[med-svn] [Git][med-team/sourmash][upstream] New upstream version 4.9.4

Sat Sep 13 11:42:03 BST 2025

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

Commits:
c61f851a by Michael R. Crusoe at 2025-09-13T09:49:15+02:00
New upstream version 4.9.4
- - - - -

160 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
- 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/-/commit/c61f851af8147f15ad138fbe8dd53c99c5122c74

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