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@ctb ctb released this 21 Mar 16:44
· 247 commits to latest since this release
v4.8.7
24ab89c
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Learn about vigilant mode.

Note: This release changes the way sourmash multigather names output files in some situations. Please see #2722 for details.

Minor new features:

  • support proper manifest creation with --relpath for sig check and sig collect (#3054)
  • fix multigather output by adding md5sum along with -U/--output-add-query-md5sum (#2722)
  • enable loading lineages from annotated gather with match_name instead of name (#3078)

Bug fixes:

  • fix output for sketch ... --singleton (#3066)
  • fix calculate_gather_stats threshold=0 bug (#3052)

Cleanup and documentation updates:

  • adjust protein ksize for record/manifest (#3019)
  • Resolve sourmash gather --help issue (#3032)
  • rework the manifest documentation; do misc cleanup (#3027)
  • add branchwater web to docs (#3018)

Developer updates:

  • make core Manifest booleans python compatible (core) (#3007)
  • safer ksize selection while still accommodating k=k*3 (#3028)
  • fix clippy beta issues (#3088)
  • tell dependabot to ignore upgrades to byteorder, chrono, once_cell, and wasm-bindgen (#3065)
  • update rust changelog for r0.13.0 in preparation for release (#3033)
  • Allow changing storage location for a collection in RevIndex (#3015)
  • Fix tox and nix configs so all tox tests execute correctly (#2992)
  • Calculate all gather stats in rust; use for rocksdb gather (#2943)
  • bump screed req to 1.1.3 (#3067)
  • bump to v4.8.7-dev (#2989)

Dependabot updates:

  • Bump DeterminateSystems/magic-nix-cache-action from 1 to 3 (#2994)
  • Bump DeterminateSystems/magic-nix-cache-action from 3 to 4 (#3085)
  • Bump DeterminateSystems/nix-installer-action from 4 to 9 (#2995)
  • Bump DeterminateSystems/nix-installer-action from 9 to 10 (#3083)
  • Bump chrono from 0.4.33 to 0.4.34 (#3000)
  • Bump conda-incubator/setup-miniconda from 3.0.1 to 3.0.2 (#3046)
  • Bump conda-incubator/setup-miniconda from 3.0.2 to 3.0.3 (#3057)
  • Bump histogram from 0.9.0 to 0.9.1 (#3002)
  • Bump itertools from 0.12.0 to 0.12.1 (#3043)
  • Bump log from 0.4.20 to 0.4.21 (#3062)
  • Bump num-iter from 0.1.43 to 0.1.44 (#2997)
  • Bump pypa/cibuildwheel from 2.16.5 to 2.17.0 (#3084)
  • Bump rayon from 1.8.1 to 1.9.0 (#3058)
  • Bump roaring from 0.10.2 to 0.10.3 (#3014)
  • Bump serde from 1.0.196 to 1.0.197 (#3045)
  • Bump serde_json from 1.0.113 to 1.0.114 (#3044)
  • Bump tempfile from 3.10.0 to 3.10.1 (#3059)
  • Bump thiserror from 1.0.56 to 1.0.57 (#2999)
  • Bump thiserror from 1.0.57 to 1.0.58 (#3082)
  • Bump wasm-bindgen from 0.2.91 to 0.2.92 (#3060)
  • Bump wasm-bindgen-test from 0.3.40 to 0.3.41 (#2996)
  • Bump wasm-bindgen-test from 0.3.41 to 0.3.42 (#3063)
  • Bump web-sys from 0.3.67 to 0.3.68 (#2998)
  • Bump web-sys from 0.3.68 to 0.3.69 (#3061)
  • Revert "Bump wasm-bindgen from 0.2.91 to 0.2.92 (#3060)" (#3064)
  • Update asv to 0.6.2 (#3025)
  • Update pytest requirement from <8.1.0,>=6.2.4 to >=6.2.4,<8.2.0 (#3075)
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