[med-svn] [Git][med-team/sourmash][master] 11 commits: New upstream version

Sat Sep 13 11:42:02 BST 2025

Michael R. Crusoe pushed to branch master at Debian Med / sourmash

Commits:
00acaf75 by Michael R. Crusoe at 2025-09-13T09:49:13+02:00
New upstream version

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c61f851a by Michael R. Crusoe at 2025-09-13T09:49:15+02:00
New upstream version 4.9.4
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8a890bc8 by Michael R. Crusoe at 2025-09-13T09:51:37+02:00
Update upstream source from tag 'upstream/4.9.4'

Update to upstream version '4.9.4'
with Debian dir c7fe954f54b3d45a843af69843c60c2753f8796d
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fc71ad22 by Michael R. Crusoe at 2025-09-13T09:51:38+02:00
Standards-Version: 4.7.2 (routine-update)

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8c1e7224 by Michael R. Crusoe at 2025-09-13T11:47:13+02:00
Refreshed patches. Dropped "skip_from-finch_feature", upstream removed the conversion from Finch in version 4.9.0.

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94051b2a by Michael R. Crusoe at 2025-09-13T11:47:19+02:00
Added a new patch to adapt to the older version of the md5 Rust crate in Debian.

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ab9c51bf by Michael R. Crusoe at 2025-09-13T11:47:19+02:00
docs: new build-dep of python3-sphinx-copybutton.

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679a5232 by Michael R. Crusoe at 2025-09-13T11:47:19+02:00
d/rules: parallelize the pytest respecting DEB_BUILD_OPTION_PARALLEL

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97dc4dfa by Michael R. Crusoe at 2025-09-13T12:00:04+02:00
Install the README

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b73a81fc by Michael R. Crusoe at 2025-09-13T12:00:34+02:00
d/rules: set MPLCONFIGDIR

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b620d7af by Michael R. Crusoe at 2025-09-13T12:31:45+02:00
routine-update: Ready to upload to unstable.

Closes: #1114393

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169 changed files:

- .git_archival.txt
- .github/dependabot.yml
- .github/workflows/asv.yml
- .github/workflows/build_wheel.yml
- .github/workflows/build_wheel_all_archs.yml
- .github/workflows/codspeed.yml
- .github/workflows/dev_envs.yml
- .github/workflows/hypothesis.yml
- .github/workflows/python.yml
- .github/workflows/rust.yml
- .pre-commit-config.yaml
- .readthedocs.yml
- Cargo.lock
- Makefile
- README.md
- binder/environment.yml
- debian/changelog
- debian/control
- + debian/patches/older-md5
- + debian/patches/pytest-auto-parallel
- debian/patches/series
- − debian/patches/skip_from-finch_feature
- debian/patches/soften-deps
- debian/rules
- debian/python3-sourmash.docs → debian/sourmash.docs
- dev.yml
- doc/classifying-signatures.md
- doc/command-line.md
- doc/conf.py
- + doc/databases-md/gtdb220.md
- + doc/databases-md/gtdb226.md
- + doc/databases-md/ncbi_euks_2025_01.md
- + doc/databases-md/ncbi_viruses_2025_01.md
- doc/databases.md
- doc/developer.md
- + doc/howto-rocksdb.md
- doc/index.md
- doc/legacy-databases.md
- + doc/release-notes/sourmash-5.0.md
- doc/release.md
- doc/requirements.md
- doc/runtime.txt
- doc/sidebar.md
- doc/sourmash-sketch.md
- doc/support.md
- doc/toc.md
- flake.lock
- flake.nix
- include/sourmash.h
- pixi.lock
- pyproject.toml
- src/core/CHANGELOG.md
- src/core/Cargo.toml
- src/core/README.md
- src/core/src/collection.rs
- src/core/src/encodings.rs
- src/core/src/errors.rs
- src/core/src/ffi/cmd/compute.rs
- src/core/src/ffi/index/mod.rs
- src/core/src/ffi/index/revindex.rs
- + src/core/src/ffi/manifest.rs
- src/core/src/ffi/mod.rs
- src/core/src/ffi/utils.rs
- − src/core/src/from.rs
- src/core/src/index/linear.rs
- src/core/src/index/mod.rs
- src/core/src/index/revindex/disk_revindex.rs
- src/core/src/index/revindex/mem_revindex.rs
- src/core/src/index/revindex/mod.rs
- src/core/src/lib.rs
- src/core/src/manifest.rs
- src/core/src/signature.rs
- src/core/src/sketch/minhash.rs
- src/core/src/wasm.rs
- src/sourmash/cli/index.py
- src/sourmash/cli/sig/check.py
- src/sourmash/cli/sig/collect.py
- src/sourmash/cli/sig/manifest.py
- src/sourmash/cli/tax/genome.py
- src/sourmash/cli/tax/metagenome.py
- src/sourmash/cli/utils.py
- src/sourmash/command_sketch.py
- src/sourmash/commands.py
- src/sourmash/index/__init__.py
- src/sourmash/index/revindex.py
- src/sourmash/manifest.py
- src/sourmash/minhash.py
- src/sourmash/save_load.py
- src/sourmash/sig/__main__.py
- src/sourmash/signature.py
- src/sourmash/tax/__main__.py
- src/sourmash/tax/tax_utils.py
- src/sourmash/utils.py
- tests/conftest.py
- tests/sourmash_tst_utils.py
- + tests/test-data/2sigs.branch_0913.rocksdb/000008.log
- + tests/test-data/2sigs.branch_0913.rocksdb/000009.sst
- + tests/test-data/2sigs.branch_0913.rocksdb/000010.sst
- + tests/test-data/2sigs.branch_0913.rocksdb/CURRENT
- + tests/test-data/2sigs.branch_0913.rocksdb/IDENTITY
- + tests/test-data/2sigs.branch_0913.rocksdb/LOCK
- + tests/test-data/2sigs.branch_0913.rocksdb/MANIFEST-000005
- + tests/test-data/2sigs.branch_0913.rocksdb/OPTIONS-000007
- + tests/test-data/3sigs.branch_0913.rocksdb/000008.log
- + tests/test-data/3sigs.branch_0913.rocksdb/000009.sst
- + tests/test-data/3sigs.branch_0913.rocksdb/000010.sst
- + tests/test-data/3sigs.branch_0913.rocksdb/CURRENT
- + tests/test-data/3sigs.branch_0913.rocksdb/IDENTITY
- + tests/test-data/3sigs.branch_0913.rocksdb/LOCK
- + tests/test-data/3sigs.branch_0913.rocksdb/MANIFEST-000005
- + tests/test-data/3sigs.branch_0913.rocksdb/OPTIONS-000007
- + tests/test-data/SRR606249.sig.gz
- + tests/test-data/prot/dayhoff.rocksdb/000008.log
- + tests/test-data/prot/dayhoff.rocksdb/000009.sst
- + tests/test-data/prot/dayhoff.rocksdb/000010.sst
- + tests/test-data/prot/dayhoff.rocksdb/CURRENT
- + tests/test-data/prot/dayhoff.rocksdb/IDENTITY
- + tests/test-data/prot/dayhoff.rocksdb/LOCK
- + tests/test-data/prot/dayhoff.rocksdb/MANIFEST-000005
- + tests/test-data/prot/dayhoff.rocksdb/OPTIONS-000007
- + tests/test-data/prot/hp.rocksdb/000008.log
- + tests/test-data/prot/hp.rocksdb/000009.sst
- + tests/test-data/prot/hp.rocksdb/000010.sst
- + tests/test-data/prot/hp.rocksdb/CURRENT
- + tests/test-data/prot/hp.rocksdb/IDENTITY
- + tests/test-data/prot/hp.rocksdb/LOCK
- + tests/test-data/prot/hp.rocksdb/MANIFEST-000005
- + tests/test-data/prot/hp.rocksdb/OPTIONS-000007
- + tests/test-data/prot/protein.rocksdb/000008.log
- + tests/test-data/prot/protein.rocksdb/000009.sst
- + tests/test-data/prot/protein.rocksdb/000010.sst
- + tests/test-data/prot/protein.rocksdb/CURRENT
- + tests/test-data/prot/protein.rocksdb/IDENTITY
- + tests/test-data/prot/protein.rocksdb/LOCK
- + tests/test-data/prot/protein.rocksdb/MANIFEST-000005
- + tests/test-data/prot/protein.rocksdb/OPTIONS-000007
- + tests/test-data/skipmers/2.skip.sig.zip
- + tests/test-data/skipmers/47.skip.sig.zip
- + tests/test-data/skipmers/63.skip.sig.zip
- + tests/test-data/track_abund/47+63.abund.rocksdb/000008.log
- + tests/test-data/track_abund/47+63.abund.rocksdb/000009.sst
- + tests/test-data/track_abund/47+63.abund.rocksdb/000010.sst
- + tests/test-data/track_abund/47+63.abund.rocksdb/CURRENT
- + tests/test-data/track_abund/47+63.abund.rocksdb/IDENTITY
- + tests/test-data/track_abund/47+63.abund.rocksdb/LOCK
- + tests/test-data/track_abund/47+63.abund.rocksdb/MANIFEST-000005
- + tests/test-data/track_abund/47+63.abund.rocksdb/OPTIONS-000007
- tests/test_api.py
- + tests/test_cmd_index.py
- tests/test_cmd_signature.py
- tests/test_cmd_signature_collect.py
- tests/test_index.py
- tests/test_index_protocol.py
- tests/test_lca_db_protocol.py
- tests/test_manifest_protocol.py
- tests/test_minhash.py
- + tests/test_moltypes.py
- tests/test_plugin_framework.py
- + tests/test_revindex.py
- tests/test_sbt.py
- tests/test_search.py
- tests/test_sketchcomparison.py
- tests/test_sourmash.py
- tests/test_sourmash_args.py
- tests/test_sourmash_sketch.py
- tests/test_sqlite_index.py
- tests/test_tax.py
- tests/test_tax_utils.py
- tox.ini

The diff was not included because it is too large.

View it on GitLab: https://salsa.debian.org/med-team/sourmash/-/compare/8589346c50966764540119ab39725904372af26d...b620d7afc05c95864d91d122fe67c996ca7d10ad

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View it on GitLab: https://salsa.debian.org/med-team/sourmash/-/compare/8589346c50966764540119ab39725904372af26d...b620d7afc05c95864d91d122fe67c996ca7d10ad
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