Major new features:

• start writing v4->v5 migration docs (#3721)
• adjust warnings around tax abund and provide v5 upgrades to tax metagenome (#3711)

Minor new features:

• try setting up --v4 and --v5 behavior differences for sig check (#3072)
• update sig manifest default rebuilding behavior for v5. (#3074)
• handle (ignore) empty taxids for bioboxes format (#3748)
• improve summary_csv for lingroups (#3758)

Cleanup and documentation updates:

• use auto-generated database list (#3754)

Developer updates:

• CI: fix dependabot config syntax, and clippy beta lints (#3762)
• CI: update to cibuildwheel 3.1.1 (#3738)
• ci: group dependabot updates by language (#3749)
• Remove docutils dep (#3769)
• bump version to 4.9.4-dev (#3715)
• disable WebAssembly builds, for now (#3724)

Dependabot updates:

• Build(ci): Bump actions/download-artifact from 4 to 5 (#3766)
• Build(deps): Bump DeterminateSystems/nix-installer-action from 17 to 18 (#3727)
• Build(deps): Bump DeterminateSystems/nix-installer-action from 18 to 19 (#3746)
• Build(deps): Bump criterion from 0.6.0 to 0.7.0 (#3741)
• Build(deps): Bump md5 from 0.7.0 to 0.8.0 (#3719)
• Build(deps): Bump memmap2 from 0.9.5 to 0.9.7 (#3732)
• Build(deps): Bump prefix-dev/setup-pixi from 0.8.10 to 0.8.11 (#3733)
• Build(deps): Bump prefix-dev/setup-pixi from 0.8.11 to 0.8.14 (#3747)
• Build(deps): Bump rand from 0.9.1 to 0.9.2 (#3743)
• Build(deps): Bump serde_json from 1.0.140 to 1.0.141 (#3742)
• [pre-commit.ci] pre-commit autoupdate (#3718)
• [pre-commit.ci] pre-commit autoupdate (#3725)
• [pre-commit.ci] pre-commit autoupdate (#3731)
• [pre-commit.ci] pre-commit autoupdate (#3737)
• [pre-commit.ci] pre-commit autoupdate (#3740)
• [pre-commit.ci] pre-commit autoupdate (#3756)

Cleanup and documentation updates:

• minor updates to release docs (#3695)
• small docs fixes and updates (#3681)

Developer updates:

• release core 0.21.0 (#3712)

Dependabot updates:

• Build(deps): Bump camino from 1.1.9 to 1.1.10 (#3669)
• Build(deps): Bump cfg-if from 1.0.0 to 1.0.1 (#3689)
• Build(deps): Bump conda-incubator/setup-miniconda from 3.1.1 to 3.2.0 (#3676)
• Build(deps): Bump getset from 0.1.5 to 0.1.6 (#3700)
• Build(deps): Bump prefix-dev/setup-pixi from 0.8.8 to 0.8.10 (#3688)
• Build(deps): Bump proptest from 1.6.0 to 1.7.0 (#3674)
• Build(deps): Bump pypa/cibuildwheel from 2.23.3 to 3.0.0 (#3687)
• Build(deps): Bump roaring from 0.10.12 to 0.11.0 (#3702)
• Build(deps): Update maturin requirement from <1.9.0,>=1 to >=1,<1.10.0 (#3699)
• Build(deps): Update pytest requirement from <8.4.0,>=6.2.4 to >=6.2.4,<8.5.0 (#3670)
• EXP: Revert "Build(deps): Bump pypa/cibuildwheel from 2.23.3 to 3.0.0 (#3687) (#3691)
• [pre-commit.ci] pre-commit autoupdate (#3668)
• [pre-commit.ci] pre-commit autoupdate (#3673)
• [pre-commit.ci] pre-commit autoupdate (#3698)

This is a patchfix to v4.9.1 (#3665) to deal with a botched source code release. Below are the updates since v4.9.0.

Minor new features:

• add cANI to sig overlap (#3644)

Bug fixes:

• make RevIndex.len() and RevIndex.signatures() use picklist, if set (#3647)

Cleanup and documentation updates:

• add rocksdb HOWTO (#3648)

Developer updates:

• try fixing inline variables in rust println! (#3640)

Dependabot updates:

• Build(deps): Update cachetools requirement from <6,>=4 to >=4,<7 (#3660)
• [pre-commit.ci] pre-commit autoupdate (#3659)
• Build(deps): Bump criterion from 0.5.1 to 0.6.0 (#3655)
• [pre-commit.ci] pre-commit autoupdate (#3654)
• Build(deps): Bump tempfile from 3.19.1 to 3.20.0 (#3639)
• [pre-commit.ci] pre-commit autoupdate (#3638)

Minor new features:

• add cANI to sig overlap (#3644)

Bug fixes:

• make RevIndex.len() and RevIndex.signatures() use picklist, if set (#3647)

Cleanup and documentation updates:

• add rocksdb HOWTO (#3648)

Developer updates:

• try fixing inline variables in rust println! (#3640)

Dependabot updates:

• Build(deps): Update cachetools requirement from <6,>=4 to >=4,<7 (#3660)
• [pre-commit.ci] pre-commit autoupdate (#3659)
• Build(deps): Bump criterion from 0.5.1 to 0.6.0 (#3655)
• [pre-commit.ci] pre-commit autoupdate (#3654)
• Build(deps): Bump tempfile from 3.19.1 to 3.20.0 (#3639)
• [pre-commit.ci] pre-commit autoupdate (#3638)

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 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.

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)

Developer updates:

• 4.8.14 release branch (#3493)

Dependabot updates:

• Bump serde_json from 1.0.134 to 1.0.135 (#3490)
• Bump roaring from 0.10.9 to 0.10.10 (#3489)
• Bump thiserror from 2.0.9 to 2.0.11 (#3488)
• Bump ouroboros from 0.18.4 to 0.18.5 (#3491)
• [pre-commit.ci] pre-commit autoupdate (#3492)

NOTE: This release adds basic support for skipmers, but they are not
yet fully supported.

Minor new features:

• add genbank plant db to docs (#3429)
• add skipmer capacity to sourmash python layer via ffi (#3446)
• add skipmers; switch to reading frame approach for translation, skipmers (#3395)
• additional moltype specification needed for sig downsample with skipmers (#3457)
• update with misc animal genomes (#3422)

Cleanup and documentation updates:

• add comment about semver and column headings (#3433)

Developer updates:

• Deps: update to rocksdb 0.23 (#3456)
• Refactor: Use to_writer/from_reader across the codebase (#3443)
• adjust Signature::name() to return Option<String> instead of filename() and md5sum() (#3434)
• bump version to 4.8.13-dev (#3474)
• fix comment in _set_num_scaled (#3451)
• propagate zipfile errors (#3431)
• update rust CHANGELOG in preparation for r0.18.0 (#3450)
• CI: github actions updates (#3476)

Dependabot updates:

• Bump itertools from 0.13.0 to 0.14.0 (#3471)
• Bump needletail from 0.6.0 to 0.6.1 (#3427)
• Bump proptest from 1.5.0 to 1.6.0 (#3437)
• Bump roaring from 0.10.7 to 0.10.8 (#3423)
• Bump roaring from 0.10.8 to 0.10.9 (#3438)
• Bump serde from 1.0.215 to 1.0.216 (#3436)
• Bump serde from 1.0.216 to 1.0.217 (#3464)
• Bump serde_json from 1.0.133 to 1.0.134 (#3453)
• Bump statrs from 0.17.1 to 0.18.0 (#3426)
• Bump tempfile from 3.14.0 to 3.15.0 (#3472)
• Bump thiserror from 2.0.3 to 2.0.6 (#3425)
• Bump thiserror from 2.0.6 to 2.0.7 (#3435)
• Bump thiserror from 2.0.7 to 2.0.8 (#3448)
• Bump thiserror from 2.0.8 to 2.0.9 (#3452)
• Update maturin requirement from <1.8.0,>=1 to >=1,<1.9.0 (#3465)
• [pre-commit.ci] pre-commit autoupdate (#3428)
• [pre-commit.ci] pre-commit autoupdate (#3439)
• [pre-commit.ci] pre-commit autoupdate (#3454)
• [pre-commit.ci] pre-commit autoupdate (#3473)

Developer updates:

• build: move ORCID to metadata in pyproject.toml, fix pixi (#3416)
• build: simplify Rust release (#3392)
• fix: Avoid re-calculating md5sum on clone and conversion to KmerMinHashBTree (#3385)
• r0.15.1 release (#3304)
• update sourmash core to r0.17.0 (#3381)
• Added union method to HLL (#3293)
• Build: upgrade to newer maturin (#3366)
• CI: use supported ubuntu for codspeed (#3350)
• Fix clippy lints from 1.83 beta (#3357)
• Implement resumability for revindex (#3275)
• add Manifest::intersect_manifest to Rust core (#3305)
• bump sourmash core to r0.17.2 (#3399)
• change sig_from_record to use scaled from Record to downsample (#3387)
• derive Hash for HashFunctions (#3344)
• enforce a single scaled on a CollectionSet (#3397)
• fix formatting from #3306 (#3307)
• have ruff ignore ipynb so as to avoid triggering an error during CI (#3325)
• improve downsampling behavior on KmerMinHash; fix RevIndex::gather bug around scaled. (#3342)
• panic when FSStorage::load_sig encounters more than one Signature in a JSON record (#3333)
• propagate error from RocksDB::open on bad directory (#3306)
• refactor calculate_gather_stats to disallow repeated downsampling (#3352)
• release core r0.17.1 (#3388)
• release sourmash rust core r0.16.0 (#3356)
• standardize on u32 for scaled, and introduce ScaledType (#3364)
• update plugin documentation for users (#3286)
• update sourmash core to r0.15.2 (#3338)
• when lingroups are provided, use them for csv_summary (#3311)
• Misc Rust updates to core (#3297)
• Resolve issue for high precision MLE estimation (#3296)

Dependabot and pre-commit CI updates:

• Bump DeterminateSystems/magic-nix-cache-action from 7 to 8 (#3319)
• Bump DeterminateSystems/nix-installer-action from 13 to 14 (#3320)
• Bump DeterminateSystems/nix-installer-action from 14 to 15 (#3374)
• Bump DeterminateSystems/nix-installer-action from 15 to 16 (#3401)
• Bump camino from 1.1.7 to 1.1.9 (#3301)
• Bump codspeed-criterion-compat from 2.6.0 to 2.7.2 (#3324)
• Bump conda-incubator/setup-miniconda from 3.0.4 to 3.1.0 (#3373)
• Bump csv from 1.3.0 to 1.3.1 (#3390)
• Bump getset from 0.1.2 to 0.1.3 (#3328)
• Bump histogram from 0.11.0 to 0.11.1 (#3377)
• Bump js-sys from 0.3.72 to 0.3.74 (#3412)
• Bump memmap2 from 0.9.4 to 0.9.5 (#3326)
• Bump myst-parser from 3.0.1 to 4.0.0 (#3277)
• Bump needletail from 0.5.1 to 0.6.0 (#3376)
• Bump pypa/cibuildwheel from 2.19.2 to 2.20.0 (#3278)
• Bump pypa/cibuildwheel from 2.20.0 to 2.21.1 (#3332)
• Bump pypa/cibuildwheel from 2.21.1 to 2.21.2 (#3345)
• Bump pypa/cibuildwheel from 2.21.2 to 2.21.3 (#3353)
• Bump pypa/cibuildwheel from 2.21.3 to 2.22.0 (#3408)
• Bump roaring from 0.10.6 to 0.10.7 (#3413)
• Bump serde from 1.0.204 to 1.0.207 (#3289)
• Bump serde from 1.0.207 to 1.0.208 (#3298)
• Bump serde from 1.0.208 to 1.0.209 (#3310)
• Bump serde from 1.0.209 to 1.0.210 (#3318)
• Bump serde from 1.0.210 to 1.0.214 (#3368)
• Bump serde from 1.0.214 to 1.0.215 (#3403)
• Bump serde_json from 1.0.120 to 1.0.121 (#3267)
• Bump serde_json from 1.0.121 to 1.0.122 (#3280)
• Bump serde_json from 1.0.122 to 1.0.124 (#3288)
• Bump serde_json from 1.0.124 to 1.0.125 (#3302)
• Bump serde_json from 1.0.125 to 1.0.127 (#3309)
• Bump serde_json from 1.0.127 to 1.0.128 (#3316)
• Bump serde_json from 1.0.128 to 1.0.132 (#3358)
• Bump serde_json from 1.0.132 to 1.0.133 (#3402)
• Bump sphinx-design from 0.5.0 to 0.6.0 (#3268)
• Bump sphinx-design from 0.6.0 to 0.6.1 (#3276)
• Bump tempfile from 3.10.1 to 3.11.0 (#3279)
• Bump tempfile from 3.11.0 to 3.12.0 (#3287)
• Bump tempfile from 3.12.0 to 3.13.0 (#3340)
• Bump tempfile from 3.13.0 to 3.14.0 (#3391)
• Bump thiserror from 1.0.63 to 1.0.64 (#3335)
• Bump thiserror from 1.0.64 to 1.0.65 (#3367)
• Bump thiserror from 1.0.65 to 1.0.68 (#3379)
• Bump thiserror from 1.0.68 to 2.0.3 (#3389)
• Bump web-sys from 0.3.69 to 0.3.70 (#3299)
• Bump web-sys from 0.3.70 to 0.3.72 (#3354)
• Bump web-sys from 0.3.72 to 0.3.74 (#3411)
• Update pytest-cov requirement from <6.0,>=4 to >=4,<7.0 (#3375)
• Update sphinx requirement from <8,>=6 to >=6,<9 (#3269)
• Upgrade rocksdb to 0.22.0, bump MSRV to 1.66 (#3383)
• [pre-commit.ci] pre-commit autoupdate (#3281)
• [pre-commit.ci] pre-commit autoupdate (#3290)
• [pre-commit.ci] pre-commit autoupdate (#3312)
• [pre-commit.ci] pre-commit autoupdate (#3330)
• [pre-commit.ci] pre-commit autoupdate (#3336)
• [pre-commit.ci] pre-commit autoupdate (#3341)
• [pre-commit.ci] pre-commit autoupdate (#3346)
• [pre-commit.ci] pre-commit autoupdate (#3360)
• [pre-commit.ci] pre-commit autoupdate (#3369)
• [pre-commit.ci] pre-commit autoupdate (#3380)
• [pre-commit.ci] pre-commit autoupdate (#3393)
• [pre-commit.ci] pre-commit autoupdate (#3404)
• [pre-commit.ci] pre-commit autoupdate (#3409)
• [pre-commit.ci] pre-commit autoupdate (#3414)

Minor new features:

• RocksDB storage and self-contained RevIndex with internal storage (#3250)

Bug fixes:

• Break ahash dep cycle by bumping to 0.7.8, nix flake update (#3243)

Cleanup and documentation updates:

• Update dev env instructions (#2990)

Developer updates:

• Use softprops/action-gh-release github action for artifact upload to release (#3273)
• Enable codspeed for Rust perf tracking (#3231)
• bump cibuildwheel for linux fixes, move wasm to use cibuildwheel too (#3241)

Dependabot updates:

• Bump actions/checkout from 3 to 4 (#3265)
• Bump moonrepo/setup-rust from 0 to 1 (#3266)
• Bump CodSpeedHQ/action from 2 to 3 (#3264)
• pre-commit autoupdate (#3270) (#3260) (#3255) (#3238)
• Bump DeterminateSystems/nix-installer-action from 12 to 13 (#3259)
• Update pytest requirement from <8.3.0,>=6.2.4 to >=6.2.4,<8.4.0 (#3258)
• Bump thiserror from 1.0.62 to 1.0.63 (#3257)
• Bump thiserror from 1.0.61 to 1.0.62 (#3254)
• Bump roaring from 0.10.5 to 0.10.6 (#3245)
• Bump serde from 1.0.203 to 1.0.204 (#3244)
• Bump counter from 0.5.7 to 0.6.0 (#3235)
• Bump log from 0.4.21 to 0.4.22 (#3236)
• Bump serde_json from 1.0.117 to 1.0.120 (#3234)

This release is accompanied by the publication of a JOSS paper: “sourmash v4: A multitool to quickly search, compare, and analyze genomic and metagenomic data sets”, our new citation handle!

Minor new features:

• check select parameters; enforce types when building manifests (#3212)
• patch-fix sig extract to no longer create empty zips (#3214)

Bug fixes:

• adjust how ANI is calculated in the revindex code. (#3218)

Cleanup and documentation updates:

• final updates for 2024 JOSS publication (#3225)
• Improve JOSS paper affiliations (#3224)
• fix DOI for Rahman Hera paper in JOSS pub. (#3221)
• upd citations, minor text (#3220)

Developer updates:

• bump sourmash core version to 0.14.1 (#3219)
• bump version to 4.8.10-dev (#3211)

Dependabot updates:

• Bump proptest from 1.4.0 to 1.5.0 (#3222)
• [pre-commit.ci] pre-commit autoupdate (#3223)
• [pre-commit.ci] pre-commit autoupdate (#3003)
• Bump histogram from 0.10.2 to 0.11.0 (#3216)
• Bump pypa/cibuildwheel from 2.19.0 to 2.19.1 (#3217)
• Bump histogram from 0.10.1 to 0.10.2 (#3207)
• Bump statrs from 0.16.1 to 0.17.1 (#3205)
• Bump roaring from 0.10.4 to 0.10.5 (#3206)
• Bump primal-check from 0.3.3 to 0.3.4 (#3208)
• Bump niffler from 2.5.0 to 2.6.0 (#3204)
• Bump pypa/cibuildwheel from 2.18.1 to 2.19.0 (#3202)