Sourmash

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”](https://joss.theoj.org/papers/10.21105/joss.06830), 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)

Minor new features:

* add `--set-name` to `sig intersect` and `sig subtract` (3162)
* upgrade `sig overlap` and `sig subtract` to load more than JSON signatures (3153)
* force continue past `tax genome` classification errors (3100)

Bug fixes:

* fix `remaining_bp` output from sourmash gather (3195)
* fix RocksDB-based gather & other rust-based infelicities revealed by plugins (3193, 3197)
* use correct denominator in f_unique_to_query (3138)

Cleanup and documentation updates:

* update JOSS for sourmash v4 (3114, 3203, 3209)
* fix links to taxonomy spreadsheets (3119)
* fix description of `f_unique_weighted` (3164)

Developer updates:

* transition internal signature loading functions (3161)
* allow get/set record.filename (3121)
* round a number that is losing precision in 15th place in `test_distance_utpy` (3126)
* disable ppc64le wheel building (3127)
* prepare to remove `sourmash compute` for sourmash v5.0 (3103)
* add rustup target x86_64-apple-darwin (3148)
* mv `.cargo/config` to `config.toml` (3147)
* fix clippy warnings about max_value (3146)
* bump to v4.8.9-dev (3135)
* update src/core/CHANGELOG.md for sourmash-rs core release r0.14.0 (3199)

Dependabot updates:

* Bump DeterminateSystems/nix-installer-action from 11 to 12 (3184)
* Bump DeterminateSystems/magic-nix-cache-action from 6 to 7 (3185)
* Bump statrs from 0.16.0 to 0.16.1 (3186)
* Bump serde from 1.0.202 to 1.0.203 (3175)
* Bump ouroboros from 0.18.3 to 0.18.4 (3176)
* Bump itertools from 0.12.1 to 0.13.0 (3166)
* Bump camino from 1.1.6 to 1.1.7 (3169)
* Bump serde from 1.0.201 to 1.0.202 (3168)
* Bump thiserror from 1.0.60 to 1.0.61 (3167)
* Bump pypa/cibuildwheel from 2.18.0 to 2.18.1 (3165)
* Bump DeterminateSystems/magic-nix-cache-action from 4 to 6 (3157)
* Bump DeterminateSystems/nix-installer-action from 10 to 11 (3156)
* Bump pypa/cibuildwheel from 2.17.0 to 2.18.0 (3155)
* Bump serde_json from 1.0.116 to 1.0.117 (3159)
* Bump thiserror from 1.0.59 to 1.0.60 (3158)
* Bump serde from 1.0.200 to 1.0.201 (3160)
* Bump roaring from 0.10.3 to 0.10.4 (3142)
* Bump histogram from 0.10.0 to 0.10.1 (3141)
* Bump getrandom from 0.2.14 to 0.2.15 (3143)
* Bump num-iter from 0.1.44 to 0.1.45 (3140)
* Bump jinja2 from 3.1.3 to 3.1.4 (3145)
* Bump serde from 1.0.199 to 1.0.200 (3144)
* Bump serde from 1.0.198 to 1.0.199 (3130)
* Bump conda-incubator/setup-miniconda from 3.0.3 to 3.0.4 (3131)
* Update pytest requirement from <8.2.0,>=6.2.4 to >=6.2.4,<8.3.0 (3132)
* Bump myst-parser from 2.0.0 to 3.0.1 (3133)
* Bump thiserror from 1.0.58 to 1.0.59 (3123)
* Bump serde_json from 1.0.115 to 1.0.116 (3124)
* Bump serde from 1.0.197 to 1.0.198 (3122)
* Update docutils requirement from <0.21,>=0.17.1 to >=0.17.1,<0.22 (3116)