4.7.0 release

[ctb]

sourmash release 4.7.0

Major new features:

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

Minor new features:

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

Cleanup and documentation updates:

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

Developer updates:

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

Dependabot updates:

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

[codecov]

Codecov Report

Merging #2497 (41b9af0) into latest (2fd1ae0) will increase coverage by 7.76%.
The diff coverage is n/a.

@@            Coverage Diff             @@
##           latest    #2497      +/-   ##
==========================================
+ Coverage   84.81%   92.58%   +7.76%     
==========================================
  Files         133      104      -29     
  Lines       14820    12026    -2794     
  Branches     2513     2513              
==========================================
- Hits        12570    11134    -1436     
+ Misses       1948      590    -1358     
  Partials      302      302              

Flag	Coverage Δ
python	92.58% <ø> (ø)
rust	?

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
src/core/src/sketch/minhash.rs
src/core/src/ffi/signature.rs
src/core/src/index/sbt/mhbt.rs
src/core/src/index/search.rs
src/core/src/ffi/utils.rs
src/core/src/index/linear.rs
src/core/src/encodings.rs
src/core/src/sketch/hyperloglog/mod.rs
src/core/src/from.rs
src/core/src/cmd.rs
... and 19 more

📣 We’re building smart automated test selection to slash your CI/CD build times. Learn more

[ctb]

Release candidate testing:

• Command line tests pass for a release candidate
• All eight release candidate wheels are built

Releasing to PyPI:

• RC tag(s)s deleted on github
• Release tag cut
• Release notes written
• All eight release wheels built
• Release wheels uploaded to pypi
• tar.gz distribution uploaded to pypi

After release to PyPI and conda-forge/bioconda packages built:

• 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 correct version