draft release notes for v4.6.0

[ctb]

Used git log --oneline v4.5.0..latest to get the list below!

Editing here: https://hackmd.io/Z3ndKHBoRCi-uWF06B7eEw

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.

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Major new features:

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

Minor new features:

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

Bug fixes:

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

Cleanup and documentation updates:

• Updated python version ([MRG] Update python version per deprecation policy #2286)
• update docs re using multiple dbs ([MRG] update docs in re using multiple files/databases on command line #2296)
• fix some tax doc issues ([MRG] fix some tax doc issues #2365)
• fix kreport documentation ([MRG] fix kreport documentation #2302)

Developer updates:

• Fix cibuildwheel actions ([MRG] fixing cross-platform cibuildwheel action for release #2384, [MRG] remove cibuildwheel action from PRs #2385, [MRG] change cargo update to do a dry-run only #2388)
• return Err for angular_similarity when abundance tracking is off ([MRG] return Err for angular_similarity when abundance tracking is off #2327)
• cargo check fixes for Rust beta (1.65) (cargo check fixes for beta (1.65) #2298)
• fix unnecessary typecasts in Rust (MRG: fix unnecessary typecasts in Rust #2366)
• fix Signature.minhash API during sourmash sketch ([MRG] fix Signature.minhash API during sourmash sketch #2329)
• fix return type of LCA_SqliteDatabase.select ([MRG] fix return type of LCA_SqliteDatabase.select #2382)

Dependabot updates:

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

[ctb]

after long last,

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

🎉

now - on to conda!!

[ctb]

conda-forge: conda-forge/sourmash-minimal-feedstock#37

bioconda: bioconda/bioconda-recipes#38205

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

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🎉