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@github-actions github-actions released this 02 Dec 16:16
· 551 commits to latest since this release
v4.6.0
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The major new feature in this release is the addition of tax summarize, which produces a human-readable summary of taxonomy databases.

The various tax functions also now support ingest of the output of tax annotate as a lineage spreadsheet - see the tax prepare documentation. This allows you to (for example) run tax summarize on the output of tax annotate.

Major new features:

  • add tax summarize and support gather-tax input to taxonomy functions (#2333)
  • report both weighted and unweighted % recovered in gather (#2301)
  • replace chernoff bounds with exact probabilities (#2268)

Minor new features:

  • switch remaining sig submodule commands over to sourmash_args sig output (#2377)
  • use modern signature saving API throughout main CLI commands. (#2338)
  • add column 3 to kreport (#2306)
  • allow gzipped gather csv inputs to tax (#2339)
  • display a better error message on attempting to write a read-only sqlite database (#2376)
  • fix manifest load function to properly catch gzip.BadGzipFile (#2375)
  • update kreport proportion for better resolution; match other tool outputs (#2331)

Bug fixes:

  • Fix multigather so that the output CSV contains all matches. (#2322)
  • remove default ksize of 31 from help message when it's not actually true. (#2295)

Cleanup and documentation updates:

  • Updated python version (#2286)
  • update docs re using multiple dbs (#2296)
  • fix some tax doc issues (#2365)
  • fix kreport documentation (#2302)

Developer updates:

  • Fix cibuildwheel actions (#2384, #2385, #2388)
  • return Err for angular_similarity when abundance tracking is off (#2327)
  • cargo check fixes for Rust beta (1.65) (#2298)
  • fix unnecessary typecasts in Rust (#2366)
  • fix Signature.minhash API during sourmash sketch (#2329)
  • fix return type of LCA_SqliteDatabase.select (#2382)

Dependabot updates:

  • Bump conda-incubator/setup-miniconda from 2.1.1 to 2.2.0 (#2363)
  • Bump counter from 0.5.6 to 0.5.7 (#2336)
  • Bump finch from 0.4.1 to 0.4.3 (#2283)
  • Bump getrandom from 0.2.7 to 0.2.8 (#2347)
  • Bump memmap2 from 0.5.7 to 0.5.8 (#2364)
  • Bump myst-parser from 0.18.0 to 0.18.1 (#2345)
  • Bump pypa/cibuildwheel from 2.11.1 to 2.11.2 (#2353)
  • Bump pypa/cibuildwheel from 2.9.0 to 2.10.2 (#2307)
  • Bump rayon from 1.5.3 to 1.6.0 (#2373)
  • Bump serde from 1.0.145 to 1.0.147 (#2348)
  • Bump serde from 1.0.147 to 1.0.148 (#2378)
  • Bump serde_json from 1.0.86 to 1.0.87 (#2349)
  • Bump serde_json from 1.0.87 to 1.0.88 (#2374)
  • Bump serde_json from 1.0.88 to 1.0.89 (#2379)
  • Bump typed-builder from 0.10.0 to 0.11.0 (#2356)
  • Update bitstring requirement from <4,>=3.1.9 to >=3.1.9,<5 (#2372)
  • Update docutils requirement from <0.18,>=0.17.1 to >=0.17.1,<0.20 (#2344)
  • Update pytest requirement from <7.2.0,>=6.2.4 to >=6.2.4,<7.3.0 (#2354)
  • Update pytest-cov requirement from <4.0,>=2.12 to >=2.12,<5.0 (#2346)
  • Version bumps (#2282)
  • Combine latest dependabot PRs: cibuildwheel, finch, serde_json (#2343)
  • Rust deps updates without MSRV bump (#2315)
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