CHANGELOG.md

Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

unreleased

[0.18.0] - 2024-12-20

MSRV: 1.66

Changes/additions:

• add skipmer capacity to sourmash python layer via ffi (#3446)
• add skipmers; switch to reading frame approach for translation, skipmers (#3395)
• Refactor: Use to_writer/from_reader across the codebase (#3443)
• adjust Signature::name() to return Option<String> instead of filename() and md5sum() (#3434)
• propagate zipfile errors (#3431)

Updates:

• Bump proptest from 1.5.0 to 1.6.0 (#3437)
• Bump roaring from 0.10.8 to 0.10.9 (#3438)
• Bump serde from 1.0.215 to 1.0.216 (#3436)
• Bump statrs from 0.17.1 to 0.18.0 (#3426)
• Bump roaring from 0.10.7 to 0.10.8 (#3423)
• Bump needletail from 0.6.0 to 0.6.1 (#3427)
• Bump web-sys from 0.3.72 to 0.3.74 (#3411)
• Bump js-sys from 0.3.72 to 0.3.74 (#3412)
• Bump roaring from 0.10.6 to 0.10.7 (#3413)
• Bump serde_json from 1.0.132 to 1.0.133 (#3402)
• Bump serde from 1.0.214 to 1.0.215 (#3403)

[0.17.2] - 2024-11-15

MSRV: 1.66

Changes/additions:

• enforce a single scaled on a CollectionSet (#3397)
• change sig_from_record to use scaled from Record to downsample (#3387)

Updates:

• Upgrade rocksdb to 0.22.0, bump MSRV to 1.66 (#3383)
• Bump thiserror from 1.0.68 to 2.0.3 (#3389)
• Bump csv from 1.3.0 to 1.3.1 (#3390)
• Bump tempfile from 3.13.0 to 3.14.0 (#3391)

[0.17.1] - 2024-11-11

Changes/additions:

• fix: Avoid re-calculating md5sum on clone and conversion to KmerMinHashBTree (#3385)
• build: simplify Rust release (#3392)

[0.17.0] - 2024-11-05

Changes/additions:

• standardize on u32 for scaled, and introduce ScaledType (#3364)
• panic when FSStorage::load_sig encounters more than one Signature in a JSON record (#3333)

Updates:

• Bump needletail from 0.5.1 to 0.6.0 (#3376)
• Bump histogram from 0.11.0 to 0.11.1 (#3377)
• Bump serde from 1.0.210 to 1.0.214 (#3368)
• Bump serde_json from 1.0.128 to 1.0.132 (#3358)
• Fix clippy lints from 1.83 beta (#3357)

[0.16.0] - 2024-10-15

MSRV: 1.65

Changes/additions:

• refactor calculate_gather_stats to disallow repeated downsampling (#3352)
• improve downsampling behavior on KmerMinHash; fix RevIndex::gather bug around scaled. (#3342)
• derive Hash for HashFunctions (#3344)

Updates:

• Bump web-sys from 0.3.70 to 0.3.72 (#3354)
• Bump tempfile from 3.12.0 to 3.13.0 (#3340)

[0.15.2] - 2024-09-25

MSRV: 1.65

Changes/additions:

• add Manifest::intersect_manifest to Rust core (#3305)
• propagate error from RocksDB::open on bad directory (#3306, #3307)

Updates:

• Bump getset from 0.1.2 to 0.1.3 (#3328)
• Bump memmap2 from 0.9.4 to 0.9.5 (#3326)
• Bump codspeed-criterion-compat from 2.6.0 to 2.7.2 (#3324)
• Bump serde_json from 1.0.127 to 1.0.128 (#3316)
• Bump serde from 1.0.209 to 1.0.210 (#3318)
• Bump serde from 1.0.208 to 1.0.209 (#3310)
• Bump serde_json from 1.0.125 to 1.0.127 (#3309)

[0.15.1] - 2024-08-20

MSRV: 1.65

Changes/additions:

• Misc Rust updates to core (#3297)
• Implement resumability for revindex (#3275)
• Resolve issue for high precision MLE estimation (#3296)
• Added union method to HLL (#3293)

Updates:

• Bump camino from 1.1.7 to 1.1.9 (#3301)
• Bump web-sys from 0.3.69 to 0.3.70 (#3299)
• Bump serde_json from 1.0.120 to 1.0.125 (#3288) (#3280) (#3267) (#3302)
• Bump serde from 1.0.204 to 1.0.208 (#3289) (#3298)
• Bump tempfile from 3.10.1 to 3.12.0 (#3279) (#3287)

[0.15.0] - 2024-07-27

MSRV: 1.65

Changes/additions:

• RocksDB storage and self-contained RevIndex with internal storage #3250
• Enable codspeed for Rust perf tracking (#3231)

Updates

• 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)
• Bump proptest from 1.4.0 to 1.5.0 (#3222)

[0.14.1] - 2024-06-19

MSRV: 1.65

Changes/additions:

• adjust how ANI is calculated in the revindex code. (#3218)

Updates:

• Bump histogram from 0.10.2 to 0.11.0 (#3216)
• 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)

[0.14.0] - 2024-06-10

MSRV: 1.65

Changes/additions:

• fix cargo fmt for updated disk_revindex.rs code (#3197)
• fix RocksDB-based gather & other rust-based infelicities revealed by plugins (#3193)
• use correct denominator in f_unique_to_query (#3138)
• fix clippy warnings about max_value (#3146)
• allow get/set record.filename (#3121)

Updates:

• 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 serde_json from 1.0.116 to 1.0.117 (#3159)
• 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 num-iter from 0.1.44 to 0.1.45 (#3140)
• Bump serde from 1.0.199 to 1.0.200 (#3144)
• Bump serde from 1.0.198 to 1.0.199 (#3130)
• Bump serde_json from 1.0.115 to 1.0.116 (#3124)
• Bump serde from 1.0.197 to 1.0.198 (#3122)
• Bump histogram from 0.9.1 to 0.10.0 (#3109)
• Bump enum_dispatch from 0.3.12 to 0.3.13 (#3102)
• Bump serde_json from 1.0.114 to 1.0.115 (#3101)
• Bump rayon from 1.9.0 to 1.10.0 (#3098)

0.13.1 - 2024-03-23

MSRV: 1.65

Changes/additions:

• Implement file parsing for webassembly (#3047)
• fix calculate_gather_stats threshold=0 bug (#3052)
• fix clippy beta issues (#3088)

Updates:

• Bump wasm-bindgen-test from 0.3.41 to 0.3.42 (#3063)
• Bump web-sys from 0.3.68 to 0.3.69 (#3061)
• Bump log from 0.4.20 to 0.4.21 (#3062)
• Bump rayon from 1.8.1 to 1.9.0 (#3058)
• Bump tempfile from 3.10.0 to 3.10.1 (#3059)
• Bump serde_json from 1.0.113 to 1.0.114 (#3044)
• Bump serde from 1.0.196 to 1.0.197 (#3045)
• Bump itertools from 0.12.0 to 0.12.1 (#3043)

0.13.0 - 2024-02-23

MSRV: 1.65

Changes/additions:

• Calculate all gather stats in rust; use for rocksdb gather (#2943)
• adjust protein ksize for record/manifest (#3019)
• Allow changing storage location for a collection in RevIndex (#3015)
• make core Manifest booleans python compatible (core) (#3007)

Updates:

• Bump roaring from 0.10.2 to 0.10.3 (#3014)
• Bump histogram from 0.9.0 to 0.9.1 (#3002)
• Bump chrono from 0.4.33 to 0.4.34 (#3000)
• Bump web-sys from 0.3.67 to 0.3.68 (#2998)
• Bump num-iter from 0.1.43 to 0.1.44 (#2997)
• Bump wasm-bindgen-test from 0.3.40 to 0.3.41 (#2996)

0.12.1 - 2024-02-10

MSRV: 1.65

Changes/additions:

• bump rust core version to r0.12.1 (#2988)
• Clean up and refactor KmerMinHash::merge in core (#2973)
• core: add scaled selection to manifest; add helper functions for collection and sig/sketch usage (#2948)
• core: enable downsample within select (#2931)

Updates:

• Deps: update typed-builder and histogram, bump MSRV to 1.65 (#2858)
• Bump tempfile from 3.9.0 to 3.10.0 (#2979)
• Bump rkyv from 0.7.43 to 0.7.44 (#2978)
• Bump memmap2 from 0.9.3 to 0.9.4 (#2958)
• Bump chrono from 0.4.31 to 0.4.33 (#2957)
• Bump serde from 1.0.195 to 1.0.196 (#2956)
• Bump serde_json from 1.0.111 to 1.0.113 (#2955)
• Bump web-sys from 0.3.66 to 0.3.67 (#2939)
• Bump wasm-bindgen-test from 0.3.39 to 0.3.40 (#2938)
• Bump rayon from 1.8.0 to 1.8.1 (#2937)
• Bump ouroboros from 0.18.2 to 0.18.3 (#2936)
• Bump histogram from 0.8.4 to 0.9.0 (#2935)
• Bump wasm-bindgen from 0.2.89 to 0.2.90 (#2925)
• Bump histogram from 0.8.3 to 0.8.4 (#2923)
• Bump serde_json from 1.0.110 to 1.0.111 (#2902)
• Bump serde from 1.0.194 to 1.0.195 (#2901)
• Bump serde_json from 1.0.108 to 1.0.110 (#2896)
• Bump ouroboros from 0.18.1 to 0.18.2 (#2894)
• Bump tempfile from 3.8.1 to 3.9.0 (#2893)
• Bump memmap2 from 0.9.2 to 0.9.3 (#2889)
• Bump memmap2 from 0.9.0 to 0.9.2 (#2882)
• Bump rkyv from 0.7.42 to 0.7.43 (#2880)
• Bump ouroboros from 0.18.0 to 0.18.1 (#2875)
• Bump once_cell from 1.18.0 to 1.19.0 (#2874)
• 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)

0.12.0 - 2023-11-26

MSRV: 1.64

Added:

• Initial implementation for Manifest, Selection, and Picklist following the Python API. (#2230)
• Collection is a new abstraction for working with a set of signatures. A collection needs a Storage for holding the signatures (on-disk, in-memory, or remotely), and a Manifest to describe the metadata for each signature. (#2230)
• Expose CSV parsing and RocksDB errors. (#2230)
• New module sourmash::index::revindex::disk_revindex with the on-disk RevIndex implementation based on RocksDB. (#2230)
• Add iter and iter_mut methods for Signature. (#2230)
• Add load_sig and save_sig methods to Storage trait for higher-level data manipulation and caching. (#2230)
• Add spec method to Storage to allow constructing a concrete Storage from a string description. (#2230)
• Add InnerStorage for synchronizing parallel access to Storage implementations. (#2230)
• Add MemStorage for keeping signatures in-memory (mostly for debugging and testing). (#2230)
• Add new branchwater feature (enabled by default), which can be disabled by downstream projects to limit bringing heavy dependencies like rocksdb. (#2230)
• Add new rkyv feature (disabled by default), making MinHash serializable with the rkyv crate. (#2230)
• Add semver checks for CI (so we bump versions accordingly, or avoid breaking changes). (#2230)
• Add cargo deny config. (#2724)
• Benchmarks for seq_to_hashes in protein mode. (#1944)
• Oxidize ZipStorage. (#1909)
• Move greyhound-core into sourmash. (#1238)
• add MinHash.kmers_and_hashes(...) and sourmash sig kmers. (#1695)
• Produce list of hashes from a sequence. (#1653)

Changed:

• Rename HashFunctions variants to follow camel-case, so Murmur64Protein instead of murmur64_protein. (#2230)
• LinearIndex is now implemented as a thin layer on top of Collection. (#2230)
• Move GatherResult to sourmash::index module. (#2230)
• Move sourmash::index::revindex to sourmash::index::mem_revindex (this is the Greyhound version of revindex, in-memory only). It was also refactored internally to build a version of a LinearIndex that will be merged in the future with sourmash::index::LinearIndex. (#2230)
• Move select method from Index trait into a separate Select trait, and implement it for Signature based on the new Selection API. (#2230)
• Move SigStore into sourmash::storage module, and remove the generic. Now it always stores Signature. Also implement Select for it. (#2230)
• Disable musllinux wheels (need to figure out how to build rocksdb for it). (#2230)
• Reorganize traits for easier wasm and native compilation. (#1836)
• Adjust dayhoff and hp encodings to tolerate stop codons in the protein sequence. (#1673)

Fixed:

• Reduce features combinations on Rust checks (takes much less time to run). (#2230)
• Build: MSRV check for 1.64. (#2680)
• maturin: move deprecated definition from Cargo.toml to pyproject.toml. (#2597)
• Fix broken crates.io badge. (#2556)
• Fix unnecessary typecasts in Rust. (#2366)
• Fix Signature.minhash API during sourmash sketch. (#2329)
• Return Err for angular_similarity when abundance tracking is off. (#2327)
• Update various descriptions to talk about k-mers, not just DNA. (#2137)
• Fix downsample_scaled in core. (#2108)
• speed up SeqToHashes translate. (#1946)
• Speed-up SeqToHashes(). (#1938)
• Fix containment calculation for nodegraphs. (#1862)
• Fix panic bug in sourmash sketch dna with bad input and --check-sequence. (#1702)
• Fix Rust panic in MinHash.seq_to_hashes. (#1701)
• Beta lints. (#2841 #2630 #2596 #2298 #1791 #1786 #1760)

Removed:

• Remove BIGSI and SBT code. (#2732)

0.11.0 - 2021-07-07

Added:

• Add HyperLogLog implementation (#1223)

Changed:

• Update MinHash.set_abundances to remove hash if 0 abund; handle negative abundances. (#1575)
• Improving MinHash.remove_many(...) performance (#1571)
• Improved intersection and union calculations (#1475)
• Bump MSRV to 1.42 (and other dep fixes) (#1461)
• Rework the find functionality for Index classes (#1392)
• Rationalize SourmashSignature.name and str(sig) (#1179)

Fixed:

• Fix needless borrows as suggested by clippy (#1636)
• Fix Rust 1.59 lints (#1600)
• Clean up clippy lints from 1.52 (#1505)
• Fix clippy lints introduced in 1.51 (#1407)
• CI/Rust: update and fix cbindgen config (#1473)
• pin needletail version to keep MSRV at 1.37 (#1393)
• Update proptest requirement from 0.9.6 to 1.0.0 (#1344)
• Fix clippy lints introduced in 1.50 and update nix configs (#1332)
• Update finch requirement from 0.3.0 to 0.4.1 (#1290)
• update rand for test, and activate "js" feature for getrandom (#1275)
• Fix new clippy warnings from Rust 1.49 (#1267)
• CI: small build fixes (#1252)

Removed:

• Remove 10x support in compute (#1229)

0.10.0 - 2020-10-08

Added:

• Add clear option to set_abundances(...) method (#1046)

Changed:

• Replace mx by scaled (#1139)

Fixed:

• Fix Rust panic error in signature creation (#1172)
• Update typed-builder requirement from 0.6.0 to 0.7.0 (#1121)
• update CI for latest branch name change (#1150)
• Update typed-builder requirement from 0.6.0 to 0.7.0 (#1121)

0.9.0 - 2020-07-13

Added:

• Cache md5sum calculation (#1058)
• Expose more of the API for wasm (signature and ComputeParameters) (#1058)
• Getters and setters for ComputeParameters (#1058)

Changed:

• Migrate from failure to thiserror (#1058)
• Bump MSRV to 1.37 (#1058)

Fixed:

• Use the derive feature in serde instead of serde_derive (#1058)
• Use nohash-hasher crate instead of previous NoHashHasher from finch.
• Update typed-builder to 0.6.0 (#1058)
• stricter niffler versions and add new gz feature to it (#1070)

0.8.0 - 2020-06-26

Added:

• compute-optimized MinHash (for small scaled or large cardinalities) (#1045)

0.7.0 - 2020-05-12

Changed:

• Hide internal representation in core (#986)

Fixed:

• update FFI and cbindgen (#986)

0.6.0 - 2020-04-28

Added:

• Nodegraph implementation based on khmer.Nodegraph (#799)

0.5.0 - 2020-02-08

Added:

• add_hash_with_abundance method in core library (#892)

Changed:

• More refactoring of MinHash comparison code (#882)
• Replace mins_push and abunds_push with set_abundances (#887)

Fixed:

• add_hash with num doesn't set abundances properly (#891)

0.4.0 - 2020-01-26

Added:

• Compute improvements: Parameter sets for defining signatures, add_protein implemented (#845)
• add_many for faster insertion of multiple hashes (#826)

Changed:

• Compare/similarity now have a downsample argument (#856)

Fixed:

• Improve sketching performance with lookup tables for complement and DNA validation (#861) (#865)
• Use tarpaulin instead of grcov (#862)
• set up publishing workflow for NPM and crates.io (#824)

0.3.0 - 2020-01-05

Added:

• Similarity with abundance method for MinHash (#808)
• Experimental support for indices in Rust (#773)
• Experimental SBT with MQF internal nodes in Rust (#772)

Changed:

• Make the sourmash crate library-only (#812)

Fixed:

• Use once_cell instead of lazy_static and lazy-init (#815)
• Fix mem leak in get_mins (#807)
• Fixes for WASI and WASM compilation (#771) (#723)