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Clean up and refactor KmerMinHash::merge in core #2973

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merged 3 commits into from
Feb 5, 2024

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Use Option::iter to simplify code in KmerMinhash::merge, as well as rewritting some checks so they are less redundant.

This wasn't quite the change I was going for, but I also noticed this lowered Python tests runtime from 58s to 49s in my dev machine, mostly because similarity is 17% faster, so might as well merge it.

@luizirber luizirber changed the title core: Clean up and refactor KmerMinHash::merge in core Clean up and refactor KmerMinHash::merge in core Feb 5, 2024
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codecov bot commented Feb 5, 2024

Codecov Report

Attention: 1 lines in your changes are missing coverage. Please review.

Comparison is base (1692eb7) 86.62% compared to head (1623a7a) 86.61%.

Files Patch % Lines
src/core/src/sketch/minhash.rs 97.56% 1 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##           latest    #2973      +/-   ##
==========================================
- Coverage   86.62%   86.61%   -0.01%     
==========================================
  Files         135      135              
  Lines       15278    15269       -9     
  Branches     2618     2618              
==========================================
- Hits        13235    13226       -9     
  Misses       1743     1743              
  Partials      300      300              
Flag Coverage Δ
hypothesis-py 25.80% <ø> (ø)
python 92.83% <ø> (ø)
rust 59.09% <97.56%> (-0.14%) ⬇️

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@luizirber luizirber merged commit 7b18302 into latest Feb 5, 2024
37 of 38 checks passed
@luizirber luizirber deleted the lirber/merge_cleanup branch February 5, 2024 03:47
ctb added a commit that referenced this pull request Feb 10, 2024
MSRV: 1.65

Changes/additions:

* 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)
@ctb ctb mentioned this pull request Feb 10, 2024
ctb added a commit that referenced this pull request Feb 10, 2024
release notes: https://hackmd.io/SCoVcWS1RhCH-ndQNWF-1A?view

# sourmash release v4.8.6 - release notes

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)
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