db/kegg/genes.rb | 6 +++--- - 1 files changed, 3 insertions(+), 3 deletions(-) + 1 file changed, 3 insertions(+), 3 deletions(-) commit ea500006ed56857139c858bdfeb98773e5ca541e Author: Naohisa Goto <ng@bioruby.org> Date: Thu Jun 28 21:36:35 2012 +0900 Rakefile: use own mktmpdir Rakefile | 59 +++++++++++++++++++++++++++++++++++++++++++---------------- - 1 files changed, 43 insertions(+), 16 deletions(-) + 1 file changed, 43 insertions(+), 16 deletions(-) commit 452fadcab61083dcb9d01ee05d300eae5cb23fee Author: Naohisa Goto <ng@bioruby.org> Date: Thu Jun 28 20:37:59 2012 +0900 .travis.yml: remove "rake regemspec" from after_install .travis.yml | 2 -- - 1 files changed, 0 insertions(+), 2 deletions(-) + 1 file changed, 2 deletions(-) commit 3fad822af3d7e558a58b71fd8ec2a7061b49f9f2 Author: Naohisa Goto <ng@bioruby.org> Date: Thu Jun 28 20:36:59 2012 +0900 regenerate bioruby.gemspec with rake regemspec bioruby.gemspec | 2 ++ - 1 files changed, 2 insertions(+), 0 deletions(-) + 1 file changed, 2 insertions(+) commit ea6e96fc654c797664b118a6326a84e4f9b1a8a3 Author: Naohisa Goto <ng@bioruby.org> Date: Thu Jun 28 20:35:49 2012 +0900 print message when doing Dir.chdir Rakefile | 17 +++++++++++------ - 1 files changed, 11 insertions(+), 6 deletions(-) + 1 file changed, 11 insertions(+), 6 deletions(-) commit c2fcd5e8cc71da38dc3c6d1f8c8d0233e47398b3 Author: Naohisa Goto <ng@bioruby.org> Date: Thu Jun 28 20:28:41 2012 +0900 In tar-install, removed dependency to regemspec Rakefile | 2 +- - 1 files changed, 1 insertions(+), 1 deletions(-) + 1 file changed, 1 insertion(+), 1 deletion(-) commit 67a7e83d516aab5d60f8263525b359be8b0ffc0b Author: Naohisa Goto <ng@bioruby.org> Date: Thu Jun 28 20:23:24 2012 +0900 @@ -764,11 +835,11 @@ * Rakefile: give up using Dir.mktmpdir because of JRuby's behavior that may be related with http://jira.codehaus.org/browse/JRUBY-5678 Rakefile | 61 ++++++++++++++++++++++++++++++++++++++++++++++--------------- - 1 files changed, 46 insertions(+), 15 deletions(-) + 1 file changed, 46 insertions(+), 15 deletions(-) commit cff098034a338bbe9579d6c7b4380c7132a38ef5 Author: Naohisa Goto <ng@bioruby.org> Date: Thu Jun 28 19:23:57 2012 +0900 @@ -776,21 +847,21 @@ * gem-integration-test, gem-install and gem-install-nodoc are removed because they are useless with Bundler Rakefile | 13 ------------- - 1 files changed, 0 insertions(+), 13 deletions(-) + 1 file changed, 13 deletions(-) commit d5c054265af4f80318cbfa5a5bbdee6125219de2 Author: Naohisa Goto <ng@bioruby.org> Date: Thu Jun 28 18:10:05 2012 +0900 .travis.yml: .gemspec is needed to install local gem .travis.yml | 1 + gemfiles/prepare-gemspec.rb | 25 +++++++++++++++++++++++++ - 2 files changed, 26 insertions(+), 0 deletions(-) + 2 files changed, 26 insertions(+) create mode 100644 gemfiles/prepare-gemspec.rb commit 05b6172123f42a1d8d46668d8a3d5f698c371704 Author: Naohisa Goto <ng@bioruby.org> Date: Thu Jun 28 17:51:43 2012 +0900 @@ -813,20 +884,20 @@ Date: Thu Jun 28 17:06:28 2012 +0900 descriptions are modified for danger operations Rakefile | 4 ++-- - 1 files changed, 2 insertions(+), 2 deletions(-) + 1 file changed, 2 insertions(+), 2 deletions(-) commit a209688952c922d9ba45c227874990bccd3da7c0 Author: Naohisa Goto <ng@bioruby.org> Date: Mon Jun 25 23:25:51 2012 +0900 regenerate bioruby.gemspec with rake regemspec bioruby.gemspec | 5 +++++ - 1 files changed, 5 insertions(+), 0 deletions(-) + 1 file changed, 5 insertions(+) commit 8f6459497be0e9ca7dc3eb2eb9606e42d97ad60c Author: Naohisa Goto <ng@bioruby.org> Date: Mon Jun 25 21:01:06 2012 +0900 @@ -848,11 +919,11 @@ 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". Rakefile | 110 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-- - 1 files changed, 107 insertions(+), 3 deletions(-) + 1 file changed, 107 insertions(+), 3 deletions(-) commit 3b400042cd361e1ab6d0fb0d8c8cce14a6c2ae10 Author: Naohisa Goto <ng@bioruby.org> Date: Mon Jun 25 20:58:13 2012 +0900 @@ -861,11 +932,11 @@ * 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. test/bioruby_test_helper.rb | 4 ++-- - 1 files changed, 2 insertions(+), 2 deletions(-) + 1 file changed, 2 insertions(+), 2 deletions(-) commit 848304b6f90310f8fa15c80ba06655ae5cae5053 Author: Naohisa Goto <ng@bioruby.org> Date: Mon Jun 25 20:42:07 2012 +0900 @@ -879,12 +950,12 @@ % 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. - test/bioruby_test_helper.rb | 49 ++++++++++++++++++++++++++++++++---------- - 1 files changed, 37 insertions(+), 12 deletions(-) + test/bioruby_test_helper.rb | 49 ++++++++++++++++++++++++++++++++----------- + 1 file changed, 37 insertions(+), 12 deletions(-) commit 9453a6773c24f866698370195fd8e767443a38b9 Author: Tomoaki NISHIYAMA <tomoakin@kenroku.kanazawa-u.ac.jp> Date: Fri Jun 1 18:06:40 2012 +0900 @@ -897,11 +968,11 @@ first id line starting with "@". * Test code is added. lib/bio/io/flatfile/autodetection.rb | 2 +- test/unit/bio/io/flatfile/test_autodetection.rb | 6 ++++++ - 2 files changed, 7 insertions(+), 1 deletions(-) + 2 files changed, 7 insertions(+), 1 deletion(-) commit 120e780c023cba06b83899c2f8a17c8fc1de4faa Author: Naohisa Goto <ng@bioruby.org> Date: Fri Jun 8 15:36:29 2012 +0900 @@ -913,12 +984,12 @@ 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. - test/unit/bio/sequence/test_common.rb | 40 +++++++++++++++++++++++++++++--- - 1 files changed, 36 insertions(+), 4 deletions(-) + test/unit/bio/sequence/test_common.rb | 40 +++++++++++++++++++++++++++++---- + 1 file changed, 36 insertions(+), 4 deletions(-) commit 20dde52f7da784d4d9ac551957700cd96e842ef6 Author: Naohisa Goto <ng@bioruby.org> Date: Sat May 19 18:14:19 2012 +0900 @@ -953,20 +1024,20 @@ Date: Thu May 10 23:13:56 2012 -0400 test_tree.rb: to use %f instead of %g to prevent odd behavior. test/unit/bio/test_tree.rb | 22 +++++++++++----------- - 1 files changed, 11 insertions(+), 11 deletions(-) + 1 file changed, 11 insertions(+), 11 deletions(-) commit 5e80e4394bf2a5e4ee472fe84ab76239b293e1b5 Author: Clayton Wheeler <cswh@umich.edu> Date: Thu May 10 23:04:55 2012 -0400 Fixed spurious JRuby failures in test_tree.rb due to floating point differences. test/unit/bio/test_tree.rb | 14 +++++++------- - 1 files changed, 7 insertions(+), 7 deletions(-) + 1 file changed, 7 insertions(+), 7 deletions(-) commit 459d4da894e9a9b9db0d793e3711dc45bae2089b Author: Artem Tarasov <lomereiter@gmail.com> Date: Thu May 10 16:23:13 2012 +0400 @@ -974,11 +1045,11 @@ * Test bug fix: Bio::TestSOFT#test_dataset: order of hash keys are not guaranteed. test/unit/bio/db/test_soft.rb | 2 +- - 1 files changed, 1 insertions(+), 1 deletions(-) + 1 file changed, 1 insertion(+), 1 deletion(-) commit 7e730691d6ec597a610dc0d4665db3598fcfde59 Author: Naohisa Goto <ng@bioruby.org> Date: Thu May 10 00:06:19 2012 +0900 @@ -988,11 +1059,11 @@ 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(-) + 6 files changed, 22 deletions(-) commit f1c398fdc3488bd18bd13ac864920ce6db4dab9e Author: Naohisa Goto <ng@bioruby.org> Date: Wed May 9 15:54:20 2012 +0900 @@ -1000,11 +1071,11 @@ * .travis.yml: comment out apt-get lines because libxml2-dev and libexpat1-dev are already installed. .travis.yml | 6 +++--- - 1 files changed, 3 insertions(+), 3 deletions(-) + 1 file changed, 3 insertions(+), 3 deletions(-) commit bc5ef4959e51f4a199d9f740b07812e9b8216255 Author: Naohisa Goto <ng@bioruby.org> Date: Wed May 9 15:47:11 2012 +0900 @@ -1023,15 +1094,15 @@ Date: Tue May 1 18:11:09 2012 +0900 config files for Travis CI continuous integration service .travis.yml | 73 ++++++++++++++++++++++++++++++++++++++ - gemfiles/Gemfile.travis-jruby1.8 | 6 +++ + 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(-) + gemfiles/Gemfile.travis-ruby1.9 | 8 +++++ + 5 files changed, 101 insertions(+) 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 @@ -1052,11 +1123,11 @@ Date: Sat Feb 25 15:26:27 2012 -0600 Bug fix: Bio::NucleicAcid.to_re("s") typo lib/bio/data/na.rb | 2 +- - 1 files changed, 1 insertions(+), 1 deletions(-) + 1 file changed, 1 insertion(+), 1 deletion(-) commit c552aa3a6773139b14ae95e79e0fb43a2f91c6fb Author: Naohisa Goto <ng@bioruby.org> Date: Thu Jan 12 22:24:37 2012 +0900 @@ -1065,57 +1136,57 @@ * Bug fix: GenomeNet BLAST server URI changed. Reported by joaocardoso via GitHub. ( https://github.com/bioruby/bioruby/issues/44 ) lib/bio/appl/blast/genomenet.rb | 3 ++- - 1 files changed, 2 insertions(+), 1 deletions(-) + 1 file changed, 2 insertions(+), 1 deletion(-) commit f33abf9bbd90c3c1e320f06447fdb54ffd094c5d Author: peterjc <p.j.a.cock@googlemail.com> Date: Fri Nov 25 11:20:08 2011 +0000 Mark echoarg2.bat and echoarg2.sh as world executable - 0 files changed, 0 insertions(+), 0 deletions(-) + 0 files changed mode change 100644 => 100755 test/data/command/echoarg2.bat mode change 100644 => 100755 test/data/command/echoarg2.sh commit d2d66f833d0b20647e8d761d2a240b99b206eaa8 Author: Naohisa Goto <ng@bioruby.org> Date: Thu Nov 24 13:32:37 2011 +0900 Bug fix: rake aborted without git bioruby.gemspec.erb | 2 +- - 1 files changed, 1 insertions(+), 1 deletions(-) + 1 file changed, 1 insertion(+), 1 deletion(-) commit c2139739988ef731d61bf1a8cdba2dc5c48393bd Author: Naohisa Goto <ng@bioruby.org> Date: Thu Nov 24 13:07:10 2011 +0900 regenerate bioruby.gemspec with rake regemspec. bioruby.gemspec | 18 ++++++++++-------- - 1 files changed, 10 insertions(+), 8 deletions(-) + 1 file changed, 10 insertions(+), 8 deletions(-) commit 6213b45d28bfea2cc8c838813b524d48c369266b Author: Naohisa Goto <ng@bioruby.org> Date: Thu Nov 24 13:05:07 2011 +0900 Added workaround for changes of a module name and file names to require. Rakefile | 21 +++++++++++++++++++-- - 1 files changed, 19 insertions(+), 2 deletions(-) + 1 file changed, 19 insertions(+), 2 deletions(-) commit 39f847cf8d453476275361078b831da43d400816 Author: Naohisa Goto <ng@bioruby.org> Date: Thu Nov 24 12:08:47 2011 +0900 Use binary mode to open files. Rakefile | 6 ++++-- - 1 files changed, 4 insertions(+), 2 deletions(-) + 1 file changed, 4 insertions(+), 2 deletions(-) commit 688779e71a27e861fb01e07f816384561b8cfe45 Author: Naohisa Goto <ng@bioruby.org> Date: Thu Nov 24 11:49:30 2011 +0900 @@ -1123,20 +1194,20 @@ * Rakefile: new tasks: test-all to run all tests, and test-network to run tests in test/network. Rakefile | 10 ++++++++++ - 1 files changed, 10 insertions(+), 0 deletions(-) + 1 file changed, 10 insertions(+) commit 53719535defcb0fefb3cf8bebe3fad6716bf7de2 Author: Naohisa Goto <ng@bioruby.org> Date: Thu Nov 24 11:28:38 2011 +0900 test/runner.rb: Run tests only in test/unit and test/functional. test/runner.rb | 22 ++++++++++++++++------ - 1 files changed, 16 insertions(+), 6 deletions(-) + 1 file changed, 16 insertions(+), 6 deletions(-) commit fb9ee403db6b447aee73ebb7f12ff5a5b73d6c52 Author: Naohisa Goto <ng@bioruby.org> Date: Wed Nov 23 20:36:36 2011 +0900 @@ -1197,11 +1268,11 @@ Test bug fix: use binmode to disable CR/LF conversion (fail on Windows) 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(-) + 2 files changed, 2 insertions(+) commit 07ce32da009baa2c4e81f6d96f45e3dac49da183 Author: Naohisa Goto <ng@bioruby.org> Date: Wed Nov 23 14:47:33 2011 +0900 @@ -1224,20 +1295,20 @@ (binmode) unless text mode option is explicitly given. 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(-) + 3 files changed, 230 insertions(+) commit 48bd150a6180d59879872bd85dd95c7ddf1a19c0 Author: Naohisa Goto <ng@bioruby.org> Date: Tue Nov 22 17:32:23 2011 +0900 Test bug fix: fixed incomplete Windows platform detection. test/unit/bio/test_command.rb | 13 +++++++++---- - 1 files changed, 9 insertions(+), 4 deletions(-) + 1 file changed, 9 insertions(+), 4 deletions(-) commit d499bcee7956b1a0a4c04aeb106e50a0839167b0 Author: Naohisa Goto <ng@bioruby.org> Date: Tue Nov 22 16:15:05 2011 +0900 @@ -1261,11 +1332,11 @@ * 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. test/unit/bio/db/test_phyloxml_writer.rb | 24 +++++++++++++++--------- - 1 files changed, 15 insertions(+), 9 deletions(-) + 1 file changed, 15 insertions(+), 9 deletions(-) commit a9022c61b98746e98a83f1cfd902e0e6b11c7bbb Author: Naohisa Goto <ng@bioruby.org> Date: Tue Nov 22 13:55:15 2011 +0900 @@ -1278,39 +1349,39 @@ to the block as an argument. When the block terminates, the object is closed. * Added tests about the above changes. lib/bio/db/phyloxml/phyloxml_parser.rb | 57 +++++++++++++++++++++++++++++--- - test/unit/bio/db/test_phyloxml.rb | 56 ++++++++++++++++++++++++++++++- + test/unit/bio/db/test_phyloxml.rb | 56 +++++++++++++++++++++++++++++-- 2 files changed, 106 insertions(+), 7 deletions(-) commit 893cbe6ca993eca08427074059c2ba03621ea889 Author: Naohisa Goto <ng@bioruby.org> Date: Sat Nov 5 00:49:10 2011 +0900 Ruby 1.9 should be fully supported, and optional requirements are revised. README.rdoc | 48 +++++++++++++++++++++++++++++++++--------------- - 1 files changed, 33 insertions(+), 15 deletions(-) + 1 file changed, 33 insertions(+), 15 deletions(-) commit 38b1715c2d6bad39560e0846781ca903b1c16eda Author: Naohisa Goto <ng@bioruby.org> Date: Fri Nov 4 22:12:38 2011 +0900 Added REFERENCE. README.rdoc | 12 ++++++++++++ - 1 files changed, 12 insertions(+), 0 deletions(-) + 1 file changed, 12 insertions(+) commit 9a766cd17236bbe1e28d6972001dd5e3ed596123 Author: Naohisa Goto <ng@bioruby.org> Date: Fri Nov 4 21:39:20 2011 +0900 Removed "setup.rb test" and added about running tests. README.rdoc | 39 ++++++++++++++++++++++++++++++++++----- - 1 files changed, 34 insertions(+), 5 deletions(-) + 1 file changed, 34 insertions(+), 5 deletions(-) commit 39737179b06366e1d5acf2e5ac930e41b3a4ee38 Author: Pjotr Prins <pjotr.public01@thebird.nl> Date: Fri Oct 14 08:58:01 2011 +0200 @@ -1339,30 +1410,30 @@ * 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. - README_DEV.rdoc | 95 +++++++++++++++++++++++++++++++++++++++++++++++++++++- - 1 files changed, 93 insertions(+), 2 deletions(-) + README_DEV.rdoc | 95 +++++++++++++++++++++++++++++++++++++++++++++++++++++-- + 1 file changed, 93 insertions(+), 2 deletions(-) commit 3c952c4a782501b21f36ece5bcab672dab12fc6d Author: Naohisa Goto <ng@bioruby.org> Date: Tue Sep 13 13:21:20 2011 +0900 README.rdoc: for release notes and changelog, about sample files. README.rdoc | 10 +++++++++- - 1 files changed, 9 insertions(+), 1 deletions(-) + 1 file changed, 9 insertions(+), 1 deletion(-) commit fba9a6c0f1f79dd567ca54ba085b6258ac8efb31 Author: Naohisa Goto <ng@bioruby.org> Date: Tue Sep 13 13:20:05 2011 +0900 RELEASE_NOTES.rdoc: mentioned about removal of rdoc.zsh. RELEASE_NOTES.rdoc | 6 +++++- - 1 files changed, 5 insertions(+), 1 deletions(-) + 1 file changed, 5 insertions(+), 1 deletion(-) commit 685b6bb7b98083e1b50e73baf4e7fa71bc9a39fa Author: Naohisa Goto <ng@bioruby.org> Date: Mon Sep 12 21:23:34 2011 +0900 @@ -1384,11 +1455,11 @@ * Deleted rdoc.zsh which is obsolete and unused. To generate rdoc html, "rake rdoc" or "rake rerdoc". See "rake -T" for more information. rdoc.zsh | 8 -------- - 1 files changed, 0 insertions(+), 8 deletions(-) + 1 file changed, 8 deletions(-) delete mode 100644 rdoc.zsh commit 272d9106cec43b0f219edd92a6f7bd3f9875a761 Author: Naohisa Goto <ng@bioruby.org> Date: Mon Sep 12 20:35:47 2011 +0900 @@ -1398,11 +1469,11 @@ * 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. ChangeLog | 64 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ - 1 files changed, 64 insertions(+), 0 deletions(-) + 1 file changed, 64 insertions(+) create mode 100644 ChangeLog commit 941493378f9884978c81d5f63ee4ed5c175d4bea Author: Naohisa Goto <ng@bioruby.org> Date: Mon Sep 12 20:28:28 2011 +0900 @@ -1412,11 +1483,11 @@ * Rakefile: add new task :rechangelog to update ChangeLog using git log. Note that the tag name (currently 1.4.2) is hardcoded in Rakefile. Rakefile | 9 +++++++++ - 1 files changed, 9 insertions(+), 0 deletions(-) + 1 file changed, 9 insertions(+) commit 1c89e6546223c3c05ea79b8ade4b493580851efa Author: Naohisa Goto <ng@bioruby.org> Date: Mon Sep 12 20:24:49 2011 +0900 @@ -1433,20 +1504,20 @@ Date: Mon Sep 12 20:22:49 2011 +0900 ChangeLog updated: add log about 1.4.2 release ChangeLog | 9 +++++++++ - 1 files changed, 9 insertions(+), 0 deletions(-) + 1 file changed, 9 insertions(+) commit 1c02ab0488e4097a2cf5c16180c3179c78e3d572 Author: Naohisa Goto <ng@bioruby.org> Date: Mon Sep 12 19:40:54 2011 +0900 New RELEASE_NOTES.rdoc for next release version. RELEASE_NOTES.rdoc | 47 +++++++++++++++++++++++++++++++++++++++++++++++ - 1 files changed, 47 insertions(+), 0 deletions(-) + 1 file changed, 47 insertions(+) create mode 100644 RELEASE_NOTES.rdoc commit 4e63e69e98c0c440ec476ef3407fcc8fd2411056 Author: Naohisa Goto <ng@bioruby.org> Date: Mon Sep 12 19:32:48 2011 +0900 @@ -1464,6 +1535,6 @@ Date: Fri Sep 2 12:02:41 2011 +0900 Bio::BIORUBY_EXTRA_VERSION set to ".5000" (unstable version). lib/bio/version.rb | 2 +- - 1 files changed, 1 insertions(+), 1 deletions(-) + 1 file changed, 1 insertion(+), 1 deletion(-)