MRG: fix linear gather in Rust #3605
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Co-authored-by: Luiz Irber <luizirber@users.noreply.github.com>
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## latest #3605 +/- ##
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- Coverage 88.49% 88.49% -0.01%
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Files 136 136
Lines 23337 23346 +9
Branches 2262 2262
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+ Hits 20653 20659 +6
- Misses 2372 2375 +3
Partials 312 312
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ready for review & merge @bluegenes @luizirber |
luizirber
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## [0.20.0] - 2025-05-06 MSRV: 1.74 Changes/additions: * fully support skip-mers at the Python level; provide documentation (#3627) * remove support for python 3.10 (#3606) * fix linear gather in Rust (#3605) * impl full mem-based `RevIndex` in Rust, and add Python support for mem- and disk-based `RevIndex` (#3545) * Minhash deserialize hashfunction errorhandling (#3560) * fix beta clippy errors (#3548) Updates: * Bump rand from 0.9.0 to 0.9.1 (#3620) * Bump roaring from 0.10.10 to 0.10.12 (#3608) * Bump log from 0.4.26 to 0.4.27 (#3587) * Bump tempfile from 3.19.0 to 3.19.1 (#3588) * Bump tempfile from 3.18.0 to 3.19.0 (#3582) * Bump serde from 1.0.218 to 1.0.219 (#3576) * Bump tempfile from 3.17.1 to 3.18.0 (#3575) * Bump histogram from 0.11.2 to 0.11.3 (#3574) * Bump serde_json from 1.0.139 to 1.0.140 (#3566) * Bump getset from 0.1.4 to 0.1.5 (#3567) * Bump needletail from 0.6.1 to 0.6.3 (#3553) * Bump serde_json from 1.0.138 to 1.0.139 (#3552) * Bump serde from 1.0.217 to 1.0.218 (#3550) * Bump log from 0.4.25 to 0.4.26 (#3549) * Bump tempfile from 3.16.0 to 3.17.1 (#3539)
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# sourmash v4.9.0 release notes This release adds two significant feature sets to sourmash, without introducing any breaking changes. First, sourmash now fully supports fast, low-memory disk-based inverted indexes based on RocksDB. This functionality has been part of [the branchwater plugin](https://github.com/sourmash-bio/sourmash_plugin_branchwater) for a while, but it is now accessible via the sourmash command line and Python API. Second, we have added skip-mer sketching to sourmash, joining DNA, protein, dayhoff, and hp encodings. Skip-mers allow more mismatches than DNA k-mers and can be useful when comparing fast-evolving sequences such as virus and phage genomes. Documentation for the RocksDB indexes and skip-mer encodings is available in the [command-line docs](https://sourmash.readthedocs.io/en/latest/command-line.html). Major new features: * Fully support fast, low-memory RocksDB indexes in Python (#3545) * Fully support skip-mers at the Python level; provide documentation (#3627) * Remove support for python 3.10 (#3606) Cleanup and documentation updates: * add default to `add_scaled_arg` in Python CLI utils (#3609) * use `match/case` in `sourmash index` implementation (#3604) * use single quotes inside sqlite statements (#3556) Developer updates: * implement manifest retrieval from Rust via FFI for `RevIndex` (#3630) * make the RocksDB handle directly accessible to external code (#3468) * fix linear gather in Rust (#3605) * fix beta clippy errors (#3548) * fix deprecations (#3613) * update Makefile with 'offline', 'wheel' (#3579) * update ubuntu image version for CI (#3623) * Minhash deserialize hashfunction errorhandling (#3560) Automated updates: * Bump DeterminateSystems/nix-installer-action from 16 to 17 (#3626) * Bump getset from 0.1.4 to 0.1.5 (#3567) * Bump histogram from 0.11.2 to 0.11.3 (#3574) * Bump log from 0.4.25 to 0.4.26 (#3549) * Bump log from 0.4.26 to 0.4.27 (#3587) * Bump needletail from 0.6.1 to 0.6.3 (#3553) * Bump prefix-dev/setup-pixi from 0.8.1 to 0.8.2 (#3538) * Bump prefix-dev/setup-pixi from 0.8.2 to 0.8.3 (#3551) * Bump prefix-dev/setup-pixi from 0.8.3 to 0.8.4 (#3602) * Bump prefix-dev/setup-pixi from 0.8.4 to 0.8.7 (#3616) * Bump prefix-dev/setup-pixi from 0.8.7 to 0.8.8 (#3621) * Bump pypa/cibuildwheel from 2.22.0 to 2.23.0 (#3564) * Bump pypa/cibuildwheel from 2.23.0 to 2.23.1 (#3581) * Bump pypa/cibuildwheel from 2.23.1 to 2.23.2 (#3603) * Bump pypa/cibuildwheel from 2.23.2 to 2.23.3 (#3625) * Bump rand from 0.9.0 to 0.9.1 (#3620) * Bump roaring from 0.10.10 to 0.10.12 (#3608) * Bump serde from 1.0.217 to 1.0.218 (#3550) * Bump serde from 1.0.218 to 1.0.219 (#3576) * Bump serde_json from 1.0.138 to 1.0.139 (#3552) * Bump serde_json from 1.0.139 to 1.0.140 (#3566) * Bump tempfile from 3.16.0 to 3.17.1 (#3539) * Bump tempfile from 3.17.1 to 3.18.0 (#3575) * Bump tempfile from 3.18.0 to 3.19.0 (#3582) * Bump tempfile from 3.19.0 to 3.19.1 (#3588) * Bump thiserror from 2.0.11 to 2.0.12 (#3565) * pre-commit autoupdate (#3547) * pre-commit autoupdate (#3563) * pre-commit autoupdate (#3573) * pre-commit autoupdate (#3580) * pre-commit autoupdate (#3586) * pre-commit autoupdate (#3607) * pre-commit autoupdate (#3615) * pre-commit autoupdate (#3619) * pre-commit autoupdate (#3624) * pre-commit autoupdate (#3633)
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Fixes #3594
The
gatherimplementation insrc/core/src/index/linear.rsincorrectly subtracted all query hashes from remaining matches, ensuring that there would only ever be one match, the first. This narrows the subtraction to just things that overlap with the intersection between query and best match.