v4.8.12

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)

v4.8.11

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)

v4.8.10

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)

v4.8.9

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)

v4.8.8

We are proud to report that sourmash v4.8.8 has been accepted after peer review by pyOpenSci! See the review here!

Major new features:

• Add pyopensci review badge (#3105)
• Implement file parsing for webassembly (#3047)

Dependabot updates:

• Bump histogram from 0.9.1 to 0.10.0 (#3109)
• Bump getrandom from 0.2.12 to 0.2.14 (#3108)
• Bump enum_dispatch from 0.3.12 to 0.3.13 (#3102)
• Bump serde_json from 1.0.114 to 1.0.115 (#3101)
• Update pytest-cov requirement from <5.0,>=4 to >=4,<6.0 (#3097)
• Bump rayon from 1.9.0 to 1.10.0 (#3098)

v4.8.7

Note: This release changes the way sourmash multigather names output files in some situations. Please see #2722 for details.

Minor new features:

• support proper manifest creation with --relpath for sig check and sig collect (#3054)
• fix multigather output by adding md5sum along with -U/--output-add-query-md5sum (#2722)
• enable loading lineages from annotated gather with match_name instead of name (#3078)

Bug fixes:

• fix output for sketch ... --singleton (#3066)
• fix calculate_gather_stats threshold=0 bug (#3052)

Cleanup and documentation updates:

• adjust protein ksize for record/manifest (#3019)
• Resolve sourmash gather --help issue (#3032)
• rework the manifest documentation; do misc cleanup (#3027)
• add branchwater web to docs (#3018)

Developer updates:

• make core Manifest booleans python compatible (core) (#3007)
• safer ksize selection while still accommodating k=k*3 (#3028)
• fix clippy beta issues (#3088)
• tell dependabot to ignore upgrades to byteorder, chrono, once_cell, and wasm-bindgen (#3065)
• update rust changelog for r0.13.0 in preparation for release (#3033)
• Allow changing storage location for a collection in RevIndex (#3015)
• Fix tox and nix configs so all tox tests execute correctly (#2992)
• Calculate all gather stats in rust; use for rocksdb gather (#2943)
• bump screed req to 1.1.3 (#3067)
• bump to v4.8.7-dev (#2989)

Dependabot updates:

• Bump DeterminateSystems/magic-nix-cache-action from 1 to 3 (#2994)
• Bump DeterminateSystems/magic-nix-cache-action from 3 to 4 (#3085)
• Bump DeterminateSystems/nix-installer-action from 4 to 9 (#2995)
• Bump DeterminateSystems/nix-installer-action from 9 to 10 (#3083)
• Bump chrono from 0.4.33 to 0.4.34 (#3000)
• Bump conda-incubator/setup-miniconda from 3.0.1 to 3.0.2 (#3046)
• Bump conda-incubator/setup-miniconda from 3.0.2 to 3.0.3 (#3057)
• Bump histogram from 0.9.0 to 0.9.1 (#3002)
• Bump itertools from 0.12.0 to 0.12.1 (#3043)
• Bump log from 0.4.20 to 0.4.21 (#3062)
• Bump num-iter from 0.1.43 to 0.1.44 (#2997)
• Bump pypa/cibuildwheel from 2.16.5 to 2.17.0 (#3084)
• Bump rayon from 1.8.1 to 1.9.0 (#3058)
• Bump roaring from 0.10.2 to 0.10.3 (#3014)
• Bump serde from 1.0.196 to 1.0.197 (#3045)
• Bump serde_json from 1.0.113 to 1.0.114 (#3044)
• Bump tempfile from 3.10.0 to 3.10.1 (#3059)
• Bump thiserror from 1.0.56 to 1.0.57 (#2999)
• Bump thiserror from 1.0.57 to 1.0.58 (#3082)
• Bump wasm-bindgen from 0.2.91 to 0.2.92 (#3060)
• Bump wasm-bindgen-test from 0.3.40 to 0.3.41 (#2996)
• Bump wasm-bindgen-test from 0.3.41 to 0.3.42 (#3063)
• Bump web-sys from 0.3.67 to 0.3.68 (#2998)
• Bump web-sys from 0.3.68 to 0.3.69 (#3061)
• Revert "Bump wasm-bindgen from 0.2.91 to 0.2.92 (#3060)" (#3064)
• Update asv to 0.6.2 (#3025)
• Update pytest requirement from <8.1.0,>=6.2.4 to >=6.2.4,<8.2.0 (#3075)

v4.8.6

Minor new features:

• re-establish tax gather reading flexibility (#2986)
• update JOSS paper per pyopensci review (#2964)
• Clean up and refactor KmerMinHash::merge in core (#2973)
• add label output & input options to compare and plot, for better customization (#2598)
• add utilities for using ictv taxonomic ranks with sourmash tax (#2608)

Bug fixes:

• Fix tax metagenome to work on gather output created with --estimate-ani-ci (#2952)
• fix gather memory usage issue by not accumulating GatherResult (#2962)
• update the CLI docs and help for search --containment and prefetch (#2971)

Documentation updates:

• update tutorial to remove bioconda & use sourmash-minimal (#2972)
• update readme with maintainers & sourmash comparison info (#2965)
• add branchwater reference; make FAQ more visible (#2984)
• update FAQ answer on k-mer size (#2899)
• update README with repostatus and pyver badges, and Windows support (#2928)
• add full column descriptions for gather and prefetch output (#2954)
• add scaled FAQ, adjust ksize answer (#2921)
• minor refactoring of gather code, small doc updates (#2953)
• Add threshold-bp and scaled relationship to faqs (#2930)

Developer updates:

• nix updates for pyopensci review (#2975)
• add scaled selection to manifest; add helper functions for collection and sig/sketch usage (#2948)
• Pre-commit updates (#2427)
• fix upload wheel CI (#2974)
• release core; bump rust core version to r0.12.1 (#2988)
• CI: macos deployment target and maturin updates (#2879)
• MRG: bump version to 4.8.6-dev, post-release (#2877)
• fix benchmark code & a few other small issues from pyOpenSci review (#2920)
• fix uploading of wheels after upload-artifact upgrade. (#2887)
• in core, enable downsample within select (#2931)

Dependabot updates:

• Bump pypa/cibuildwheel from 2.16.4 to 2.16.5 (#2981)
• Bump tempfile from 3.9.0 to 3.10.0 (#2979)
• Bump rkyv from 0.7.43 to 0.7.44 (#2978)
• Bump actions/cache from 3 to 4 (#2933)
• Bump actions/download-artifact from 3 to 4 (#2884)
• Bump actions/upload-artifact from 3 to 4 (#2883)
• Bump cachix/cachix-action from 13 to 14 (#2926)
• Bump cachix/install-nix-action from 24 to 25 (#2927)
• Bump chrono from 0.4.31 to 0.4.33 (#2957)
• Bump getrandom from 0.2.11 to 0.2.12 (#2924)
• Bump histogram from 0.8.3 to 0.8.4 (#2923)
• Bump histogram from 0.8.4 to 0.9.0 (#2935)
• Bump jinja2 from 3.1.2 to 3.1.3 (#2922)
• Bump memmap2 from 0.9.0 to 0.9.2 (#2882)
• Bump memmap2 from 0.9.2 to 0.9.3 (#2889)
• Bump memmap2 from 0.9.3 to 0.9.4 (#2958)
• Bump mymindstorm/setup-emsdk from 13 to 14 (#2934)
• Bump ouroboros from 0.18.1 to 0.18.2 (#2894)
• Bump ouroboros from 0.18.2 to 0.18.3 (#2936)
• Bump pypa/cibuildwheel from 2.16.2 to 2.16.4 (#2960)
• Bump rayon from 1.8.0 to 1.8.1 (#2937)
• Bump rkyv from 0.7.42 to 0.7.43 (#2880)
• Bump serde from 1.0.194 to 1.0.195 (#2901)
• Bump serde from 1.0.195 to 1.0.196 (#2956)
• Bump serde_json from 1.0.108 to 1.0.110 (#2896)
• Bump serde_json from 1.0.110 to 1.0.111 (#2902)
• Bump serde_json from 1.0.111 to 1.0.113 (#2955)
• Bump shlex from 1.1.0 to 1.3.0 (#2940)
• Bump supercharge/redis-github-action from 1.7.0 to 1.8.0 (#2885)
• Bump tempfile from 3.8.1 to 3.9.0 (#2893)
• Bump thiserror from 1.0.50 to 1.0.51 (#2881)
• Bump thiserror from 1.0.51 to 1.0.56 (#2897)
• Bump wasm-bindgen from 0.2.89 to 0.2.90 (#2925)
• Bump wasm-bindgen-test from 0.3.39 to 0.3.40 (#2938)
• Bump web-sys from 0.3.66 to 0.3.67 (#2939)
• Update pytest requirement from <7.5.0,>=6.2.4 to >=6.2.4,<8.1.0 (#2959)

v4.8.5

This release drops support for Python < 3.10, and also reorganizes and expands the documentation substantially!

Major new features:

• Drop Python 3.8 and 3.9, default to Python 3.10 for most CI tasks (#2848)
• Revise documentation structure; add internals page. (#2184)
• Adjust documentation to recommend tax over lca for taxonomic analysis (#2777)

Bug fixes:

• make sourmash plot labels/indices arguments make sense (#2790)

Cleanup and documentation updates:

• Various minor updates to docs (#2854)
• Deps: update typed-builder and histogram, bump MSRV to 1.65 (#2858)
• Fix wheel building and semver checks post r0.12.0 (#2857)
• Added seed to parameter strings #1732 (#2836)
• Add link for developer documentation to sidebar (#2847)
• add explicit install tutorial (#2826)
• fix many minor documentation nits (#2814)
• update docs for tax grep: only searches tax (#2789)
  *add usage docs for sig import/ingest (#2785)

Developer updates:

• Feat: on-disk RevIndex based on RocksDB (#2230)
• Fix many warnings from PYTHONDEVMODE=1 (#2849)
• Build: Fix Rust 1.75 beta lints; flake update (#2841)
• try pinning maturin to <1.3.0 to fix dev build CI (#2799)
• minor updates to release procedure after 4.8.4 (#2783)
• run rust checks always (#2787)
• add __all__ to sig/__main__.py (#2778)
• bump version to 4.8.5-dev (#2766)

Dependabot updates:

• Bump ouroboros from 0.18.0 to 0.18.1 (#2875)
• Bump once_cell from 1.18.0 to 1.19.0 (#2874)
• Bump actions/setup-python from 4 to 5 (#2873)
• Bump cachix/cachix-action from 12 to 13 (#2861)
• Bump conda-incubator/setup-miniconda from 3.0.0 to 3.0.1 (#2860)
• Bump cachix/install-nix-action from 23 to 24 (#2859)
• Bump rkyv from 0.7.40 to 0.7.42 (#2863)
• Bump csv from 1.2.0 to 1.3.0 (#2862)
• Bump roaring from 0.10.1 to 0.10.2 (#2865)
• Bump web-sys from 0.3.65 to 0.3.66 (#2864)
• Bump byteorder from 1.4.3 to 1.5.0 (#2866)
• Bump proptest from 1.3.1 to 1.4.0 (#2837)
• Bump getrandom from 0.2.10 to 0.2.11 (#2839)
• Bump web-sys from 0.3.64 to 0.3.65 (#2838)
• Bump wasm-bindgen-test from 0.3.37 to 0.3.39 (#2853)
• Bump wasm-bindgen from 0.2.88 to 0.2.89 (#2850)
• Bump mymindstorm/setup-emsdk from 12 to 13 (#2851)
• Bump conda-incubator/setup-miniconda from 2.2.0 to 3.0.0 (#2852)
• Bump wasm-bindgen from 0.2.87 to 0.2.88 (#2834)
• Bump serde_json from 1.0.107 to 1.0.108 (#2829)
• Bump tempfile from 3.8.0 to 3.8.1 (#2828)
• Bump bytecount from 0.6.5 to 0.6.7 (#2830)
• Bump bytecount from 0.6.4 to 0.6.5 (#2822)
• Bump thiserror from 1.0.49 to 1.0.50 (#2823)
• Bump actions/setup-node from 3 to 4 (#2821)
• Bump rustix from 0.37.20 to 0.37.25 (#2817)
• Bump pypa/cibuildwheel from 2.16.1 to 2.16.2 (#2808)
• Bump memmap2 from 0.8.0 to 0.9.0 (#2807)
• Bump byteorder from 1.4.3 to 1.5.0 (#2806)
• Bump pypa/cibuildwheel from 2.16.0 to 2.16.1 (#2797)
• Bump thiserror from 1.0.48 to 1.0.49 (#2796)
• Bump proptest from 1.2.0 to 1.3.1 (#2795)
• Bump bytecount from 0.6.3 to 0.6.4 (#2794)
• Bump memmap2 from 0.7.1 to 0.8.0 (#2780)
• Bump rayon from 1.7.0 to 1.8.0 (#2782)
• Bump docker/setup-qemu-action from 2 to 3 (#2767)
• Bump pypa/cibuildwheel from 2.15.0 to 2.16.0 (#2768)
• Bump serde_json from 1.0.106 to 1.0.107 (#2769)
• Bump chrono from 0.4.30 to 0.4.31 (#2771)

v4.8.4

We are proud to release sourmash v4.8.4, now with even fewer bugs!

In addition to the patches and updates below, we would like to announce the availability of branchwater, a sourmash plugin that supports fast, low-memory, and multithreaded search, compare, and gather operations. branchwater v0.8.0 is now available and is between 10 and 100 times faster and lower memory than sourmash. (However, it does not support all the sourmash features; that will come with time!) Please give it a try!

Last but not least, we would like to ask people who use sourmash regularly to fill out this form so that we can include your information in some of our upcoming requests for funding support. Your use will not be made public but your support will help us continue to develop sourmash!

On to the release notes for sourmash v4.8.4!

Bug fixes:

• fix exponential time explosion in sig check (#2762)
• fix duplicate md5 in picklist problem (#2747)
• avoid compressing sig files in directory output twice (#2752)

Developer updates:

• Remove BIGSI and SBT code from Rust layer (#2732)
• bump version to 4.8.4-dev (#2720)
• build: updates spun off mastiff PR (#2723)
• Build: Remove deprecated system_packages from readthedocs (#2740)
• build: remove specific tooling that breaks s390x (#2725)
• Add cargo deny and bump deps now that MSRV is 1.64 (#2724)

Dependabot updates:

• Bump serde_json from 1.0.105 to 1.0.106 (#2757)
• Bump actions/checkout from 2 to 4 (#2746)
• Bump supercharge/redis-github-action from 1.6.0 to 1.7.0 (#2745)
• Bump cachix/install-nix-action from 22 to 23 (#2744)
• Bump ouroboros from 0.17.2 to 0.18.0 (#2743)
• Bump chrono from 0.4.26 to 0.4.30 (#2755)
• Bump thiserror from 1.0.47 to 1.0.48 (#2742)
• Bump thiserror from 1.0.44 to 1.0.47 (#2730)
• Bump serde_json from 1.0.104 to 1.0.105 (#2731)
• Bump actions/upload-artifact from 1 to 3 (#2729)

v4.8.3

Minor new features:

• add support for -E/--extension to sig split (#2712)
• add a sourmash.cli.parse_args([...]) function (#2691)
• update plugin support for argparse usage/description/epilog (#2696)

Cleanup and documentation updates:

• add gtdb-rs214 info (#2618, #2621, #2690)
• update JOSS paper for v4 (#1361)
• fix tutorial notebook links (#2633)
• Update URL for sourmash/fig.py (#2586)
• change matching_hashes.sig to matching-hashes.sig in documentation (#2713)
• patch lineage_summary documentation (#2693)
• switch dib-lab links to sourmash-bio links in .md files (#2588)

Developer updates:

• add upload token for codecov (#2632)
• build: fix clippy lints and MSRV check (#2680)
• maturin: move deprecated definition from Cargo.toml to pyproject.toml (#2597)
• update the core documentation building packages: Sphinx, myst-parser, and docutils (#2657)
• update the dependabot config to allow automatic rebases (#2634)
• update version to 4.8.3-dev (#2584)
• Build: bump maturin to 1.x (#2650)
• Clippy beta (1.70) fix (#2596)
• Fix clippy lint introduced in 1.71 beta (#2630)
• fix release procedure based on v4.8.0 release (#2551)
• Update docutils requirement from <0.20,>=0.17.1 to >=0.17.1,<0.21 (#2611)
• Update pytest requirement from <7.4.0,>=6.2.4 to >=6.2.4,<7.5.0 (#2659)
• Fix: update a manifest test to use temp directory (#2689)

Dependabot updates:

• Bump cachix/install-nix-action from 20 to 21 (#2625)
• Bump cachix/install-nix-action from 21 to 22 (#2651)
• Bump chrono from 0.4.24 to 0.4.25 (#2628)
• Bump chrono from 0.4.25 to 0.4.26 (#2636)
• Bump criterion from 0.3.6 to 0.5.1 (#2629)
• Bump getrandom from 0.2.9 to 0.2.10 (#2645)
• Bump log from 0.4.17 to 0.4.18 (#2623)
• Bump log from 0.4.18 to 0.4.19 (#2641)
• Bump log from 0.4.19 to 0.4.20 (#2715)
• Bump memmap2 from 0.5.10 to 0.6.1 (#2613)
• Bump memmap2 from 0.6.1 to 0.6.2 (#2626)
• Bump memmap2 from 0.6.2 to 0.7.0 (#2643)
• Bump memmap2 from 0.7.0 to 0.7.1 (#2658)
• Bump once_cell from 1.17.1 to 1.17.2 (#2622)
• Bump once_cell from 1.17.2 to 1.18.0 (#2635)
• Bump ouroboros from 0.15.6 to 0.17.0 (#2654)
• Bump ouroboros from 0.17.0 to 0.17.2 (#2687)
• Bump proptest from 1.1.0 to 1.2.0 (#2627)
• Bump pypa/cibuildwheel from 2.12.1 to 2.12.3 (#2590)
• Bump pypa/cibuildwheel from 2.12.3 to 2.13.0 (#2624)
• Bump pypa/cibuildwheel from 2.13.0 to 2.13.1 (#2642)
• Bump pypa/cibuildwheel from 2.13.1 to 2.14.0 (#2673)
• Bump pypa/cibuildwheel from 2.14.0 to 2.14.1 (#2681)
• Bump pypa/cibuildwheel from 2.14.1 to 2.15.0 (#2716)
• Bump serde from 1.0.160 to 1.0.162 (#2609)
• Bump serde from 1.0.162 to 1.0.163 (#2612)
• Bump serde from 1.0.163 to 1.0.164 (#2644)
• Bump serde from 1.0.164 to 1.0.166 (#2666)
• Bump serde from 1.0.166 to 1.0.168 (#2679)
• Bump serde_json from 1.0.100 to 1.0.103 (#2682)
• Bump serde_json from 1.0.103 to 1.0.104 (#2701)
• Bump serde_json from 1.0.96 to 1.0.97 (#2653)
• Bump serde_json from 1.0.97 to 1.0.99 (#2660)
• Bump serde_json from 1.0.99 to 1.0.100 (#2675)
• Bump supercharge/redis-github-action from 1.5.0 to 1.6.0 (#2700)
• Bump tempfile from 3.5.0 to 3.6.0 (#2639)
• Bump tempfile from 3.6.0 to 3.7.0 (#2686)
• Bump tempfile from 3.7.0 to 3.7.1 (#2705)
• Bump thiserror from 1.0.40 to 1.0.43 (#2674)
• Bump thiserror from 1.0.43 to 1.0.44 (#2685)
• Bump wasm-bindgen from 0.2.84 to 0.2.86 (#2615)
• Bump wasm-bindgen from 0.2.86 to 0.2.87 (#2640)
• Bump wasm-bindgen-test from 0.3.34 to 0.3.36 (#2620)
• Bump wasm-bindgen-test from 0.3.36 to 0.3.37 (#2656)
• Bump web-sys from 0.3.61 to 0.3.63 (#2619)
• Bump web-sys from 0.3.63 to 0.3.64 (#2655)