From 0f48dc56d2cabc29916250b829964f6a1c47110d Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Thu, 5 Dec 2024 13:47:19 -0800 Subject: [PATCH] MRG: 4.8.12 release branch (#3417) 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) --- flake.nix | 2 +- pyproject.toml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/flake.nix b/flake.nix index a9d567db5d..732f4b59de 100644 --- a/flake.nix +++ b/flake.nix @@ -62,7 +62,7 @@ sourmash = python.buildPythonPackage ( commonArgs // rec { pname = "sourmash"; - version = "4.8.11"; + version = "4.8.12"; format = "pyproject"; cargoDeps = rustPlatform.importCargoLock { diff --git a/pyproject.toml b/pyproject.toml index 9dc3d023a3..6c61b6dda5 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -9,7 +9,7 @@ build-backend = 'maturin' name = "sourmash" description = "tools for comparing biological sequences with k-mer sketches" readme = "README.md" -version = "4.8.11" +version = "4.8.12" authors = [ { name="Luiz Irber" },