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Accepted sra-sdk 3.0.3+dfsg-2 (source) into unstable

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Format: 1.8
Date: Fri, 20 Jan 2023 17:57:36 -0500
Source: sra-sdk
Architecture: source
Version: 3.0.3+dfsg-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Aaron M. Ucko <ucko@debian.org>
Closes: 1024155 1025278
Changes:
 sra-sdk (3.0.3+dfsg-2) unstable; urgency=medium
 .
   * Upload to unstable.
   * .gitignore: Update patterns corresponding to test output.
   * debian/control:
     - Drop vestigial versioned dependency on libncbi-wvdb2.
     - Limit architecture-dependent packages to amd64 and arm64.  The only
       other architecture ncbi-vdb supports is x32, but these tools require
       a 64-bit address space.
   * debian/not-installed: Refresh.
     - Correct location of explicitly tagged lib*-static.a.
     - Drop spurious entries (with hardcoded amd64 paths, no less).
   * debian/patches/fix_ngs-c++-underlinkage.patch (new): Link libngs-c++
     against all internal dependencies.  Hold off for now on linking
     against libncbi-vdb, though anyone looking to substitute libncbi-wvdb
     would need to contrive to supply a suitable definition of
     KDBManagerMakeRead.
   * debian/patches/label_online_tests.patch: Extend as needed.  All
     existing labels confirmed to remain appropriate.
   * debian/patches/link_vdb_dynamically.patch: Extend prior to building
     tests again.  To wit, additionally cover makeinputs, from
     tools/loaders/general-loader/test. (All other tests were already OK at
     this point.)
   * debian/patches/prefer_dynamic_libraries.patch: Comment out upstream
     logic that favored static linkage.
   * debian/rules:
     - Skip rpaths, not needed even for libhdf5.
     - Explicitly enable tests, disabled by default these days.
     - Update test cleanup logic to allow for build area reuse.
   * debian/salsa-ci.yml: Retire remaining customizations.
 .
 sra-sdk (3.0.3+dfsg-1) experimental; urgency=medium
 .
   [ Andreas Tille ]
   * Breaks+Replaces: libncbi-vdb-dev (<< 3), libngs-sdk-dev (<< 3)
     Closes: #1024155
 .
   [ Aaron M. Ucko ]
   * New upstream version.
   * .gitignore:
     - Unhardcode architecture name in build tree (obj-*).
     - Ignore build results under ngs/ngs-python (dist, ngs.egg-info).
   * debian/{control,salsa-ci.yml}: Build against libncbi-vdb-dev 3.0.1+.
   * debian/copyright: Account for layout changes as of 3.0.1 and drop
     references to content removed upstream, both in Files-Excluded and in
     special cases.
   * debian/patches: Update for 3.0.1+; in particular, account for layout
     changes and better support for using system libraries.
   * debian/rules:
     - Correctly accommodate multiple supported Python versions.  (I'd
       insufficiently adapted ncbi-ngs's relevant logic.)
     - Account for layout changes and CMAKE_INSTALL_LIBDIR support (with
       the latter yielding multiarch paths).
     - Clean up newly generated files under ngs/ngs-python.
   * debian/{rules,sra-toolkit.install}: Move sratools and *-orig to a new
     /usr/lib/sra-toolkit directory; repoint symlinks accordingly.
     (Closes: #1025278.)
   * Standards-Version: 4.6.2 (routine-update)
 .
 sra-sdk (3.0.0+dfsg-1) experimental; urgency=medium
 .
   [ Andreas Tille ]
   * New upstream version
   * Standards-Version: 4.6.1 (routine-update)
   * Build-Depends: default-jdk, flex, bison
 .
   [ Aaron M. Ucko ]
   * debian/control:
     - Account for consolidation of ngs-sdk (albeit with some intervening
       changes, notably library restructuring); take the opportunity to add
       a -java-doc package.0
     - Let python3-ngs bypass libncbi-ngs-dev and use libncbi-ngs3 directly.
     - Drop build dependency on libvdb-sqlite-dev, now internal to sra-sdk.
   * debian/libngs-java-doc.javadoc: Enable javadoc installation.
   * debian/{libngs-java.{jlibs,poms},ngs-java.pom(.asc)}: Adopt (and adapt)
     from ngs-sdk.
   * debian/*ngs*.examples (new): Install upstream NGS examples.
   * debian/not-installed: Ignore usr/jar/*.jar (installed elsewhere, via
     jh_installlibs), usr/lib64/lib*-static.a, usr/share/examples*
     (installed elsewhere, via dh_installexamples), and
     usr/share/javadoc/ngs-doc (installed elsewhere, via jh_installjavadoc).
   * debian/patches/use_debian_packaged_re2.patch: Comment out an
     inappropriate add_dependencies call in test/sharq/CMakeLists.txt.
   * Add more patches for remaining build issues: fix_javadoc_build.patch,
     link_magic_dynamically.patch, link_vdb_dynamically.patch, and
     use_debian_packaged_compression_libs.patch.
   * debian/patches/use_soversions.patch (new): Give shared libraries
     proper versioned SONAMEs; use them from the Python bindings.
   * debian/rules:
     - Adopt (and adapt) assorted build logic from ngs-sdk.
     - Pass VDB header path via -DVDB_INCDIR rather than via general
       compilation flags.
     - Install configuration files explicitly; the CMake setup insists on
       putting them in the wrong place for us.
     - Extend bin deversioning to *+ (i.e., kar+).
   * debian/salsa-ci.yml: Use ncbi-vdb's aptly repo to get 3.x for now.
 .
   [ Pierre Gruet ]
   * debian/control:
     - Add missing build dependencies on liblzma-dev and libsam-extract-dev.
     - Mark libngs-java as Architecture: all; loosen its dependencies on
       libncbi-ngs-dev slightly to account for possible binNMUs.
     - Introduce a libngs-jni package, on which libngs-java can and will
       depend in lieu of libncbi-ngs-dev (or patching source to support
       using libncbi-ngs3 directly).
   * debian/libngs-java-doc.lintian-overrides: Override complaints about
     javadoc-embedded jQuery per the discussion starting at
     https://lists.debian.org/debian-java/2018/06/msg00020.html.
   * debian/libngs-jni.links.in: Provide a general formula for libngs-jni's
     central symlink.
   * debian/rules: Add logic to fill in the specifics.
 .
   [ Aaron M. Ucko ]
   * (debian/).gitignore (new): Ignore build and (offline) test results.
   * debian/control:
     - Make python3-ngs (safely!) Architecture: all too.
     - Attempt Architecture: any for sra-toolkit (modulo B-D availability).
       This setting matches architecture-dependent NGS packages'; if it
       doesn't work out, we'll want to rein them all in for simplicity.
     - Honor ${misc:Depends} for libngs-java per Lintian.
   * debian/copyright: Reflect a full inventory, including convenience
     copies of several third-party libraries for which it would be good to
     substitute existing packages at some point.
   * debian/patches/label_online_tests (new): Label tests that involve data
     retrieval as "online".
   * debian/patches/reflect_code_donations.patch (new): Clean up stray
     licenseless copyright statements per consultation with upstream (as
     quoted in the patch's header).
   * debian/patches/use_stock_magic.patch (new): Let copycat use the stock
     magic-number database in /usr/share/misc.
   * debian/rules:
     - Skip tests labeled "online" to avoid breaking on
       autobuilders, which require builds to work fully offline.
     - Refrain from shipping .gitignore files alongside examples.
     - Clean up after tests (offline ones, anyway).
   * Remove trailing whitespace in debian/changelog (routine-update)
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Files:
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