Sourmash

Major new features:

* Add taxonomic utilities for LINs (2469, 2468, 2519, 2518)

Minor new features:

* update prefetch/gather output to be clearer (2543)

Cleanup and documentation updates:

* update version of screed to >= 1.1,<2 (2415)
* minor fixes to release docs after v4.7.0 (2498)

Developer updates:

* Remove pkg_resources usage (2505)
* Add LICENSE and test data to sdist (2490)
* Build pyodide wheels in CI (2433)
* Update nix deps (2506)
* bump to pyodide 0.23 (2545)

Dependabot updates:

* Bump serde_json from 1.0.94 to 1.0.95 (2540)
* Bump needletail from 0.5.0 to 0.5.1 (2541)
* Bump serde from 1.0.156 to 1.0.158 (2534)
* Bump thiserror from 1.0.39 to 1.0.40 (2533)
* Bump typed-builder from 0.13.0 to 0.14.0 (2527)
* Bump serde from 1.0.152 to 1.0.156 (2530)
* Bump minimum rust version to 1.60 (2528)
* Bump myst-parser from 0.19.1 to 1.0.0 (2525)
* Bump chrono from 0.4.23 to 0.4.24 (2524)
* Bump pypa/cibuildwheel from 2.12.0 to 2.12.1 (2523)
* Bump myst-parser from 0.18.1 to 0.19.1 (2507)
* Bump rayon from 1.6.1 to 1.7.0 (2515)
* Bump tempfile from 3.3.0 to 3.4.0 (2514)
* Bump needletail from 0.4.1 to 0.5.0 (2512)
* Bump memmap2 from 0.5.9 to 0.5.10 (2516)
* Bump thiserror from 1.0.38 to 1.0.39 (2509)
* Bump mymindstorm/setup-emsdk from 11 to 12 (2508)
* Bump serde_json from 1.0.93 to 1.0.94 (2510)
* Bump typed-builder from 0.12.0 to 0.13.0 (2511)

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)

This is a quick patch-fix for sourmash v4.6.0, which introduced bug https://github.com/sourmash-bio/sourmash/issues/2390. This bug broke `sourmash sketch ... -o <file>` with multiple ksizes, so that `.zip` and `.sqldb` output files contained only one ksize.

Bug fixes:
- fix `sourmash sketch ... -o <file>.zip` bug introduced in 2329 and released in v4.6.0 (2391)
- disable cibuildwheel on PRs again (2389)

The major new feature in this release is the addition of [`tax summarize`](https://sourmash.readthedocs.io/en/latest/command-line.html#sourmash-tax-summarize-print-summary-information-for-lineage-spreadsheets-or-taxonomy-databases), 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](https://sourmash.readthedocs.io/en/latest/command-line.html#sourmash-tax-prepare-prepare-and-or-combine-taxonomy-files). 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)

sourmash v4.5.0 provides several minor bug fixes, as well as a number of new features.

This release also includes two minor Python API breaking changes - by default, `SourmashSignature` objects loaded from files are "frozen", and we force explicit keyword arguments on `MinHash` object construction.

Finally, this release updates the sourmash documentation with several new tutorials, including one on using `sourmash tax` to classify metagenomes with MAGs + GTDB.

Bug fixes

* Fix `sourmash tax` argument parsing for multiple `-g` and `-t` arguments (2218)
* Prevent loading multiple independent gather results files in `sourmash tax` (2244)
* Fix `query_abundance` column when `--ignore-abundance` is set in gather (2251)
* fix pickle protocol to properly adjust `ksize` in `__getstate__` (2265)
* clean up zip error handling for bad zip files (2270)

Minor new features

* Use the bias factor for containment when estimating ANI (2057)
* add human output format to `sourmash tax`; provide tutorials (2158)
* add kreport output format to tax metagenome (2239, 2249)
* add `--distance-matrix` option to `sourmash compare` (2225)
* update database load UX for `gather` etc. (2204)
* add generic support for gzipped and zipfile CSVs (2195)
* implement `tax grep` to produce identifier picklists from taxonomies (2178)

Cleanup and documentation fixes

* add `sourmash tax` tutorial (2158)
* revise command-line docs for `sourmash sig` subcommands (1714, 1717)
* Clarify containment direction for matrix output (2215)
* Add ANGUS tutorial to docs (1114)
* update links to static rmd (1177)
* update `search` documentation, help, and output. (2222)
* Fix signature filter command (2159)
* fix notification message about query scaled (2183)
* adjust gather output width on terminal (2176)

Developer updates

* Add `FrozenSourmashSignature` (1610)
* force explicit kwargs on MinHash constructor (2174)
* fix ReadTheDocs by using a more recent conda version (2231)
* refactor and add tests for containment direction for ANI calculation (2215)
* fix `test_storage_convert` to allow success of `sourmash convert` (2232)
* Updating `tests/test_sourmash.py::test_storage_convert` to use `runtmp` fixture instead of `utils.TempDirectory()` (1739)
* Bump pypa/cibuildwheel from 2.8.1 to 2.9.0 (2207)
* use stderr for test output printing (2217)
* fix for sphinx 5.10 (2147)

Minor new features:
* use and report ANI from `tax genome` summarization (2005)

Performance improvements:
* avoid instantiating a hashes class (2132)

Cleanup and documentation fixes:
* update various descriptions to talk about k-mers, not just DNA (2137)

Developer updates:
* fix docs building for pip 22.2 (2143)
* change dependabot rebase-strategy to disabled for rust dependencies (2142)
* Rust deps and nix flakes updates (2141)
* add `pytest-xdist` and `-n4` to pytest and tox configs (2138)
* update release instructions after v4.4.2 (2131)