ruby-bio (2.0.4-1) unstable; urgency=medium
* New upstream version 2.0.4
* Update copyright
* Bump Standards-Version to 4.6.1 (no changes needed)
-- Nilesh Patra <nilesh@debian.org> Sun, 09 Oct 2022 13:54:56 +0530
ruby-bio (2.0.3-1) unstable; urgency=medium
* New upstream version 2.0.3
* Remove ruby-3.0.patch, merged upstream
-- Nilesh Patra <nilesh@debian.org> Sat, 06 Nov 2021 20:53:44 +0530
ruby-bio (2.0.2-3) unstable; urgency=medium
* Add myself to uploaders
* Pull upstream patch to fix FTBFS with ruby-3.0 (Closes: #996138)
-- Nilesh Patra <nilesh@debian.org> Fri, 05 Nov 2021 19:27:49 +0530
ruby-bio (2.0.2-2) unstable; urgency=medium
* Team Upload.
* Switch to ruby-tests.rake instead of ruby-tests.rb
-- Nilesh Patra <nilesh@debian.org> Mon, 18 Oct 2021 09:47:13 +0000
ruby-bio (2.0.2-1) unstable; urgency=medium
* Team Upload.
[ Cédric Boutillier ]
* [ci skip] Update team name
* [ci skip] Add .gitattributes to keep unwanted files
out of the source package
[ Debian Janitor ]
* Bump debhelper from old 12 to 13.
[ Nilesh Patra ]
* New upstream version 2.0.2
* Bump Standards-Version to 4.6.0 (no changes needed)
* d/control: Use ${ruby:Depends} instead of "ruby | ruby-interpreter"
-- Nilesh Patra <nilesh@debian.org> Mon, 18 Oct 2021 01:10:13 +0530
ruby-bio (2.0.1-2) unstable; urgency=medium
* Team upload
* Add Breaks for ruby-crb-blast
-- Utkarsh Gupta <utkarsh@debian.org> Mon, 06 Apr 2020 02:17:20 +0530
ruby-bio (2.0.1-1) unstable; urgency=medium
* Team upload.
[ Utkarsh Gupta ]
* Add salsa-ci.yml
[ Debian Janitor ]
* Trim trailing whitespace.
* Use secure copyright file specification URI.
* Update standards version, no changes needed.
* Set debhelper-compat version in Build-Depends.
[ Samyak Jain ]
* New upstream version 2.0.1
* Updates d/control
* Refresh d/patches
* Removes unwanted patch
-- Samyak Jain <samyak.jn11@gmail.com> Tue, 03 Mar 2020 16:42:09 +0530
ruby-bio (1.5.2-1) unstable; urgency=medium
* Team upload.
* New upstream version
* debhelper 12
* Standards-Version: 4.3.0
* Update watch file
-- Andreas Tille <tille@debian.org> Mon, 28 Jan 2019 21:12:21 +0100
ruby-bio (1.5.1-1) unstable; urgency=medium
* Team upload.
[ Andreas Tille ]
* New upstream version
* debhelper 11
* cme fix dpkg-control
- Standards-Version: 4.1.4
- Point Vcs-fields to Salsa
- Sorting of fields
[ Chris Hofstaedtler ]
* Fix format specifier crash
-- Chris Hofstaedtler <zeha@debian.org> Sun, 22 Jul 2018 07:58:08 +0000
ruby-bio (1.5.0-2) unstable; urgency=medium
* restore fix_definition_CutSymbol_in_test_cut_symbol.patch to avoid
transient FTBFS because of undefined CutSymbol class
* Bump Standards-Version to 3.9.7 (no changes needed)
* Use https in Vcs-* fields
* Fix syntax of copyright file
-- Cédric Boutillier <boutil@debian.org> Thu, 03 Mar 2016 21:32:25 +0100
ruby-bio (1.5.0-1) unstable; urgency=medium
* Team upload.
* New upstream version (Closes: #804068)
* Remove upstream-applied patch fix_shebang_for_examples
* Refresh Debian packaging using dh-make-ruby -w. Bumps Standard-Version
to 3.9.6.
-- Christian Hofstaedtler <zeha@debian.org> Sun, 08 Nov 2015 22:16:50 +0000
ruby-bio (1.4.3.0001-2) unstable; urgency=low
* debian/ruby-tests.rb: choose to define external encoding if Encoding is
defined instead of checking version of Ruby, which was too strict.
(Closes: #720240)
* Tighten dependency on ruby-libxml and gem2deb to ensure Ruby 2.0 support.
(Closes: #730644)
* Bump Standards-Version to 3.9.5 (no changes needed)
-- Cédric Boutillier <boutil@debian.org> Tue, 24 Dec 2013 21:18:56 +0100
ruby-bio (1.4.3.0001-1) unstable; urgency=low
* Imported Upstream version 1.4.3.0001
* debian/control:
+ remove obsolete DM-Upload-Allowed flag
+ use canonical URI in Vcs-* fields
+ build-depend on ruby-test-unit
+ bump Standards-Version to 3.9.4 (no changes needed)
+ update my email address
+ drop transitional packages
* debian/patches:
+ drop disable-test-soap.patch, fixed upstream
+ drop fix_definition_CutSymbol_in_test_cut_symbol.patch, fixed upstream
+ drop do_not_rely_on_keys_order_for_hashes.patch, fixed upstream
+ omit chi2 tests instead of commenting them out
+ add remove_rubygems.patch: remove requirement on rubygems from bin/bioruby
* debian/ruby-tests.rb: do not exclude manually tests requiring network in
ruby-tests.rb, now moved to a dedicated directory by upstream
* remove debian/source/lintian-overrides, related to transitional packages
* install KNOWN_ISSUES.rdoc as documentation
* provide more complete copyright information
-- Cédric Boutillier <boutil@debian.org> Tue, 06 Aug 2013 23:19:36 +0200
ruby-bio (1.4.2-3) unstable; urgency=low
[ Andreas Tille ]
* debian/upstream: Add citation information according to
https://wiki.debian.org/UpstreamMetadata (Closes: #675061)
[ Cédric Boutillier ]
* Add myself to Uploaders:
* Bump Standards-Version: to 3.9.3 (no changes needed)
* Update debian/copyright to cover also setup.rb, sample/* and
test/data/uniprot/p53_human.uniprot
* debian/patches:
+ add disable_tests_using_chi2.patch, disabling randomly failing tests
+ add do_not_rely_on_keys_order_for_hashes.patch, fixing FTBFS
(Closes: #674337)
+ add fix_shebang_for_examples.patch, ensuring the shebang in
sample/biofetch.rb is correct
* Build-depend on gem2deb >= 0.3.0
* Register HTML tutorials in doc-base
-- Cédric Boutillier <cedric.boutillier@gmail.com> Mon, 25 Jun 2012 11:34:26 +0200
ruby-bio (1.4.2-2) unstable; urgency=low
* Remove some tests depending on a access to the Internet. Closes: #654985
* Add fix_definition_CutSymbol_in_test_cut_symbol.patch to ensure that
Bio::RestrictionEnzyme::CutSymbol is defined
* Set to extra the priority of transitional packages
* Depends on ruby-libxml instead of libxml-ruby
-- Cédric Boutillier <cedric.boutillier@gmail.com> Fri, 17 Feb 2012 15:22:29 +0100
ruby-bio (1.4.2-1) unstable; urgency=low
* New upstream version.
+ Fixes build failure. Closes: #642035.
* fix typos in debian/copyright.
* document disable-test-soap.patch.
-- Lucas Nussbaum <lucas@debian.org> Sun, 25 Sep 2011 11:01:38 +0200
ruby-bio (1.4.1-2) unstable; urgency=low
* Switch to gem2deb packaging. Rename binary and source package, introduce
transitional packages.
-- Lucas Nussbaum <lucas@debian.org> Thu, 28 Jul 2011 17:25:55 +0200
bioruby (1.4.1-1) unstable; urgency=low
* New upstream version
* debian/control:
- Standards-Version: 3.9.1 (no changes needed)
- Added Recommends: hmmer, mafft, muscle, probcons, sim4, t-coffee
which are called in lib/bio/appl
- Added Suggests: clustalw (non-free), emboss (large and thus not
always wanted on the system just for BioRuby development)
* Source format 3.0 (quilt)
-- Andreas Tille <tille@debian.org> Thu, 25 Nov 2010 16:04:31 +0100
bioruby (1.4.0-2) unstable; urgency=low
* Fixed long description
Closes: #453022
* New upstream version from past upload just
Closes: #524180
-- Andreas Tille <tille@debian.org> Fri, 22 Jan 2010 16:26:50 +0100
bioruby (1.4.0-1) unstable; urgency=low
* New upstream version
-- Andreas Tille <tille@debian.org> Thu, 21 Jan 2010 11:42:04 +0100
bioruby (1.3.1-1) unstable; urgency=low
* debian/control:
- Group maintenance in Debian Med team
- Added myself as uploader
- Standards-Version: 3.8.3 (no changes needed)
- Debhelper >= 7.1
- Homepage and Vcs fileds
-- Andreas Tille <tille@debian.org> Sun, 04 Oct 2009 09:15:28 +0200
bioruby (1.1.0-1) unstable; urgency=low
* New upstream version
+ Bioruby is now distributed under the same terms as ruby itself.
This gives you the option of using the GPL or a similar copyleft
license. See /usr/share/doc/libbio-ruby/copyright for details on the
alternate license.
+ Lots of new and obsolete classes, see the upstream changelog for details
+ BioRuby shell rewritten to utilize the rails generators
+ Many bugfixes
* Re-work build system to utilize install.rb instead of my custom rules file
+ Enable unit tests in the build
+ Don't hardcode the binary names when hacking off the .rb suffix. Use
wildcards and a for loop to rename them
+ Remove the libbio-ruby1.8.dirs file. The directories get installed by
the install.rb now
+ The docs are built by install.rb now, so don't do custom stuff for them
in debian/rules
+ Move building the manpages to the build-stamp target, rather than the
build target
+ Add ruby to build-depends
-- David Nusinow <dnusinow@debian.org> Sun, 22 Jul 2007 18:42:39 -0400
bioruby (1.0.0-1) unstable; urgency=low
* New upstream version
* Add the bioruby shell program
* Add the Changes-0.7.html doc describing updates since 0.6.x
* Bump standards version to 3.7.2.0. No changes needed.
* Bump debhelper compat to 5
* Move debhelper to build-depends from build-depends-indep
-- David Nusinow <dnusinow@debian.org> Thu, 17 Aug 2006 00:28:21 +0000
bioruby (0.6.4-1) unstable; urgency=low
* New upstream release
+ siRNA designer class is contributed by Itoshi Nikaido.
(lib/bio/util/sirna.rb)
+ fastacmd wrapper is contributed by Shinji Shigenobu.
(lib/bio/io/fastacmd.rb)
+ bl2seq parser is contributed by Tomoaki Nishiyama.
(lib/bio/appl/bl2seq/report.rb)
+ new application execution factory is provided.
(lib/bio/command.rb)
+ FlatFile class can accept Blast results, Spidey, Blat, Sim4 and some
KEGG formats (KO, GLYCAN, REACTION)
+ some methods are added to SPTr class proposed by Luca Pireddu.
(lib/bio/db/embl/sptr.rb)
+ external2go parser is added. (lib/bio/db/go.rb)
+ improved amino/nucleic data classes to have some handy methods.
(lib/bio/data/)
+ fixed hmmer parser (by Masashi Fujita) and remote execution of blast and
fasta using GenomeNet.
+ some English documentations are added. (doc/)
* Re-organize debian/rules handling of docs
+ Ship new English tutorial and KEGG_API. These are turned to html with rd2
+ Put document building commands in the build target instead of configure
+ Add commands to remove generated documents in the clean target
+ Put package building commands in binary-indep where they belong
* Add build-dependency on rdtool to build html docs using rd2
* Minor debian/copyright cleanup to get rid of stupid lintian warning about
boilerplate
* Change Build-Depends to Build-Depends-Indep
* Update standards version to 3.6.2. No changes needed.
* Add ruby1.8 to recommends for libbio-ruby1.8
-- David Nusinow <dnusinow@debian.org> Thu, 1 Sep 2005 14:04:35 -0400
bioruby (0.6.2-3) unstable; urgency=low
* Add watch file
-- David Nusinow <dnusinow@debian.org> Thu, 7 Apr 2005 22:12:44 -0400
bioruby (0.6.2-2) unstable; urgency=low
* Depend on libruby1.8 instead of ruby1.8 to bring in line with ruby policy
* Add Recommends on blast2 for local blast
* Depend on docbook-to-man; closes: #302360
-- David Nusinow <dnusinow@debian.org> Tue, 1 Feb 2005 00:25:45 -0500
bioruby (0.6.2-1) unstable; urgency=low
* Initial Release.
-- David Nusinow <dnusinow@debian.org> Mon, 31 Jan 2005 11:11:55 -0500