release notes for sourmash v4.6.0

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)

ctb commented 1 year ago

after long last,

https://github.com/sourmash-bio/sourmash/releases/tag/v4.6.0

🎉

now - on to conda!!

ctb commented 1 year ago

conda-forge: https://github.com/conda-forge/sourmash-minimal-feedstock/pull/37

bioconda: https://github.com/bioconda/bioconda-recipes/pull/38205

ctb commented 1 year ago

[x] PyPI page updated
[x] Zenodo DOI successfully minted upon new github release - see search results
[x] pip install sourmash installs the correct version
[x] mamba create -n smash-release -y sourmash installs the corr

ctb commented 1 year ago

🎉

sourmash-bio / sourmash

draft release notes for v4.6.0 #2387

release notes for sourmash v4.6.0