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@ctb ctb released this 03 Mar 13:48
· 460 commits to latest since this release
v4.7.0
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sourmash release 4.7.0

Major new features:

  • provide an initial plugin architecture for sourmash that supports new signature saving & loading mechanisms (#2428)
  • add plugin support for new command-line subcommands (#2438)
  • debias all containment values (#2243)

Minor new features:

  • Use RankLineageInfo to simplify reading lineages (#2467)
  • store taxids in lineageDB (#2466)
  • Use new tax classes for taxonomic summarization (#2443)
  • add tax summarization dataclasses for safety and flexibility (#2439)
  • add --scaled to sourmash compare (#2414)
  • replace lca_utils.LineagePair with tax_utils.LineagePair (#2441)
  • Add new classes for lineage manipulation (#2437)

Cleanup and documentation updates:

  • ReadTheDocs updates (#2445)
  • update sourmash compare command-line docs (#2400)

Developer updates:

  • fix python tests by bumping tox and pip cache versions (#2424)
  • Update sphinx requirement from <6,>=4.4.0 to >=4.4.0,<7 (#2430)
  • Build: replace milksnake with maturin (#2393)
  • importlib_metadata is a dependency on old Python versions (#2484)
  • Release docs: use two separate sed commands (#2483)
  • minor fixes to release behavior (#2479)
  • Use screed and maturin from nixpkgs in flake.nix (#2481)
  • update release procedure after v4.6.0 and v4.6.1 (#2386)
  • Update makefile and docs (#2432)

Dependabot updates:

  • Bump once_cell from 1.17.0 to 1.17.1 (#2488)
  • Bump ouroboros from 0.15.5 to 0.15.6 (#2487)
  • Bump memmap2 from 0.5.8 to 0.5.9 (#2486)
  • Bump supercharge/redis-github-action from 1.4.0 to 1.5.0 (#2485)
  • Bump proptest from 1.0.0 to 1.1.0 (#2460)
  • Bump web-sys from 0.3.60 to 0.3.61 (#2461)
  • Bump serde_json from 1.0.91 to 1.0.93 (#2471)
  • Bump wasm-bindgen-test from 0.3.33 to 0.3.34 (#2463)
  • Bump cachix/install-nix-action from 18 to 19 (#2459)
  • Bump wasm-bindgen from 0.2.83 to 0.2.84 (#2464)
  • Bump typed-builder from 0.11.0 to 0.12.0 (#2451)
  • Bump bumpalo from 3.9.1 to 3.12.0 (#2450)
  • Bump pypa/cibuildwheel from 2.11.4 to 2.12.0 (#2447)
  • Bump bzip2 from 0.4.3 to 0.4.4 (#2444)
  • Bump once_cell from 1.14.0 to 1.17.0 (#2429)
  • Bump serde from 1.0.151 to 1.0.152 (#2423)
  • Bump pypa/cibuildwheel from 2.11.3 to 2.11.4 (#2422)
  • Bump serde_json from 1.0.89 to 1.0.91 (#2418)
  • Bump serde from 1.0.150 to 1.0.151 (#2419)
  • Bump thiserror from 1.0.37 to 1.0.38 (#2417)
  • Bump finch from 0.4.3 to 0.5.0 (#2416)
  • Bump rayon from 1.6.0 to 1.6.1 (#2404)
  • Bump serde from 1.0.149 to 1.0.150 (#2403)
  • Bump pypa/cibuildwheel from 2.11.2 to 2.11.3 (#2402)
  • Bump serde from 1.0.148 to 1.0.149 (#2397)
  • Bump capnp from 0.14.5 to 0.14.11 (#2396)
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