MRG: 4.8.12 release branch

[ctb]

Developer updates:

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

Dependabot and pre-commit CI updates:

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

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 86.41%. Comparing base (1f92aa0) to head (616eb0d).
Report is 1 commits behind head on latest.

Additional details and impacted files

@@           Coverage Diff           @@
##           latest    #3417   +/-   ##
=======================================
  Coverage   86.41%   86.41%           
=======================================
  Files         137      137           
  Lines       16103    16103           
  Branches     2219     2219           
=======================================
  Hits        13916    13916           
  Misses       1880     1880           
  Partials      307      307           

Flag	Coverage Δ
hypothesis-py	25.43% <ø> (ø)
python	92.40% <ø> (ø)
rust	62.08% <ø> (ø)

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