ruby-bio (2.0.6-1) unstable; urgency=medium

  * Team Upload.

  [ Lucas Nussbaum ]
  * debian/gbp.conf: Add for DEP-14
  * debian/gbp.conf: remove trailing empty lines
  * debian/.gitattributes: remove
  * debian/salsa-ci.yml: use team-specific include

  [ Nilesh Patra ]
  * New upstream version 2.0.6
  * Change Recommends from blast2 => ncbi-blast+-legacy
    Closes: #1116111
  * Bump Standards-Version to 4.7.2 (no changes needed)
  * Drop myself from uploaders

 -- Nilesh Patra <nilesh@debian.org>  Fri, 26 Sep 2025 16:59:33 +0530

ruby-bio (2.0.5-1) unstable; urgency=medium

  [ Debian Janitor ]
  * Update standards version to 4.6.2, no changes needed.

  [ Lucas Nussbaum ]
  * New upstream version 2.0.5

 -- Lucas Nussbaum <lucas@debian.org>  Sun, 03 Mar 2024 14:21:49 +0100

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
