Releases · sourmash-bio/sourmash

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)

Assets 8

05 Dec 22:07

ctb

v4.8.12

0f48dc5

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)

Assets 8

31 Jul 16:11

luizirber

v4.8.11

7f72671

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)

Assets 8

29 Jun 18:26

github-actions

v4.8.10

9590033

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)

Assets 7

11 Jun 01:05

ctb

v4.8.9

55c0c45

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)

Assets 8

09 Apr 22:10

ctb

v4.8.8

a387d22

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)

Assets 9

21 Mar 16:44

ctb

v4.8.7

24ab89c

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)

Assets 9

10 Feb 23:29

ctb

v4.8.6

47a6ee0

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)

Assets 8

12 Dec 19:51

github-actions

v4.8.5

5ae9ebc

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)

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