python-biopython (1.86+dfsg-1ubuntu1) resolute; urgency=medium

  * Do not treat Sphinx warnings as errors (LP: #2147029)

 -- Graham Inggs <ginggs@ubuntu.com>  Wed, 08 Apr 2026 17:38:55 +0000

python-biopython (1.86+dfsg-1build1) resolute; urgency=medium

  * No-change rebuild to drop Python 3.13 bits.

 -- Matthias Klose <doko@ubuntu.com>  Fri, 20 Mar 2026 11:18:05 +0100

python-biopython (1.86+dfsg-1) unstable; urgency=medium

  * New upstream version 1.86+dfsg
  * croak-on-muscle5.patch: delete: affected code erased upstream.
  * muscle3.patch: delete: affected code erased upstream.
  * skip-scipy-in-codonalign.patch: delete: #1086108 is resolved.
  * bwa-output.patch: delete: affected code erased upstream.
  * d/control: drop redundant Rules-Requires-Root: no.
  * d/rules: cleanup list of excluded tests.
  * d/{rules,t/run-unit-test}: skip test_pairwise_aligner.py on i386.

 -- Étienne Mollier <emollier@debian.org>  Wed, 29 Oct 2025 23:16:49 +0100

python-biopython (1.85+dfsg-5) unstable; urgency=medium

  * bwa-output.patch: new: fix a test failure. (Closes: #1114298)
  * d/control: build depends on python3-numpy-dev:any.
    Lintian flagged that dh_numpy3 needed python3-numpy-dev:any.
  * d/watch: update to file format version 5.
  * d/patches/*: normalize dep3 headers.
  * d/python3-biopython.lintian-overrides: delete.
    The spelling override that was within is not needed anymore.
  * d/control: uncondionally deploy some build-dependencies.
    Several of the packages that were initially marked as <!nocheck>
    turned out to be actually needed outside check context. (Closes: #1103472)
  * d/rules: isolate a code segment irrelevant with nocheck profile.

 -- Étienne Mollier <emollier@debian.org>  Sat, 13 Sep 2025 12:12:17 +0200

python-biopython (1.85+dfsg-4) unstable; urgency=medium

  * Team upload.
  * Restore deleted line as it seems to break autopkgtests.

 -- Santiago Vila <sanvila@debian.org>  Fri, 11 Apr 2025 21:30:00 +0200

python-biopython (1.85+dfsg-3) unstable; urgency=medium

  * Team upload.
  * Fix build with nocheck.
  * Update standards-version.

 -- Santiago Vila <sanvila@debian.org>  Fri, 11 Apr 2025 19:00:00 +0200

python-biopython (1.85+dfsg-2) unstable; urgency=medium

  * Skip the Tutorial test on s390x. Closes: #1095105.

 -- Michael R. Crusoe <crusoe@debian.org>  Thu, 06 Feb 2025 15:44:29 +0100

python-biopython (1.85+dfsg-1) unstable; urgency=medium

  * Team upload

  [ Étienne Mollier ]
  * d/t/mini-ccd.cif: include definition of SO4 molecule.
    The definition originates from PDB's components.cif as of 2024-10-30.
    This resolves the noisy warning when running test_PDB_DSSP.

  [ Michael R. Crusoe ]
  * New upstream version
  * Refreshed patches.
  * Added python3-igraph as a recommend package and test dependency for
    use with Bio.Phylo.
  * d/rules: resume running the Tutorial tests everywhere.

 -- Michael R. Crusoe <crusoe@debian.org>  Wed, 29 Jan 2025 17:02:52 +0100

python-biopython (1.84+dfsg-4) unstable; urgency=medium

  * skip-scipy-in-codonalign.patch: comment about #1086108.
    Bug #1086108 may be related and the patch removed once resolved.
  * d/t/mini-ccd.cif: new: provide subset of data needed by the libcifpp.
  * d/copyright: document origin of mini-ccd.cif.
  * d/rules: configure libcifpp to use the mini-ccd.cif.
    By instructing the libcifpp to use a local data directory with the
    mini-ccd.cif providing the missing components.cif PDB/DSSP related
    tests depending on a working libcifpp are back in "fair enough"
    working conditions.  The original components.cif is more than 400M and
    changes constantly, making it problematic to maintain through Debian
    packages while at the same time keeping it useful for end users,
    Thanks to Maarten L. Hekkelman <maarten@hekkelman.com> (Closes: #1086156)
  * d/t/run-unit-test: also fix PDB/dssp for autopkgtest.

 -- Étienne Mollier <emollier@debian.org>  Wed, 30 Oct 2024 21:45:42 +0100

python-biopython (1.84+dfsg-3) unstable; urgency=medium

  * skip-scipy-in-codonalign.patch: also skip on mips64el.
    The symptom of scipy processing hanging up appeared already in
    riscv64, now on mips64el.
  * d/rules: skip test of BWA on mips64el.

 -- Étienne Mollier <emollier@debian.org>  Fri, 18 Oct 2024 11:30:13 +0200

python-biopython (1.84+dfsg-2) unstable; urgency=medium

  * d/t/run-unit-test: disable PDB_binary_cif for s390x in autopkgtest too.

 -- Étienne Mollier <emollier@debian.org>  Tue, 24 Sep 2024 19:44:19 +0200

python-biopython (1.84+dfsg-1) unstable; urgency=medium

  * Migrate Biopython 1.84 from experimental to unstable.
  * d/salsa-ci.yml: disable build path variation in reprotest.
  * d/rules: normalize HOME; this stabilizes build reproducibility.
  * d/rules: skip PDB_bcif on s390x architecture.

 -- Étienne Mollier <emollier@debian.org>  Mon, 23 Sep 2024 19:04:17 +0200

python-biopython (1.84+dfsg-1~0exp1) experimental; urgency=medium

  * New upstream version 1.84+dfsg
  * d/watch: fix debian version mangling.
  * d/copyright: update copyright years.
  * fix-use-of-unversioned-python.patch: delete: hunk removed upstream.
  * reproduciblebuild.patch: delete: file disappeared upstream.
  * croak-on-muscle5.patch: refresh.
  * muscle3.patch: unfuzz.
  * seqxml-parser.patch: delete: issue fixed upstream.
  * skip-scipy-in-codonalign.patch: unfuzz.
  * d/rules: condensate dh_installdocs target to ease readability.
  * d/rules: cleanup irrelevant comments and more readable dh_auto_test.
  * d/t/run-unit-test: Tutorial.tex does not exist anymore.
  * d/t/run-unit-test: new PDB tests require compressed bcif files.
  * d/rules: replace distclean target by clean in Doc/.
  * d/control: documentation now depends on Sphinx and side modules.
  * d/rules: explicitly make html documentation.
  * d/copyright: do not advertise LGPL since it is not in use.
  * d/rules: cleanup documentation from embeding and privacy breaches.
  * d/control: documentation depends on libjs-sphinx and libjs-jquery.
  * d/python-biopython-doc.docs: install sphinx html artifacts.
  * d/python-biopython-doc.doc-base: update location of the Tutorial.
  * d/python-biopython-doc.examples: new: install examples.
  * d/python-biopython-doc.lintian-overrides: flag another empty test file.
  * fix-type-cast-i386.patch: new: fix PDB test failure on 32-bit.
  * d/TODO: build reproducibility needs fixing.

 -- Étienne Mollier <emollier@debian.org>  Mon, 16 Sep 2024 22:34:06 +0200

python-biopython (1.83+dfsg1-5) unstable; urgency=medium

  * Team upload.
  * Cherry-pick patch from upstream to fix FTBFS with Python 3.13.
    Closes: #1081665
  * Remove constraints unnecessary since bullseye (oldstable):
    + python3-biopython: Drop versioned constraint on ncbi-blast+ (>= 2.10.1-3)
      in Recommends.
  * d/control: adjust build-deps to be more cross-build friendly.
  * Fix some of the DEP-3 patch metadata

 -- Michael R. Crusoe <crusoe@debian.org>  Sat, 14 Sep 2024 13:51:11 +0200

python-biopython (1.83+dfsg1-4) unstable; urgency=medium

  * skip-scipy-in-codonalign.patch: new: skip scipy tests on riscv64.
    This patch is introduced to give some breath to Risc-V CI runners while
    the core of the problem is investigated. (Closes: #1079439)
  * d/rules: skip ncbi tools tests due to #1079439.
  * d/rules: update list of excluded tests due to missing packages.

 -- Étienne Mollier <emollier@debian.org>  Wed, 04 Sep 2024 21:44:05 +0200

python-biopython (1.83+dfsg1-3) unstable; urgency=medium

  * Replace skip-xmlio-tests.patch by seqxml-parser.patch.
    Instead of skipping the test, upstream introduced a change that fixed
    the XML parser for use with the newer version of expat. (Closes: #1064147)
  * d/control: declare compliance to standards version 4.7.0.
  * d/python3-biopython.lintian-overrides: update file name.

 -- Étienne Mollier <emollier@debian.org>  Wed, 22 May 2024 15:14:56 +0200

python-biopython (1.83+dfsg1-2) unstable; urgency=medium

  * Team upload.
  * Drop emboss from test dependencies on emboss due to #1069098.

 -- Andrius Merkys <merkys@debian.org>  Wed, 17 Apr 2024 07:32:28 -0400

python-biopython (1.83+dfsg1-1) unstable; urgency=medium

  * New upstream pseudo-version 1.83+dfsg1.
    This is a minor version bump to include the new test artifact necessary
    to allow the test suite to pass on big endian architectures.  The nature
    of the change makes it unsuitable to represent using the regular d/patches
    series.  See upstream issue 4658[1] for further information.
    [1}: https://github.com/biopython/biopython/issues/4658
  * d/rules: skip test Tutorial on non-amd64.

 -- Étienne Mollier <emollier@debian.org>  Wed, 20 Mar 2024 21:10:02 +0100

python-biopython (1.83+dfsg-1) unstable; urgency=medium

  [ Andreas Tille ]
  * New upstream version
  * Exclude emboss from Build-Depends for 32bit architectures since
    emboss will be removed for these architectures (see #1062371)

  [ Étienne Mollier ]
  * skip-xmlio-tests.patch: new: skip test failures.
    This works around #1064147 so it is not a serious failure anymore.
    The problem being still latent, said bug is not closed for now.
  * d/t/run-unit-test: deploy newly needed test data.
  * d/control: reduce availability of test dependencies.
    Following the 64-bit time_t migration, and the removal of several
    Debian Med packages from the 32-bit archives, these items are not
    generally available anymore, and only checked on amd64 architecture.

 -- Étienne Mollier <emollier@debian.org>  Sun, 10 Mar 2024 21:00:41 +0100

python-biopython (1.81+dfsg-3) unstable; urgency=medium

  * d/control: remove dependency on python3-unittest2. (Closes: #1058967)

 -- Étienne Mollier <emollier@debian.org>  Tue, 19 Dec 2023 15:06:46 +0100

python-biopython (1.81+dfsg-2) unstable; urgency=medium

  * python3.12.patch: new: fix ftbfs with python3.12.
    Thanks to Antonio (Closes: #1055708)
  * d/control: remove obsolete comment.
  * d/control: move to dh-sequence-python3.

 -- Étienne Mollier <emollier@debian.org>  Sat, 11 Nov 2023 11:16:46 +0100

python-biopython (1.81+dfsg-1) unstable; urgency=medium

  * Migrate biopython 1.81 to unstable.
  * Merges fixes from python-biopython 1.80+dfsg-6.

 -- Étienne Mollier <emollier@debian.org>  Mon, 10 Jul 2023 22:50:52 +0200

python-biopython (1.81+dfsg-0+exp1) experimental; urgency=medium

  * New upstream version 1.81+dfsg
  * d/control: remove obsolete version constraint on dssp.
  * numpy-1.24.patch: remove: applied upstream.
  * muscle3.patch: fix typo in patch description.
  * remove-distutils-import.patch: add.

 -- Étienne Mollier <emollier@debian.org>  Sun, 09 Jul 2023 20:21:39 +0200

python-biopython (1.80+dfsg-6) unstable; urgency=medium

  * d/control: depend on python3-reportlab (>= 4.0.4-1~). (Closes: #1040776)

 -- Étienne Mollier <emollier@debian.org>  Mon, 10 Jul 2023 22:27:12 +0200

python-biopython (1.80+dfsg-5) unstable; urgency=medium

  [ Andreas Tille ]
  * Drop nocheck profile from hevea since its also needed to create doc
    (Closes: #1036174)

  [ Lukas Märdian ]
  * avoid the python3-renderpm dependency (Closes: #1039565)

  [ Étienne Mollier ]
  * d/rules: disable install-doc target with nodoc profile.
  * d/control: enable numpy outside nocheck build profile.
  * d/*.lintian-overrides: make the spelling override more generic.

 -- Étienne Mollier <emollier@debian.org>  Sun, 09 Jul 2023 17:48:34 +0200

# Older entries have been removed from this changelog.
# To read the complete changelog use `apt changelog python3-biopython`.
