sra-sdk (3.2.1+dfsg-6ubuntu2) stonking; urgency=medium

  * No-change rebuild against libabsl20260526

 -- Graham Inggs <ginggs@ubuntu.com>  Wed, 08 Jul 2026 09:02:33 +0000

sra-sdk (3.2.1+dfsg-6ubuntu1) resolute; urgency=medium

  * Merge with Debian; remaining changes:
    - Disable LTO; this causes a misbuild that makes fastq-dump segfault.

 -- Matthias Klose <doko@ubuntu.com>  Sat, 28 Feb 2026 08:42:51 +0100

sra-sdk (3.2.1+dfsg-6) unstable; urgency=medium

  * debian/control: Build-depend on pkgconf.
  * debian/patches/support_glibc_2.43.patch (new): Comment out
    test/search/agrep-main.c's gratuitous redefinition of index as an alias
    for strchr, which interacted poorly with C23 const-preserving generics.
    (Closes: #1128753.)
  * debian/patches/support_libre2-11.patch: Obtain re2's dependencies from
    pkgconf rather than hardcoding absl_string_view.  (Closes: #1126172,
    modulo the need for a rebuilt re2.)
  * Update watch file format version to 5.
  * Add dversionmangle for repack versioning in debian/watch.
  * Use GitHub template in watch file instead of explicit
    Source/Matching-Pattern.
  * Reorder Files paragraphs in debian/copyright by directory depth.
  * Remove duplicate values for fields Entry, Entry, Entry, Name, Name in
    debian/upstream/metadata.
  * debputy lint --auto-fix (routine-update)

 -- Aaron M. Ucko <ucko@debian.org>  Fri, 27 Feb 2026 17:45:36 -0500

sra-sdk (3.2.1+dfsg-5) unstable; urgency=medium

  * debian/patches/bypass-libxml2-ATTRIBUTE_UNUSED.patch (new): Fix builds
    with libxml2 2.14+, which don't define ATTRIBUTE_UNUSED publically.
    (Closes: #1106622.)

 -- Aaron M. Ucko <ucko@debian.org>  Sat, 16 Aug 2025 23:39:09 -0400

sra-sdk (3.2.1+dfsg-4ubuntu6) resolute; urgency=medium

  * No-change rebuild for abseil soname.

 -- Matthias Klose <doko@ubuntu.com>  Thu, 22 Jan 2026 08:55:23 +0100

sra-sdk (3.2.1+dfsg-4ubuntu5) questing; urgency=medium

  * Fix build with libxml 2.14.x.

 -- Matthias Klose <doko@ubuntu.com>  Wed, 28 May 2025 14:27:42 +0200

sra-sdk (3.2.1+dfsg-4ubuntu4) questing; urgency=medium

  * No-change rebuild for libxml2 soname change.

 -- Matthias Klose <doko@ubuntu.com>  Mon, 26 May 2025 14:23:23 +0200

sra-sdk (3.2.1+dfsg-4ubuntu3) questing; urgency=medium

  * No-change rebuild for libxml2 soname change.

 -- Matthias Klose <doko@ubuntu.com>  Tue, 20 May 2025 12:19:57 +0200

sra-sdk (3.2.1+dfsg-4ubuntu2) questing; urgency=medium

  * Rebuild against latest abseil

 -- Jeremy Bícha <jbicha@ubuntu.com>  Sat, 03 May 2025 11:13:20 -0400

sra-sdk (3.2.1+dfsg-4ubuntu1) plucky; urgency=low

  * Merge from Debian unstable. Remaining changes:
    - Disable LTO; this causes a misbuild that makes fastq-dump segfault.

 -- Gianfranco Costamagna <locutusofborg@debian.org>  Thu, 17 Apr 2025 09:58:24 +0200

sra-sdk (3.2.1+dfsg-4) unstable; urgency=medium

  * debian/patches: Add two patches for GCC 15 support.  (Closes: #1097930.)
    - fix_bm_for_gcc15.patch: BitMagic cherry-pick, location adjusted.
    - include_cstdint_for_gcc15.patch: Compensate for libstdc++ changes.
  * debian/rules: Explicitly direct pybuild to use distutils.  It can
    otherwise misfire when bypassing the test suite, which includes a
    setup.py run.  (Closes: #1103330.)

 -- Aaron M. Ucko <ucko@debian.org>  Wed, 16 Apr 2025 15:44:48 -0400

sra-sdk (3.2.1+dfsg-3ubuntu1) plucky; urgency=low

  * Merge from Debian unstable. Remaining changes:
    - Disable LTO; this causes a misbuild that makes fastq-dump segfault.

 -- Gianfranco Costamagna <locutusofborg@debian.org>  Thu, 10 Apr 2025 17:12:28 +0200

sra-sdk (3.2.1+dfsg-3) unstable; urgency=medium

  * Upload to unstable.
  * debian/salsa-ci.yml: Disable use of experimental (build-)deps again.

 -- Aaron M. Ucko <ucko@debian.org>  Wed, 09 Apr 2025 21:31:32 -0400

sra-sdk (3.2.1+dfsg-2) experimental; urgency=medium

  * debian/control: Build-depend on python3-setuptools.
  * debian/patches/fix_arm64_build.patch: Correct parenthesis placement.
  * debian/patches/setuptools.patch (new): Substitute setuptools for
    distutils (retired) in ngs/ngs-python/setup.py.
  * debian/rules:
    - Set PIP_BREAK_SYSTEM_PACKAGES for upstream's test suite.
    - Substitute pybuild for direct setup.py invocation and clean up after
      it.
  * .gitignore: Add .pc (belatedly) and .pybuild.

 -- Aaron M. Ucko <ucko@debian.org>  Wed, 09 Apr 2025 20:41:31 -0400

sra-sdk (3.2.1+dfsg-1) experimental; urgency=medium

  [ Andreas Tille ]
  * New upstream version 3.1.1.
  * Fix Python3.12 string syntax
    Closes: #1087096
  * Do not fail if clean target debian/libngs-jni.links does not exist

  [ Aaron M. Ucko ]
  * New upstream version 3.2.1.
  * debian/control:
    - Tighten libncbi-vdb-dev build dependency as usual; add one on
      python3-vdb (provided by ncbi-vdb-data for now, to be split off
      post-Trixie.)
    - Drop vestigial build dependency on libfuse-dev.  (Closes: #1084404.)
  * debian/copyright: Update GPL logistics (see #1080497) and bm and
    spdlog paths.
  * debian/patches: Update accordingly.  Notably:
    - label_online_tests.patch: Add a couple dozen additional tests.
    - missing_include.patch: Drop, superfluous at this point.
    - support_libre2-11.patch: Cover new additions to
      fastq_defline_matcher.hpp.
    - use_debian_packaged_re2.patch: Cover new test-sharq-reader.
  * debian/rules:
    - Stop generating and installing debian.kfg, taken over by
      ncbi-vdb-data.
    - Clean up additional build output.
  * debian/salsa-ci.yml: Reenable use of experimental (build-)deps for now.
  * debian/tests/control: Per Stefano Rivera (thanks!), declare a
    dependency on ca-certificates and the need for Internet access.
    (Closes: #1099933.)
  * .gitignore: Add, belatedly.
  * Standards-Version: 4.7.2 (routine-update)

 -- Aaron M. Ucko <ucko@debian.org>  Tue, 08 Apr 2025 21:51:58 -0400

sra-sdk (3.0.9+dfsg-7.1ubuntu1) plucky; urgency=low

  * Merge from Debian unstable. Remaining changes:
    - Disable LTO; this causes a misbuild that makes fastq-dump segfault.

 -- Gianfranco Costamagna <locutusofborg@debian.org>  Wed, 12 Mar 2025 08:31:47 +0100

sra-sdk (3.0.9+dfsg-7.1) unstable; urgency=medium

  * Non-maintainer upload.
  * Build-Depend on python3-setuptools, used in the test suite.
    (Closes: #1099911)

 -- Stefano Rivera <stefanor@debian.org>  Sun, 09 Mar 2025 10:33:36 -0400

sra-sdk (3.0.9+dfsg-7ubuntu2) plucky; urgency=medium

  * No-change rebuild against libhdf5-310

 -- Miriam España Acebal <miriam.espana@canonical.com>  Sun, 26 Jan 2025 11:08:27 +0000

sra-sdk (3.0.9+dfsg-7ubuntu1) plucky; urgency=low

  * Merge from Debian unstable. Remaining changes:
    - Disable LTO; this causes a misbuild that makes fastq-dump segfault.

 -- Gianfranco Costamagna <locutusofborg@debian.org>  Wed, 30 Oct 2024 17:46:43 +0100

sra-sdk (3.0.9+dfsg-7) unstable; urgency=medium

  * Upload to unstable to join Mbed TLS 3.x.  (See #1075868.)
  * debian/salsa-ci.yml: Comment out aptly setup, no longer needed.
  * Add changelog entries for 3.0.3+dfsg-7 through -9 to placate dgit.

 -- Aaron M. Ucko <ucko@debian.org>  Thu, 17 Oct 2024 22:48:06 -0400

sra-sdk (3.0.9+dfsg-6) experimental; urgency=medium

  * Team upload
  * Adding missing #include <algorithm> to use std::transform

 -- Pierre Gruet <pgt@debian.org>  Tue, 20 Aug 2024 22:46:44 +0200

sra-sdk (3.0.9+dfsg-5) experimental; urgency=medium

  * Team upload
  * Building against HDF5/1.14.4.3

 -- Pierre Gruet <pgt@debian.org>  Tue, 20 Aug 2024 09:45:01 +0200

sra-sdk (3.0.9+dfsg-4) experimental; urgency=medium

  * Team upload
  * Removing unneeded markdown and discount from B-D

 -- Pierre Gruet <pgt@debian.org>  Fri, 12 Jul 2024 07:48:57 +0200

sra-sdk (3.0.9+dfsg-3) experimental; urgency=medium

  * debian/control: Build depend on libabsl-dev so binaries using libre2
    (sharq and relevant tests) can unconditionally link against
    -labsl_string_view for simplicitly.
  * debian/patches/support_libre2-11.patch (new): Prepare for (but don't
    require!) newer libre2 versions where re2::StringPiece has changed
    from a custom class to a typedef for absl::string_view, whose API is
    somewhat different.  (Closes: #1053411.)

 -- Aaron M. Ucko <ucko@debian.org>  Sun, 05 May 2024 22:45:27 -0400

sra-sdk (3.0.9+dfsg-2) experimental; urgency=medium

  * debian/patches/fix_arm64_build.patch (new): Fix arm64 builds by
    tweaking BitMagic to treat __aarch64__ like __arm64__.

 -- Aaron M. Ucko <ucko@debian.org>  Fri, 12 Apr 2024 19:32:51 -0400

sra-sdk (3.0.9+dfsg-1) experimental; urgency=medium

  [ Andreas Tille ]
  * New upstream version

  [ Aaron M. Ucko ]
  * debian/control:
    - Tighten libncbi-vdb-dev requirement to (>= 3.0.9+dfsg~) per
      upstream expectations; this stack has to stay in experimental as
      long as mbed TLS 3 does, calling for explicit hints.
    - Drop explicit B-D on python3-distutils, currently redundant with
      dh-python (which depends on it via python3-setuptools) and found
      unnecessary regardless in Ubuntu.  (Closes: #1065961.)
  * debian/patches/label_online_tests.patch:
    - Correctly place test/internal/vdb-diff/CMakeLists.txt's change; its
      set_tests_properties call accidentally wound up ahead of the
      corresponding add_test calls.
    - Label 55 additional tests as needing network access.
  * debian/salsa-ci.yml: Try to ensure availability of experimental VDB,
    both by setting RELEASE to experimental and by reinstating aptly, now
    using job 5576517.
  * debian/sra-toolkit.links: Drop; its only entry has dangled since
    vdb-get retired (in upstream version 3.0.1).  (Closes: #1040391.)
  * Standards-Version: 4.7.0 (routine-update)

 -- Aaron M. Ucko <ucko@debian.org>  Fri, 12 Apr 2024 18:02:49 -0400

sra-sdk (3.0.3+dfsg-9ubuntu1) oracular; urgency=low

  * Merge from Debian unstable. Remaining changes:
    - Disable LTO; this causes a misbuild that makes fastq-dump segfault.

 -- Gianfranco Costamagna <locutusofborg@debian.org>  Tue, 03 Sep 2024 20:17:13 +0200

sra-sdk (3.0.3+dfsg-9) unstable; urgency=medium

  * Team upload
  * Building against HDF5/1.14.4.3 (Closes: #1078882)

 -- Pierre Gruet <pgt@debian.org>  Tue, 20 Aug 2024 09:40:26 +0200

sra-sdk (3.0.3+dfsg-8ubuntu1) oracular; urgency=low

  * Merge from Debian unstable. Remaining changes:
    - Disable LTO; this causes a misbuild that makes fastq-dump segfault.

 -- Gianfranco Costamagna <locutusofborg@debian.org>  Fri, 12 Jul 2024 08:18:50 +0200

sra-sdk (3.0.3+dfsg-8) unstable; urgency=medium

  * Team upload.
  * Removing B-D on markdown or discount for building the doc
  * Building with python3-setuptools instead of removed python3-distutils

 -- Pierre Gruet <pgt@debian.org>  Thu, 11 Jul 2024 14:39:57 +0200

sra-sdk (3.0.3+dfsg-7ubuntu1) oracular; urgency=medium

  * Merge from Debian unstable. Remaining changes:
    - Disable LTO; this causes a misbuild that makes fastq-dump segfault.
    - Drop build-dependency on python3-distutils, see #1065961

 -- Gianfranco Costamagna <locutusofborg@debian.org>  Fri, 24 May 2024 22:09:26 +0200

sra-sdk (3.0.3+dfsg-7) unstable; urgency=medium

  * debian/control: Build depend on libabsl-dev so binaries using libre2
    (sharq and relevant tests) can unconditionally link against
    -labsl_string_view for simplicitly.
  * debian/patches/support_libre2-11.patch (new): Prepare for (but don't
    require!) newer libre2 versions where re2::StringPiece has changed
    from a custom class to a typedef for absl::string_view, whose API is
    somewhat different.  (Closes: #1053411.)

 -- Aaron M. Ucko <ucko@debian.org>  Sun, 05 May 2024 22:15:17 -0400

sra-sdk (3.0.3+dfsg-6ubuntu7) oracular; urgency=medium

  * Rebuild against new libre2-11.

 -- Gianfranco Costamagna <locutusofborg@debian.org>  Fri, 24 May 2024 19:34:45 +0200

sra-sdk (3.0.3+dfsg-6ubuntu6) oracular; urgency=medium

  * Rebuild against new libre11.

 -- Gianfranco Costamagna <locutusofborg@debian.org>  Fri, 24 May 2024 10:38:36 +0200

sra-sdk (3.0.3+dfsg-6ubuntu5) noble; urgency=medium

  * No-change rebuild for CVE-2024-3094

 -- William Grant <wgrant@ubuntu.com>  Mon, 01 Apr 2024 15:51:57 +1100

sra-sdk (3.0.3+dfsg-6ubuntu4) noble; urgency=medium

  * Drop build-dependency on python3-distutils, see #1065961

 -- Graham Inggs <ginggs@ubuntu.com>  Sat, 23 Mar 2024 12:37:41 +0000

sra-sdk (3.0.3+dfsg-6ubuntu3) noble; urgency=medium

  * No-change rebuild against libhdf5-103-1t64

 -- Steve Langasek <steve.langasek@ubuntu.com>  Wed, 13 Mar 2024 18:05:54 +0000

sra-sdk (3.0.3+dfsg-6ubuntu2) noble; urgency=medium

  * No-change rebuild against libssl3t64

 -- Steve Langasek <steve.langasek@ubuntu.com>  Mon, 04 Mar 2024 21:25:51 +0000

sra-sdk (3.0.3+dfsg-6ubuntu1) mantic; urgency=medium

  * Merge from Debian unstable. Remaining changes:
    - Disable LTO; this causes a misbuild that makes fastq-dump segfault.

 -- Steve Langasek <steve.langasek@ubuntu.com>  Mon, 17 Jul 2023 22:16:18 -0700

sra-sdk (3.0.3+dfsg-6) unstable; urgency=high

  * debian/rules: Expand $(DEB_HOST_MULTIARCH) in libngs-java.links.in.
    (Closes: #1039621.)

 -- Aaron M. Ucko <ucko@debian.org>  Tue, 27 Jun 2023 22:14:41 -0400

# Older entries have been removed from this changelog.
# To read the complete changelog use `apt changelog libncbi-ngs3`.
