[Debian-med-packaging] sra-sdk_3.4.1+dfsg-1_source.changes ACCEPTED into unstable

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Accepted:

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Format: 1.8
Date: Sun, 27 Sep 2026 21:07:56 -0400
Source: sra-sdk
Architecture: source
Version: 3.4.1+dfsg-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Changed-By: Aaron M. Ucko <ucko at debian.org>
Closes: 1144917
Changes:
 sra-sdk (3.4.1+dfsg-1) unstable; urgency=medium
 .
   * New upstream release.
     - test-sra no longer crashes under glibc 2.43.  (Closes: #1144917.)
   * debian/control:
     - Bump libngs-c++-dev Breaks/Replaces on libncbi-vdb-dev to (<< 3.4)
       per libkapp.a takeover.  (NB: sra-sdk took over the name and the
       main() wrapper, but ncbi-vdb retained the remaining content under
       the name libvdbapp.a.)
     - Bump B-D on libncbi-vdb-dev to (>= 3.4.1+dfsg~) and add one on
       python3-setuptools-whl to support Test_NGS_Python_install's patch.
   * debian/copyright: Revisit per licenserecon (lrc).
     - Add stanzas for bxzstr, rwqueue, SparkKMer.java, sse2neon.h,
       taskflow (complete with internal special cases), and tsl.
     - Wildcard (N. Lohmann's) json.hpp.
     - Extend BitMagic (libs/inc/bm) date range.
     - Formally rename BSD-3-clause-CLI11 to BSD-3-clause, uncontended.
   * debian/not-installed: Broaden lib*ngs*-static.a to lib*-static.a.
   * debian/patches: Update existing patches for new release.  Notably:
     - bypass-libxml2-ATTRIBUTE_UNUSED.patch, fix_bm_for_gcc15.patch:
       Disable (fully superseded).
     - include_cstdint_for_gcc15.patch: Drop superseded portion.
     - label_online_tests.patch: Resync; leave out Test_NGS_Python_install.
     - link_vdb_dynamically.patch, prefer_dynamic_libraries.patch: Drop
       build/env.cmake changes; we can now set DYNAMIC_LINK=ON instead.
     - setuptools.patch: Repurpose somewhat.  (setup.py has already
       migrated to setuptools, but the new accompanying test-install.sh
       [Test_NGS_Python_install] uses pip and needs patching to take
       infrastructure wheels from the local filesystem rather than PyPI.)
     - support_libre2-11.patch, use_debian_packaged_*.patch: Resync.
   * debian/patches/not_just_ubuntu.patch (new): Don't use a build-wide
     Python virtual env. under Debian (or any other derivative) either.
   * debian/patches/public_version-hash.patch (new): In
     tools/loaders/sharq/version.h, #include <kapp/version-hash.h> without
     a leading ../libs/, which works only when building against uninstalled
     VDB.  (As of 3.4.1, Debian's installation makes the header public.)
   * debian/patches/tiny_csra_shell.patch (new): Run
     test/external/fasterq-dump/tiny_csra.sh under bash per its use of [[.
     (As is, it could never officially fail.  No further changes needed,
     though.)
   * debian/rules:
     - Don't clean "expected" (golden) *.orig files.  To that end, move
       custom cleanup logic to override_dh_clean (vs. _autoclean).
     - override_dh_auto_install: Add libkapp.a* to libngs-c++-dev.
     - execute_after_dh_auto_build (new): Take over javadoc invocation from
       the upstream build system, which no longer ever runs javadoc itself.
     - override_dh_auto_configure: Set the new DYNAMIC_LINK option to ON,
       thereby linking dynamically against dependencies in most cases.
       (Some portions of the tree still need patching to do so.)
   * debian/tests/run-unit-test: Stop testing cache-mgr, retired upstream.
   * Standards-Version: 4.7.4 (routine-update)
   * Reflow Uploaders field (cme)
   * Remove Priority field (cme)
   * Drop 'Rules-Requires-Root: no' from d/control (routine-update)
   * Reformat the Last-Update date as ISO YYYY-MM-DD.
   * No tab in license text (routine-update)
 .
 sra-sdk (3.2.1+dfsg-7) UNRELEASED; urgency=medium
 .
   * Fix watch file
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Files:
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