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

python-biopython (1.80+dfsg-4) unstable; urgency=medium

  * Team Upload.
  * Cherry-pick upstream patch to fix problems with
    numpy 1.24 (Closes: #1027253)

 -- Nilesh Patra <nilesh@debian.org>  Thu, 29 Dec 2022 18:52:07 +0530

python-biopython (1.80+dfsg-3) unstable; urgency=medium

  * muscle3.patch: ensure muscle3 is default even if unavailable.
    This fixes the test_doctest failure which occurs because of a
    mismatch between "muscle" and "muscle3" when none of them is
    available.
  * d/control: declare compliance to standards version 4.6.2.

 -- Étienne Mollier <emollier@debian.org>  Fri, 23 Dec 2022 20:22:29 +0100

python-biopython (1.80+dfsg-2) unstable; urgency=medium

  * d/NEWS: fix typo in news item.
  * d/control: bring back t_coffee tests since upstream version revert.
    Closes: #1022307
  * d/control: restore muscle3 instead of plain muscle (version 5).
    Closes: #1009118
  * port_tutorial_to_muscle3.patch: add; fix doctest failures.

 -- Étienne Mollier <emollier@debian.org>  Sun, 04 Dec 2022 19:15:42 +0100

python-biopython (1.80+dfsg-1) unstable; urgency=medium

  * Migrate biopython 1.80 from experimental to unstable.
    Closes: #1024986, #1024858, #1024855, #1025014, #1025022

 -- Étienne Mollier <emollier@debian.org>  Mon, 28 Nov 2022 22:19:25 +0100

python-biopython (1.80+dfsg-1~0exp0) experimental; urgency=medium

  * New upstream version
  * Standards-Version: 4.6.1 (routine-update)
  * Set upstream metadata fields: Security-Contact.
  * privacy_breach_ie9.patch: refresh.
  * adjust-test_GraphicsBitmaps.patch: delete; applied upstream.
  * spelling.patch: delete; applied upstream.
  * mkdssp4.patch: delete; fixed upstream.
  * d/control: remove test dependency on problematic packages; muscle 5
    wrapping is unsupported upstream, and t_coffee suffers from segmentation
    faults documented in #1022570
  * croak-on-muscle5.patch: add; raise RuntimeError with muscle 5.
  * d/NEWS: describe incompatibility with muscle 5; also describe possible
    workarounds.
  * d/not-installed: add tree1 and other_trees.
  * d/*.lintian-overrides: refresh override.
  * debian/python3-biopython.lintian-overrides: override typo; the reported
    spelling error does not seem to match anything meaningful on the side of
    the source code.
  * d/s/lintian-overrides: indicate location of Restriction.md, source of
    Restriction.html.
  * d/copyright: bump copyright years.
  * muscle3.patch: add; default to use muscle3 command if available.
    This is in preparation of the availability of a dedicated muscle3
    package with the explicitly versioned command, since muscle 5 is a very
    different program but can be installed in parallel.

 -- Étienne Mollier <emollier@debian.org>  Thu, 24 Nov 2022 18:39:22 +0100

python-biopython (1.79+dfsg-3) unstable; urgency=medium

  [ Peter Michael Green ]
  * Restrict architecture list of muscle build-dependency to reflect
    architectures where the current version of muscle is available.
    (Closes: #1006667)

  [ Étienne Mollier ]
  * d/control,d/python3-biopython.links: move from w3-dtd-mathml to slightly
    more recent w3c-sgml-lib.
    Thanks to Peter Green and Vincent Lefevre.
  * Remove d/python3-biopython.lintian-overrides; not in use anymore.

 -- Étienne Mollier <emollier@debian.org>  Sat, 05 Mar 2022 15:36:12 +0100

python-biopython (1.79+dfsg-2) unstable; urgency=medium

  * Move w3-dtd-mathml from Suggests to Depends to avoid dangling symlink
    mathml2.dtd

 -- Andreas Tille <tille@debian.org>  Thu, 17 Feb 2022 20:15:09 +0100

python-biopython (1.79+dfsg-1) unstable; urgency=medium

  * Migrate from Experimental to Unstable.
  * Mark spelling.patch as not needing forward.
    It seems that the file being package might not exists in upcoming
    Biopython versions anymore.
  * adjust-test_GraphicsBitmaps.patch: forwarded upstream.
  * d/control: breaks ncbi-acc-download (<< 0.2.7-2~)

 -- Étienne Mollier <emollier@debian.org>  Fri, 22 Oct 2021 18:10:48 +0200

python-biopython (1.79+dfsg-1~0exp0) experimental; urgency=medium

  * New upstream version
  * d/copyright: update years per LICENSE file.
  * Refresh patches:
    + mkdssp4.patch:
      - renamed from mkdssp4.path, fixing typo in the file extension,
      - skip failing test_PDB_DSSP due to mkdssp 4 too recent,
      - updated patch author's email address;
    + following renderpm upgrade, add adjust-test_GraphicsBitmaps.patch to
      properly skip again the test failing due to missing font;
    + add spelling.patch to fix new spelling-error-in-binary caught by lintian.

 -- Étienne Mollier <emollier@debian.org>  Sat, 16 Oct 2021 12:30:51 +0200

python-biopython (1.78+dfsg-6) unstable; urgency=medium

  * d/control: bump python3-renderpm to python3-biopython dependency.
    (Closes: #995689)

 -- Étienne Mollier <emollier@debian.org>  Mon, 11 Oct 2021 22:25:02 +0200

python-biopython (1.78+dfsg-5) unstable; urgency=medium

  * d/control: update uploader address
  * d/watch: fix broken url to github
  * d{,/tests}/control: add full_suite autopkgtest (Closes: #986410)
  * Standards-Version: 4.6.0 (routine-update)
  * Use secure URI in Homepage field.

 -- Étienne Mollier <emollier@debian.org>  Sun, 22 Aug 2021 21:56:28 +0200

python-biopython (1.78+dfsg-4) unstable; urgency=medium

  * Add mkdssp4.patch. (Closes: #976542)
  * Standards-Version: 4.5.1 (routine-update)
  * Bump dependency on dssp version 4.0.0.

 -- Étienne Mollier <etienne.mollier@mailoo.org>  Sat, 05 Dec 2020 23:32:40 +0100

python-biopython (1.78+dfsg-3) unstable; urgency=medium

  * Bumped ncbi-blast+ version requirement to 2.10.1-3
  * Made sure run-unit-test did not attempt memory allocation override
  * debian/not-installed made more generic for various python versions
    (Closes: #972381)

 -- Étienne Mollier <etienne.mollier@mailoo.org>  Sat, 17 Oct 2020 13:59:04 +0200

python-biopython (1.78+dfsg-2) unstable; urgency=medium

  * Bumped build requirement on ncbi-blast+ 2.10.1-2 and greater:
      - fixed building on mipsel;
      - removed patch working around makeblastdb bug in v5, now unnecessary.
  * Cleaned up patches:
      - added DEP3 description to blastdbv4-tests-filter-archs.patch;
      - reviewed and forwarded patches upstream when applicable.

 -- Étienne Mollier <etienne.mollier@mailoo.org>  Fri, 02 Oct 2020 23:18:07 +0200

python-biopython (1.78+dfsg-1) unstable; urgency=medium

  * Bumped build requirement on ncbi-blast+ 2.10.0-3 and greater,
  * Reworked the patch working around makeblastd bug in v5 to fall back in v4
    only on architectures on which corrections are yet to be implemented.
  * Removed patches applied upstream.
  * New upstream version
  * debhelper-compat 13 (routine-update)
  * Improved build reproducibility

 -- Étienne Mollier <etienne.mollier@mailoo.org>  Wed, 09 Sep 2020 22:53:13 +0200

python-biopython (1.77+dfsg-3) unstable; urgency=medium

  [ Etienne Mollier ]
  * Forwarded implementation of makeblastdb's `-blastdb_version` flag to
    upstream.  (minor change)

  [ Andreas Tille ]
  * Adapt to python3-scipy by taking over pull request
      https://github.com/biopython/biopython/pull/2998
    as quilt patch.
    Closes: #966928

 -- Etienne Mollier <etienne.mollier@mailoo.org>  Mon, 22 Jun 2020 19:21:47 +0200

python-biopython (1.77+dfsg-2) unstable; urgency=medium

  * Declared python3-biopython breaks: cnvkit (<< 0.9.7-1~) (Closes: #962944)

 -- Etienne Mollier <etienne.mollier@mailoo.org>  Tue, 16 Jun 2020 22:12:00 +0200

python-biopython (1.77+dfsg-1) unstable; urgency=medium

  * Team upload.
  * New upstream version.
  * Test makeblastdb using format version 4, this is to work around issues on
    32 bits CPU architectures.  Closes: #960756.

  [ Steffen Moeller ]
  * Also clean .pygtex and .pygstyle files in Doc

 -- Etienne Mollier <etienne.mollier@mailoo.org>  Thu, 11 Jun 2020 20:10:34 +0200

python-biopython (1.76+dfsg-2) unstable; urgency=medium

  * Team upload.

  [ Michael R. Crusoe ]
  * debian/control: mark the -doc package as Multi-Arch: foreign

  [ Dylan Aïssi ]
  * Add upstream patch to fix tests with new NCBI BLAST DB v5 (Closes: #959587)

  [ Andreas Tille ]
  * Standards-Version: 4.5.0 (routine-update)
  * Add salsa-ci file (routine-update)
  * Rules-Requires-Root: no (routine-update)
  * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository,
    Repository-Browse.
  * Refer to specific version of license GPL-2+.

 -- Dylan Aïssi <daissi@debian.org>  Fri, 15 May 2020 11:40:33 +0200

python-biopython (1.76+dfsg-1) unstable; urgency=medium

  * Team upload.
  * New upstream version
  * Remove patches applied upstream:
    fix_doctests, ppc64el_precision, python_3.8_iteration_fix.patch
  * Remove patches missing from debian/patches/series.

 -- Michael R. Crusoe <michael.crusoe@gmail.com>  Fri, 20 Dec 2019 11:00:46 -0800

python-biopython (1.75+dfsg-4) unstable; urgency=medium

  * Team upload.
  * Patch added to reduce the required precision for one part of the
    test_phenotype_fit.TestPhenoMicro test

 -- Michael R. Crusoe <michael.crusoe@gmail.com>  Tue, 17 Dec 2019 11:35:41 +0100

python-biopython (1.75+dfsg-3) unstable; urgency=medium

  * Team upload.
  * Restrict where we test phyml for now.

 -- Michael R. Crusoe <michael.crusoe@gmail.com>  Mon, 16 Dec 2019 22:15:00 +0100

python-biopython (1.75+dfsg-2) unstable; urgency=medium

  [ Michael R. Crusoe ]
  * Team upload.
  * Skip PDB_ResidueDepth test, as http://mgltools.scripps.edu/packages/MSMS
    is not yet packaged for Debian
  * Skip test_mmtf{,_online} as https://github.com/rcsb/mmtf-python is not yet
    packaged for Debian
  * Added missing test dependencies: python-unittest2, python{,3}-networkx,
    samtools
  * i386: build-dep on raxml for testing purposes
  * debian/patches/arm64.patch from upstream to fix the PairwiseAligner
  * debian/patches/fix_doctest: from me to fix the Bio.Cluster._cluster doctests
    Now the tests are required to pass again.

  [ Andreas Tille ]
  * Drop Python2 package
    Closes: #937606

 -- Michael R. Crusoe <michael.crusoe@gmail.com>  Sun, 15 Dec 2019 14:38:14 +0100

python-biopython (1.75+dfsg-1) unstable; urgency=medium

  * New upstream version
    Closes: #944242
  * debhelper-compat 12
  * Standards-Version: 4.4.1
  * Remove trailing whitespace in debian/rules
  * autopkgtest: s/ADTTMP/AUTOPKGTEST_TMP/g
  * Set upstream metadata fields: Repository.
  * Build-Depends: python3-pygments
  * Python 3.8 iteration fix from upstream
  * Ignore remaining build time test errors since these are discussed with
    upstream and will be fixed soon.  On the other hand latest version of
    biopython is needed to fix bugs in other Debian Med packages.
  * Seems explicit Depends: python is needed now for Python2 packages
  * Remove test test_Tutorial.py which is bound to fail from autopkgtest

 -- Andreas Tille <tille@debian.org>  Wed, 04 Dec 2019 17:29:48 +0100

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