[med-svn] [Git][med-team/diamond-aligner][master] 8 commits: Packaging update (routine-update)

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Med / diamond-aligner


Commits:
49a681a7 by Andreas Tille at 2026-10-19T12:01:27+02:00
Packaging update (routine-update)

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cc3c3480 by Andreas Tille at 2026-10-19T12:01:36+02:00
New upstream version

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38da2abb by Andreas Tille at 2026-10-19T12:01:37+02:00
New upstream version 2.2.8
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d04dfe4f by Andreas Tille at 2026-10-19T12:02:27+02:00
Update upstream source from tag 'upstream/2.2.8'

Update to upstream version '2.2.8'
with Debian dir d9566ae3ec9b3f55ac3b756a3d935e193e16b8a6
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36f2af06 by Andreas Tille at 2026-10-19T12:02:30+02:00
Changes made by cme

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82b63046 by Andreas Tille at 2026-10-19T11:02:39+01:00
Remove duplicate values for fields Bug-Database, Bug-Submit, Repository-Browse, Repository-Browse in debian/upstream/metadata.

Changes-By: lintian-brush
Fixes: lintian: source: upstream-metadata-yaml-invalid
See-also: https://lintian.debian.org/tags/upstream-metadata-yaml-invalid.html

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d5bbd4fd by Andreas Tille at 2026-10-19T11:02:40+01:00
Set upstream metadata fields: Bug-Submit, Repository-Browse.

Changes-By: lintian-brush
Fixes: lintian: source: upstream-metadata-missing-repository [debian/upstream/metadata]
Fixes: lintian: source: upstream-metadata-missing-bug-tracking [debian/upstream/metadata]
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-repository.html
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-bug-tracking.html

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c7308e0e by Andreas Tille at 2026-10-19T12:10:57+02:00
routine-update: Ready to upload to unstable

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64 changed files:

- CITATION.cff
- CMakeLists.txt
- debian/changelog
- debian/control
- debian/upstream/metadata
- src/ChangeLog
- src/align/align.cpp
- src/align/extend.cpp
- src/align/gapped_score.cpp
- + src/align/new/extension.h
- + src/align/new/extension_pipeline.cpp
- + src/align/new/extension_pipeline.h
- + src/align/new/sw.h
- + src/align/new/thread_pool.h
- src/align/target.h
- src/align/ungapped.cpp
- src/basic/basic.cpp
- src/basic/config.cpp
- src/basic/config.h
- src/basic/const.h
- src/basic/statistics.h
- src/cluster/combine_blocks.cpp
- src/cluster/data.cpp
- src/cluster/file_array.h
- src/cluster/input_buffer.h
- src/cluster/len_sort.cpp
- src/cluster/merge.cpp
- src/cluster/multinode.cpp
- src/cluster/multinode.h
- src/cluster/output.cpp
- src/cluster/search.cpp
- src/dp/swipe/anchored.h → src/dp/anchored_swipe/anchored.h
- + src/dp/anchored_swipe/anchored_wrapper.cpp
- src/dp/swipe/config.h → src/dp/anchored_swipe/config.h
- src/dp/dp.h
- src/dp/score_profile.cpp → src/dp/long_profile/score_profile.cpp
- src/dp/score_profile.h → src/dp/long_profile/score_profile.h
- src/dp/scan_diags.cpp
- src/dp/scan_diags.h
- src/dp/score_vector_int16.h
- src/dp/score_vector_int8.h
- − src/dp/swipe/anchored_wrapper.cpp
- src/output/blast_pairwise_format.cpp
- src/output/blast_tab_format.cpp
- src/output/output_sink.cpp
- src/search/hit_buffer.cpp
- src/search/lin_index/lin_index.cpp
- src/search/lin_index/lin_index.h
- src/search/lin_index/scan.cpp
- + src/search/lin_index/web_graph.cpp
- + src/search/lin_index/web_graph.h
- src/search/setup.cpp
- src/stats/cbs.cpp
- + src/test/anchored-swipe.out
- src/test/linclust.out
- + src/test/new-ext.out
- src/test/realign.out
- src/test/test.cmake
- src/tools/benchmark.cpp
- src/tools/greedy_vertex_cover.cpp
- src/tools/tools.h
- src/util/options/option.h
- src/util/simd/transpose.h
- src/util/simd/transpose16x16.h


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/diamond-aligner/-/compare/ee616ec0e76f3e4d7ba7a8f2b6771e5211ce97a7...c7308e0ecc2847173adfde64dc658acf49a06493

-- 
View it on GitLab: https://salsa.debian.org/med-team/diamond-aligner/-/compare/ee616ec0e76f3e4d7ba7a8f2b6771e5211ce97a7...c7308e0ecc2847173adfde64dc658acf49a06493
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