# 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)