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@ctb ctb released this 10 Feb 23:29
· 288 commits to latest since this release
v4.8.6
47a6ee0
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Learn about vigilant mode.

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)
Assets 8
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