[med-svn] [Git][med-team/ncbi-vdb][master] 10 commits: New upstream version 3.2.1+dfsg

Aaron M. Ucko (@ucko) gitlab at salsa.debian.org
Wed Apr 9 03:04:43 BST 2025 


Aaron M. Ucko pushed to branch master at Debian Med / ncbi-vdb


Commits:
1234be86 by Aaron M. Ucko at 2025-04-02T21:06:48-04:00
New upstream version 3.2.1+dfsg
- - - - -
909f6142 by Aaron M. Ucko at 2025-04-02T21:07:34-04:00
Merge tag 'upstream/3.2.1+dfsg'

Upstream version 3.2.1(+dfsg).

- - - - -
ca4aede0 by Aaron M. Ucko at 2025-04-07T10:37:19-04:00
debian/patches/fix_{cmake,x32}.patch: Formaly update for 3.2.1.

- - - - -
28daac0f by Aaron M. Ucko at 2025-04-07T20:44:19-04:00
Specify /usr/lib/ncbi-vdb schema path more broadly and cleanly.

* debian/control: Have ncbi-vdb-data replace sra-toolkit << 3.2 over
  debian.kfg.
* debian/debian.kfg: New; taken over from sra-toolkit, augmented with a
  central /vdb/schema/paths = "/usr/lib/ncbi-vdb" setting.
* debian/ncbi-vdb-data.install: Install debian.kfg to /etc/ncbi.
* debian/rules: Stop injecting /usr/lib/ncbi-vdb/ into schema include
  directives.

- - - - -
4d9e5894 by Aaron M. Ucko at 2025-04-07T20:55:37-04:00
Install py_vdb/vdb.py, as part of ncbi-vdb-data for now.

* debian/control:
  - Move python3 to main Build-Depends (from -Arch) and add dh-python.
  - Have ncbi-vdb-data (for now) incorporate a virtual python3-vdb
    package, to be split out into a regular package post-Trixie.
* debian/ncbi-vdb-data.install: Install py_vdb/vdb.py to
  /usr/lib/python3/dist-packages.
* debian/patches/python-use-default-runtime.patch (new): Bypass upstream's
  logic for locating VDB shared libraries in favor of tacking on .3 and
  honoring the system search path.
* debian/rules: Enable DebHelper's Python 3 addon.
* debian/.gitignore: Ignore generated maintainer script fragments.

- - - - -
94276f17 by Aaron M. Ucko at 2025-04-07T20:55:46-04:00
debian/control: shlibs:Depends -> devlibs:Depends for -dev packages.

Belatedly have -dev packages depend on ${devlibs:Depends} (from
d-shlibs) rather than the inapplicable ${shlibs:Depends}.

- - - - -
49199d61 by Aaron M. Ucko at 2025-04-08T21:48:49-04:00
.gitignore: Ignore Debian additions.

- - - - -
e77d60e2 by Aaron M. Ucko at 2025-04-08T21:48:49-04:00
Standards-Version: 4.7.2 (routine-update)

- - - - -
029f2ba7 by Aaron M. Ucko at 2025-04-08T21:48:49-04:00
debian/copyright: Substitute a URL for the FSF's postal address.

See #1080497.

- - - - -
d8f8d38e by Aaron M. Ucko at 2025-04-08T21:48:49-04:00
Finalize ncbi-vdb 3.2.1+dfsg-1 for experimental.

- - - - -


297 changed files:

- .gitignore
- CHANGES.md
- build/Makefile.env
- build/Makefile.vers
- build/common.cmake
- debian/.gitignore
- debian/changelog
- debian/control
- debian/copyright
- + debian/debian.kfg
- + debian/ncbi-vdb-data.install
- debian/patches/fix_cmake.patch
- debian/patches/fix_x32.patch
- + debian/patches/python-use-default-runtime.patch
- debian/patches/series
- debian/rules
- interfaces/insdc/sra.h
- interfaces/insdc/sra.vschema
- interfaces/kdb/consistency-check.h
- interfaces/kdb/database.h
- interfaces/kdb/kdb-priv.h
- interfaces/kdb/manager.h
- interfaces/vdb/page-map-priv.h → interfaces/kdb/page-map-priv.h
- libs/vdb/page-map.h → interfaces/kdb/page-map.h
- interfaces/kfc/ctx.h
- interfaces/kfg/kfg-priv.h
- interfaces/klib/vdb_release_version.h
- interfaces/ncbi/vdb-blast.h
- − interfaces/search/grep.h
- − interfaces/search/nucstrstr.h
- − interfaces/search/ref-variation.h
- interfaces/vdb/manager.h
- interfaces/vdb/table.h
- interfaces/vdb/vdb-priv.h
- interfaces/vfs/manager.h
- interfaces/vfs/path-priv.h
- interfaces/vfs/path.h
- libs/CMakeLists.txt
- libs/axf/align-ref-name.c
- libs/axf/cigar.c
- libs/axf/get-sam-flags.c
- libs/axf/ref-preserve_qual.c
- libs/axf/ref-restore-read.c
- libs/axf/refseq.c
- libs/axf/restore-read.c
- libs/axf/seq-restore-linkage-group.c
- libs/axf/wgs.c
- libs/axf/wgs.h
- libs/blast/blast-mgr.c
- libs/cloud/aws-auth.c
- libs/cloud/aws.c
- libs/cloud/cloud.c
- libs/cloud/gcp.c
- libs/kapp/args.c
- libs/kapp/main.c
- libs/kdb/CMakeLists.txt
- + libs/kdb/ColumnBlob.hpp
- + libs/kdb/RColumnBlob.cpp
- libs/kdb/wcolumnblob.c → libs/kdb/WColumnBlob.cpp
- libs/kdb/btree.c
- interfaces/search/smith-waterman.h → libs/kdb/coldata.c
- interfaces/search/extern.h → libs/kdb/coldata.h
- libs/kdb/column-cc.c
- libs/kdb/columnblob-base.c → libs/kdb/columnblob-base.cpp
- libs/kdb/database-base.c
- libs/kdb/database-cc.c
- libs/kdb/dbmgr-cmn.c
- libs/kdb/index-base.c
- libs/kdb/index-cmn.c
- libs/kdb/index-cmn.h
- libs/kdb/kdb-cmn.c
- libs/kdb/kdb-cmn.h
- libs/kdb/libkdb.vers.h
- libs/kdb/manager-base.c
- libs/kdb/manager-base.h
- libs/vdb/page-map.c → libs/kdb/page-map.c
- libs/kdb/rcoldata.c
- libs/kdb/rcoldata.h
- libs/kdb/rcolidx.c
- libs/kdb/rcolidx2.c
- libs/kdb/rcolumn.c
- − libs/kdb/rcolumnblob.c
- libs/kdb/rcolumnblob.h
- libs/kdb/rdatabase.c
- libs/kdb/rdbmgr.c
- libs/kdb/rdbmgr.h
- libs/kdb/rindex.c
- libs/kdb/rmeta.c
- libs/kdb/rtable.c
- libs/kdb/rtrieidx-v2.c
- libs/kdb/table-base.c
- libs/kdb/table-cc.c
- libs/kdb/wcoldata.c
- libs/kdb/wcoldata.h
- libs/kdb/wcolumn.c
- libs/kdb/wcolumnblob.h
- libs/kdb/wdatabase.c
- libs/kdb/wdbmgr.c
- libs/kdb/widxblk.c
- libs/kdb/windex.c
- libs/kdb/wkdb.c
- libs/kdb/wmeta.c
- libs/kdb/wtable.c
- libs/kdb/wtrieidx-v1.c
- libs/kdb/wtrieidx-v2.c
- libs/kdbtext/api-manager.cpp
- libs/kdbtext/column.cpp
- libs/kdbtext/column.hpp
- libs/kdbtext/columnblob.cpp
- libs/kdbtext/columnblob.hpp
- libs/kdbtext/manager.cpp
- libs/kfg/kfg-priv.h
- libs/kfg/ngc.c
- libs/kfs/arc.c
- libs/kfs/cacheteefile3.c
- libs/kfs/unix/sysdll.c
- libs/kns/http-file.c
- libs/kns/http-priv.h
- libs/kns/http-request.c
- libs/kns/manager.c
- libs/krypto/CMakeLists.txt
- libs/krypto/aes-byte.c
- libs/krypto/aes-priv.h
- libs/krypto/aes_core.c
- libs/ncbi-vdb/CMakeLists.txt
- libs/ncbi-vdb/libncbi-vdb.vers
- − libs/search/CMakeLists.txt
- − libs/search/Makefile
- − libs/search/agrep-dp.c
- − libs/search/agrep-myers.c
- − libs/search/agrep-myersunltd.c
- − libs/search/agrep-wumanber.c
- − libs/search/fgrep-aho.c
- − libs/search/fgrep-boyermoore.c
- − libs/search/fgrep-dumb.c
- − libs/search/nucstrstr.c
- − libs/search/search-priv.h
- − libs/search/search.c
- − libs/search/sw-search.c
- libs/sra/reader-cmn.c
- libs/sra/reader-fastq.c
- libs/sra/reader-illumina.c
- libs/sra/reader-sff.c
- libs/sra/sracache.c
- libs/sra/sratbl-cmn.c
- libs/sra/wsratbl.c
- libs/sraxf/dna-from-color.c
- libs/sraxf/dynamic-454-read-descriptor.c
- libs/sraxf/extract-coordinates.c
- libs/sraxf/extract-name_coord.c
- libs/sraxf/extract-name_fmt.c
- libs/sraxf/extract-spot_name.c
- libs/sraxf/format-spot-name.c
- libs/sraxf/fpcodec.c
- libs/sraxf/index_lookup.c
- libs/sraxf/make-position.c
- libs/sraxf/normalize.c
- libs/sraxf/process-position.c
- libs/sraxf/qual4_decode.c
- libs/sraxf/qual4_encode.c
- libs/sraxf/read-desc.c
- libs/sraxf/read-seg-from-readn.c
- libs/sraxf/rewrite-spot-name.c
- libs/sraxf/rna-flag-common.c
- libs/sraxf/set-rna-flag.c
- libs/sraxf/spot-check.c
- libs/sraxf/stats.c
- libs/sraxf/syn_quality.c
- libs/sraxf/tokenize-spot_name-454.c
- libs/sraxf/tokenize-spot_name-abi.c
- libs/sraxf/tokenize-spot_name-generic-fastq.c
- libs/sraxf/tokenize-spot_name-helicos.c
- libs/sraxf/tokenize-spot_name-illumina.c
- libs/sraxf/tokenize-spot_name-ion-torrent.c
- libs/sraxf/use-rna-flag.c
- libs/sraxf/v0-decompress-local.h
- libs/sraxf/v0-decompress.c
- libs/sraxf/varloc.c
- libs/vdb/CMakeLists.txt
- libs/vdb/blob.c
- libs/vdb/bytecode.c
- libs/vdb/column-cmn.c
- libs/vdb/compare.c
- libs/vdb/cursor-table.c
- libs/vdb/database-cmn.c
- libs/vdb/database-depend.c
- libs/vdb/dbmgr-cmn.c
- libs/vdb/delta_average.c
- libs/vdb/index_lookup.c
- libs/vdb/index_project.c
- libs/vdb/libvdb.vers.h
- libs/vdb/linker-int.c
- libs/vdb/linker-priv.h
- libs/vdb/merge.c
- libs/vdb/prod-cmn.c
- libs/vdb/redimension.c
- libs/vdb/split.c
- libs/vdb/transpose.c
- libs/vdb/wcolumn.c
- libs/vdb/wcursor.c
- libs/vdb/wphys.c
- libs/vfs/manager.c
- libs/vfs/names4-response.c
- libs/vfs/path-priv.h
- libs/vfs/path.c
- libs/vfs/remote-services.c
- libs/vfs/resolver-priv.h
- libs/vfs/resolver.c
- libs/vfs/sdl-response.c
- libs/vfs/services-cache.c
- libs/vfs/services-priv.h
- libs/vfs/services.c
- libs/vfs/srv-response.c
- py_vdb/L1-manager.py
- py_vdb/L10-fastq.py
- py_vdb/L11-table_copy.py
- py_vdb/L2-table_read.py
- py_vdb/L3-table_write.py
- py_vdb/L4-database_read.py
- py_vdb/L5-database_write.py
- py_vdb/L6-meta_read.py
- py_vdb/L7-table-rnd-write.py
- py_vdb/L8-import-csv.py
- py_vdb/L9-index_usage.py
- + py_vdb/find_ncbi_vdb.py
- py_vdb/vdb.py
- test/CMakeLists.txt
- test/kdb/CMakeLists.txt
- test/kdb/kdb.hpp
- test/kdb/remote_open_test.cpp
- test/vdb/test-pagemap.cpp → test/kdb/test-pagemap.cpp
- + test/kdb/test-rblob.cpp
- test/kdb/test-rcolumn.cpp
- test/kdb/test-rdatabase.cpp
- test/kdb/test-rtable.cpp
- + test/kdb/test-wblob.cpp
- test/kdb/test-wcolumn.cpp
- test/kdb/test-wmanager.cpp
- test/kdb/test-wtable.cpp
- + test/kdb/testdb.kar
- libs/search/.gitignore → test/kdb/testdb/tbl/SEQUENCE/col/READ/data
- + test/kdb/testdb/tbl/SEQUENCE/col/READ/idx
- + test/kdb/testdb/tbl/SEQUENCE/col/READ/idx0
- test/kdbtext/test-blob.cpp
- test/kdbtext/test-column.cpp
- test/kfg/kfgtest.cpp
- test/kns/CMakeLists.txt
- test/kns/knstest.cpp
- test/kns/test-connect.cpp
- test/kns/test-http-request.cpp
- + test/kns/test-opt-bitmap.cpp
- test/kns/test-proxy-with-scheme.cpp
- test/kns/test-proxy-with-scheme.sh
- test/kns/test-proxy-with-scheme_failure.cpp
- test/ktst/CMakeLists.txt
- + test/ktst/tsan.suppressions
- test/schema/CMakeLists.txt
- test/schema/test-schema-diff.sh
- − test/schema/test_VDB-5250.py
- − test/schema/test_VDB-5251.py
- test/schema/wb-test-schema-ast.cpp
- − test/search/CMakeLists.txt
- − test/search/Makefile
- − test/search/PerfCounter.h
- − test/search/agrep-main.c
- − test/search/search-vdb.cpp
- − test/search/search-vdb.h
- − test/search/test-agrep.cpp
- test/vdb/CMakeLists.txt
- test/vdb/WVDB_Fixture.hpp
- test/vdb/test-VDB-4156.cpp
- libs/search/debug.h → test/vdb/test-VDBManagerGetObjVersion.cpp
- + test/vdb/test-linker.cpp
- test/vdb/test-textvdb.cpp
- test/vdb/test-vdb.cpp
- test/vdb/test-view.cpp
- test/vdb/test-wvdb.cpp
- test/vfs/CMakeLists.txt
- + test/vfs/SRR045450/SRR045450.sra
- + test/vfs/SRR599578/SRR599578.sralite
- test/vfs/Test_VFS_resolver_dflt.cpp
- + test/vfs/data/SRR053325.sra
- + test/vfs/data/SRR600096.sralite
- test/vfs/test-json-response.cpp
- test/vfs/test-resolver-with-log.cpp
- test/vfs/test-sdl-response.cpp
- + test/vfs/test-vfs-resolve.cpp
- libs/kdb/columnblob-base.h → test/vfs/test-vpath-open-read-update.cpp
- + test/vfs/test-vpath-open-read-update.h
- + test/vfs/test-vpath-open-read.cpp
- + test/vfs/test-vpath-open-read.h
- + test/vfs/test-vpath-open-update-read.cpp
- + test/vfs/test-vpath-open-update-read.h
- + test/vfs/test-vpath-open-update-update.cpp
- + test/vfs/test-vpath-open-update-update.h
- + test/vfs/test-vpath-open.hpp
- test/vfs/test_VFS_cache_sdl.cpp


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View it on GitLab: https://salsa.debian.org/med-team/ncbi-vdb/-/compare/1055c9c8d9f039e45015fc2a29773d7c2ea87ce6...d8f8d38e8361eebbcdc81b08e1d42f7054dd8f1c

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View it on GitLab: https://salsa.debian.org/med-team/ncbi-vdb/-/compare/1055c9c8d9f039e45015fc2a29773d7c2ea87ce6...d8f8d38e8361eebbcdc81b08e1d42f7054dd8f1c
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