MRG: 4.8.6 release branch

[ctb]

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 (MRG: re-establish tax gather reading flexibility #2986)
• update JOSS paper per pyopensci review (MRG: update JOSS paper per pyopensci review #2964)
• Clean up and refactor KmerMinHash::merge in core (Clean up and refactor KmerMinHash::merge in core #2973)
• add label output & input options to compare and plot, for better customization (MRG: add label output & input options to compare and plot, for better customization #2598)
• add utilities for using ictv taxonomic ranks with sourmash tax (MRG: 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 (MRG: Fix tax metagenome to work on gather output created with --estimate-ani-ci #2952)
• fix gather memory usage issue by not accumulating GatherResult (MRG: fix gather memory usage issue by not accumulating GatherResult #2962)
• update the CLI docs and help for search --containment and prefetch (MRG: update the CLI docs and help for search --containment and prefetch #2971)

Documentation updates:

• update tutorial to remove bioconda & use sourmash-minimal (MRG: update tutorial to remove bioconda & use sourmash-minimal #2972)
• update readme with maintainers & sourmash comparison info (MRG: update readme with maintainers & sourmash comparison info #2965)
• add branchwater reference; make FAQ more visible (MRG: docs: add branchwater reference; make FAQ more visible #2984)
• update FAQ answer on k-mer size (MRG: update FAQ answer on k-mer size #2899)
• update README with repostatus and pyver badges, and Windows support (MRG: update README with repostatus and pyver badges, and Windows support #2928)
• add full column descriptions for gather and prefetch output (MRG: add full column descriptions for gather and prefetch output #2954)
• add scaled FAQ, adjust ksize answer (MRG: add scaled FAQ, adjust ksize answer #2921)
• minor refactoring of gather code, small doc updates (MRG: minor refactoring of gather code, small doc updates #2953)
• Add threshold-bp and scaled relationship to faqs ([MRG] Adding threshold-bp and scaled relationship to faqs #2930)

Developer updates:

• nix updates for pyopensci review (nix updates for pyopensci review #2975)
• add scaled selection to manifest; add helper functions for collection and sig/sketch usage (MRG: core: add scaled selection to manifest; add helper functions for collection and sig/sketch usage #2948)
• Pre-commit updates (Pre-commit updates #2427)
• fix upload wheel CI (MRG: fix upload wheel CI #2974)
• release core; bump rust core version to r0.12.1 (MRG: bump rust core version to r0.12.1 #2988)
• CI: macos deployment target and maturin updates (CI: macos deployment target and maturin updates #2879)
• MRG: bump version to 4.8.6-dev, post-release (MRG: bump version to 4.8.6-dev, post-release #2877)
• fix benchmark code & a few other small issues from pyOpenSci review (MRG: fix benchmark code & a few other small issues from pyOpenSci review #2920)
• fix uploading of wheels after upload-artifact upgrade. (MRG: fix uploading of wheels after upload-artifact upgrade. #2887)
• in core, enable downsample within select (MRG: in core, enable downsample within select #2931)

Dependabot updates:

• Bump pypa/cibuildwheel from 2.16.4 to 2.16.5 (Bump pypa/cibuildwheel from 2.16.4 to 2.16.5 #2981)
• Bump tempfile from 3.9.0 to 3.10.0 (Bump tempfile from 3.9.0 to 3.10.0 #2979)
• Bump rkyv from 0.7.43 to 0.7.44 (Bump rkyv from 0.7.43 to 0.7.44 #2978)
• Bump actions/cache from 3 to 4 (Bump actions/cache from 3 to 4 #2933)
• Bump actions/download-artifact from 3 to 4 (Bump actions/download-artifact from 3 to 4 #2884)
• Bump actions/upload-artifact from 3 to 4 (Bump actions/upload-artifact from 3 to 4 #2883)
• Bump cachix/cachix-action from 13 to 14 (Bump cachix/cachix-action from 13 to 14 #2926)
• Bump cachix/install-nix-action from 24 to 25 (Bump cachix/install-nix-action from 24 to 25 #2927)
• Bump chrono from 0.4.31 to 0.4.33 (Bump chrono from 0.4.31 to 0.4.33 #2957)
• Bump getrandom from 0.2.11 to 0.2.12 (Bump getrandom from 0.2.11 to 0.2.12 #2924)
• Bump histogram from 0.8.3 to 0.8.4 (Bump histogram from 0.8.3 to 0.8.4 #2923)
• Bump histogram from 0.8.4 to 0.9.0 (Bump histogram from 0.8.4 to 0.9.0 #2935)
• Bump jinja2 from 3.1.2 to 3.1.3 (Bump jinja2 from 3.1.2 to 3.1.3 #2922)
• Bump memmap2 from 0.9.0 to 0.9.2 (Bump memmap2 from 0.9.0 to 0.9.2 #2882)
• Bump memmap2 from 0.9.2 to 0.9.3 (Bump memmap2 from 0.9.2 to 0.9.3 #2889)
• Bump memmap2 from 0.9.3 to 0.9.4 (Bump memmap2 from 0.9.3 to 0.9.4 #2958)
• Bump mymindstorm/setup-emsdk from 13 to 14 (Bump mymindstorm/setup-emsdk from 13 to 14 #2934)
• Bump ouroboros from 0.18.1 to 0.18.2 (Bump ouroboros from 0.18.1 to 0.18.2 #2894)
• Bump ouroboros from 0.18.2 to 0.18.3 (Bump ouroboros from 0.18.2 to 0.18.3 #2936)
• Bump pypa/cibuildwheel from 2.16.2 to 2.16.4 (Bump pypa/cibuildwheel from 2.16.2 to 2.16.4 #2960)
• Bump rayon from 1.8.0 to 1.8.1 (Bump rayon from 1.8.0 to 1.8.1 #2937)
• Bump rkyv from 0.7.42 to 0.7.43 (Bump rkyv from 0.7.42 to 0.7.43 #2880)
• Bump serde from 1.0.194 to 1.0.195 (Bump serde from 1.0.194 to 1.0.195 #2901)
• Bump serde from 1.0.195 to 1.0.196 (Bump serde from 1.0.195 to 1.0.196 #2956)
• Bump serde_json from 1.0.108 to 1.0.110 (Bump serde_json from 1.0.108 to 1.0.110 #2896)
• Bump serde_json from 1.0.110 to 1.0.111 (Bump serde_json from 1.0.110 to 1.0.111 #2902)
• Bump serde_json from 1.0.111 to 1.0.113 (Bump serde_json from 1.0.111 to 1.0.113 #2955)
• Bump shlex from 1.1.0 to 1.3.0 (Bump shlex from 1.1.0 to 1.3.0 #2940)
• Bump supercharge/redis-github-action from 1.7.0 to 1.8.0 (Bump supercharge/redis-github-action from 1.7.0 to 1.8.0 #2885)
• Bump tempfile from 3.8.1 to 3.9.0 (Bump tempfile from 3.8.1 to 3.9.0 #2893)
• Bump thiserror from 1.0.50 to 1.0.51 (Bump thiserror from 1.0.50 to 1.0.51 #2881)
• Bump thiserror from 1.0.51 to 1.0.56 (Bump thiserror from 1.0.51 to 1.0.56 #2897)
• Bump wasm-bindgen from 0.2.89 to 0.2.90 (Bump wasm-bindgen from 0.2.89 to 0.2.90 #2925)
• Bump wasm-bindgen-test from 0.3.39 to 0.3.40 (Bump wasm-bindgen-test from 0.3.39 to 0.3.40 #2938)
• Bump web-sys from 0.3.66 to 0.3.67 (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 (Update pytest requirement from <7.5.0,>=6.2.4 to >=6.2.4,<8.1.0 #2959)

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Comparison is base (7edcf14) 86.63% compared to head (b644174) 86.63%.

Additional details and impacted files

@@           Coverage Diff           @@
##           latest    #2963   +/-   ##
=======================================
  Coverage   86.63%   86.63%           
=======================================
  Files         135      135           
  Lines       15390    15390           
  Branches     2624     2624           
=======================================
  Hits        13333    13333           
  Misses       1756     1756           
  Partials      301      301           

Flag	Coverage Δ
hypothesis-py	25.56% <ø> (ø)
python	92.85% <ø> (ø)
rust	59.41% <ø> (ø)

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