Sourmash

Minor new features:

* re-establish `tax` gather reading flexibility (2986)
* update JOSS paper per pyopensci review (2964)
* Clean up and refactor `KmerMinHash::merge` in core (2973)
* add label output & input options to `compare` and `plot`, for better customization (2598)
* add utilities for using ictv taxonomic ranks with `sourmash tax` (2608)

Bug fixes:

* Fix `tax metagenome` to work on gather output created with `--estimate-ani-ci` (2952)
* fix gather memory usage issue by not accumulating `GatherResult` (2962)
* update the CLI docs and help for `search --containment` and `prefetch` (2971)

Documentation updates:

* update tutorial to remove bioconda & use sourmash-minimal (2972)
* update readme with maintainers & sourmash comparison info (2965)
* add branchwater reference; make FAQ more visible (2984)
* update FAQ answer on k-mer size (2899)
* update README with repostatus and pyver badges, and Windows support (2928)
* add full column descriptions for `gather` and `prefetch` output (2954)
* add scaled FAQ, adjust ksize answer (2921)
* minor refactoring of gather code, small doc updates (2953)
* Add threshold-bp and scaled relationship to faqs (2930)

Developer updates:

* nix updates for pyopensci review (2975)
* add scaled selection to manifest; add helper functions for collection and sig/sketch usage (2948)
* Pre-commit updates (2427)
* fix upload wheel CI (2974)
* release core; bump rust core version to r0.12.1 (2988)
* CI: macos deployment target and maturin updates (2879)
* MRG: bump version to 4.8.6-dev, post-release (2877)
* fix benchmark code & a few other small issues from pyOpenSci review (2920)
* fix uploading of wheels after upload-artifact upgrade. (2887)
* in core, enable downsample within select (2931)

Dependabot updates:

* Bump pypa/cibuildwheel from 2.16.4 to 2.16.5 (2981)
* Bump tempfile from 3.9.0 to 3.10.0 (2979)
* Bump rkyv from 0.7.43 to 0.7.44 (2978)
* Bump actions/cache from 3 to 4 (2933)
* Bump actions/download-artifact from 3 to 4 (2884)
* Bump actions/upload-artifact from 3 to 4 (2883)
* Bump cachix/cachix-action from 13 to 14 (2926)
* Bump cachix/install-nix-action from 24 to 25 (2927)
* Bump chrono from 0.4.31 to 0.4.33 (2957)
* Bump getrandom from 0.2.11 to 0.2.12 (2924)
* Bump histogram from 0.8.3 to 0.8.4 (2923)
* Bump histogram from 0.8.4 to 0.9.0 (2935)
* Bump jinja2 from 3.1.2 to 3.1.3 (2922)
* Bump memmap2 from 0.9.0 to 0.9.2 (2882)
* Bump memmap2 from 0.9.2 to 0.9.3 (2889)
* Bump memmap2 from 0.9.3 to 0.9.4 (2958)
* Bump mymindstorm/setup-emsdk from 13 to 14 (2934)
* Bump ouroboros from 0.18.1 to 0.18.2 (2894)
* Bump ouroboros from 0.18.2 to 0.18.3 (2936)
* Bump pypa/cibuildwheel from 2.16.2 to 2.16.4 (2960)
* Bump rayon from 1.8.0 to 1.8.1 (2937)
* Bump rkyv from 0.7.42 to 0.7.43 (2880)
* Bump serde from 1.0.194 to 1.0.195 (2901)
* Bump serde from 1.0.195 to 1.0.196 (2956)
* Bump serde_json from 1.0.108 to 1.0.110 (2896)
* Bump serde_json from 1.0.110 to 1.0.111 (2902)
* Bump serde_json from 1.0.111 to 1.0.113 (2955)
* Bump shlex from 1.1.0 to 1.3.0 (2940)
* Bump supercharge/redis-github-action from 1.7.0 to 1.8.0 (2885)
* Bump tempfile from 3.8.1 to 3.9.0 (2893)
* Bump thiserror from 1.0.50 to 1.0.51 (2881)
* Bump thiserror from 1.0.51 to 1.0.56 (2897)
* Bump wasm-bindgen from 0.2.89 to 0.2.90 (2925)
* Bump wasm-bindgen-test from 0.3.39 to 0.3.40 (2938)
* Bump web-sys from 0.3.66 to 0.3.67 (2939)
* Update pytest requirement from <7.5.0,>=6.2.4 to >=6.2.4,<8.1.0 (2959)

This release drops support for Python < 3.10, and also reorganizes and expands the documentation substantially!

Major new features:

* Drop Python 3.8 and 3.9, default to Python 3.10 for most CI tasks (2848)
* Revise documentation structure; add internals page. (2184)
* Adjust documentation to recommend `tax` over `lca` for taxonomic analysis (2777)

Bug fixes:

* make `sourmash plot` labels/indices arguments make sense (2790)

Cleanup and documentation updates:

* Various minor updates to docs (2854)
* Deps: update typed-builder and histogram, bump MSRV to 1.65 (2858)
* Fix wheel building and semver checks post r0.12.0 (2857)
* Added seed to parameter strings 1732 (2836)
* Add link for developer documentation to sidebar (2847)
* add explicit install tutorial (2826)
* fix many minor documentation nits (2814)
* update docs for tax grep: only searches tax (2789)
*add usage docs for `sig import/ingest` (2785)

Developer updates:

* Feat: on-disk RevIndex based on RocksDB (2230)
* Fix many warnings from `PYTHONDEVMODE=1` (2849)
* Build: Fix Rust 1.75 beta lints; flake update (2841)
* try pinning maturin to <1.3.0 to fix dev build CI (2799)
* minor updates to release procedure after 4.8.4 (2783)
* run rust checks always (2787)
* add `__all__` to `sig/__main__.py` (2778)
* bump version to 4.8.5-dev (2766)

Dependabot updates:

* Bump ouroboros from 0.18.0 to 0.18.1 (2875)
* Bump once_cell from 1.18.0 to 1.19.0 (2874)
* Bump actions/setup-python from 4 to 5 (2873)
* Bump cachix/cachix-action from 12 to 13 (2861)
* Bump conda-incubator/setup-miniconda from 3.0.0 to 3.0.1 (2860)
* Bump cachix/install-nix-action from 23 to 24 (2859)
* Bump rkyv from 0.7.40 to 0.7.42 (2863)
* Bump csv from 1.2.0 to 1.3.0 (2862)
* Bump roaring from 0.10.1 to 0.10.2 (2865)
* Bump web-sys from 0.3.65 to 0.3.66 (2864)
* Bump byteorder from 1.4.3 to 1.5.0 (2866)
* Bump proptest from 1.3.1 to 1.4.0 (2837)
* Bump getrandom from 0.2.10 to 0.2.11 (2839)
* Bump web-sys from 0.3.64 to 0.3.65 (2838)
* Bump wasm-bindgen-test from 0.3.37 to 0.3.39 (2853)
* Bump wasm-bindgen from 0.2.88 to 0.2.89 (2850)
* Bump mymindstorm/setup-emsdk from 12 to 13 (2851)
* Bump conda-incubator/setup-miniconda from 2.2.0 to 3.0.0 (2852)
* Bump wasm-bindgen from 0.2.87 to 0.2.88 (2834)
* Bump serde_json from 1.0.107 to 1.0.108 (2829)
* Bump tempfile from 3.8.0 to 3.8.1 (2828)
* Bump bytecount from 0.6.5 to 0.6.7 (2830)
* Bump bytecount from 0.6.4 to 0.6.5 (2822)
* Bump thiserror from 1.0.49 to 1.0.50 (2823)
* Bump actions/setup-node from 3 to 4 (2821)
* Bump rustix from 0.37.20 to 0.37.25 (2817)
* Bump pypa/cibuildwheel from 2.16.1 to 2.16.2 (2808)
* Bump memmap2 from 0.8.0 to 0.9.0 (2807)
* Bump byteorder from 1.4.3 to 1.5.0 (2806)
* Bump pypa/cibuildwheel from 2.16.0 to 2.16.1 (2797)
* Bump thiserror from 1.0.48 to 1.0.49 (2796)
* Bump proptest from 1.2.0 to 1.3.1 (2795)
* Bump bytecount from 0.6.3 to 0.6.4 (2794)
* Bump memmap2 from 0.7.1 to 0.8.0 (2780)
* Bump rayon from 1.7.0 to 1.8.0 (2782)
* Bump docker/setup-qemu-action from 2 to 3 (2767)
* Bump pypa/cibuildwheel from 2.15.0 to 2.16.0 (2768)
* Bump serde_json from 1.0.106 to 1.0.107 (2769)
* Bump chrono from 0.4.30 to 0.4.31 (2771)

We are proud to release sourmash v4.8.4, now with even fewer bugs!

In addition to the patches and updates below, we would like to announce the availability of [branchwater](https://github.com/sourmash-bio/pyo3_branchwater), a sourmash plugin that supports **fast, low-memory, and multithreaded** search, compare, and gather operations. [branchwater v0.8.0](https://github.com/sourmash-bio/pyo3_branchwater/releases/tag/v0.8.0) is now available and is between 10 and 100 times faster and lower memory than sourmash. (However, it does not support all the sourmash features; that will come with time!) Please give it a try!

Last but not least, we would like to ask people who use sourmash regularly to [fill out this form](https://docs.google.com/forms/d/e/1FAIpQLSePkHGaJqFSwiBZ9PwudV309fqQ6i9f9s4BVTBQpqXCuglJfw/viewform) so that we can include your information in some of our upcoming requests for funding support. Your use will not be made public but your support _will_ help us continue to develop sourmash!

On to the release notes for sourmash v4.8.4!

Bug fixes:

* fix exponential time explosion in `sig check` (2762)
* fix duplicate md5 in picklist problem (2747)
* avoid compressing sig files in directory output twice (2752)

Developer updates:

* Remove BIGSI and SBT code from Rust layer (2732)
* bump version to 4.8.4-dev (2720)
* build: updates spun off mastiff PR (2723)
* Build: Remove deprecated system_packages from readthedocs (2740)
* build: remove specific tooling that breaks s390x (2725)
* Add cargo deny and bump deps now that MSRV is 1.64 (2724)

Dependabot updates:

* Bump serde_json from 1.0.105 to 1.0.106 (2757)
* Bump actions/checkout from 2 to 4 (2746)
* Bump supercharge/redis-github-action from 1.6.0 to 1.7.0 (2745)
* Bump cachix/install-nix-action from 22 to 23 (2744)
* Bump ouroboros from 0.17.2 to 0.18.0 (2743)
* Bump chrono from 0.4.26 to 0.4.30 (2755)
* Bump thiserror from 1.0.47 to 1.0.48 (2742)
* Bump thiserror from 1.0.44 to 1.0.47 (2730)
* Bump serde_json from 1.0.104 to 1.0.105 (2731)
* Bump actions/upload-artifact from 1 to 3 (2729)

Minor new features:

* add support for `-E/--extension` to sig split (2712)
* add a `sourmash.cli.parse_args([...])` function (2691)
* update plugin support for argparse usage/description/epilog (2696)

Cleanup and documentation updates:

* add gtdb-rs214 info (2618, 2621, 2690)
* update JOSS paper for v4 (1361)
* fix tutorial notebook links (2633)
* Update URL for sourmash/fig.py (2586)
* change `matching_hashes.sig` to `matching-hashes.sig` in documentation (2713)
* patch lineage_summary documentation (2693)
* switch dib-lab links to sourmash-bio links in .md files (2588)

Developer updates:

* add upload token for codecov (2632)
* build: fix clippy lints and MSRV check (2680)
* maturin: move deprecated definition from Cargo.toml to pyproject.toml (2597)
* update the core documentation building packages: Sphinx, myst-parser, and docutils (2657)
* update the dependabot config to allow automatic rebases (2634)
* update version to 4.8.3-dev (2584)
* Build: bump maturin to 1.x (2650)
* Clippy beta (1.70) fix (2596)
* Fix clippy lint introduced in 1.71 beta (2630)
* fix release procedure based on v4.8.0 release (2551)
* Update docutils requirement from <0.20,>=0.17.1 to >=0.17.1,<0.21 (2611)
* Update pytest requirement from <7.4.0,>=6.2.4 to >=6.2.4,<7.5.0 (2659)
* Fix: update a manifest test to use temp directory (2689)

Dependabot updates:

* Bump cachix/install-nix-action from 20 to 21 (2625)
* Bump cachix/install-nix-action from 21 to 22 (2651)
* Bump chrono from 0.4.24 to 0.4.25 (2628)
* Bump chrono from 0.4.25 to 0.4.26 (2636)
* Bump criterion from 0.3.6 to 0.5.1 (2629)
* Bump getrandom from 0.2.9 to 0.2.10 (2645)
* Bump log from 0.4.17 to 0.4.18 (2623)
* Bump log from 0.4.18 to 0.4.19 (2641)
* Bump log from 0.4.19 to 0.4.20 (2715)
* Bump memmap2 from 0.5.10 to 0.6.1 (2613)
* Bump memmap2 from 0.6.1 to 0.6.2 (2626)
* Bump memmap2 from 0.6.2 to 0.7.0 (2643)
* Bump memmap2 from 0.7.0 to 0.7.1 (2658)
* Bump once_cell from 1.17.1 to 1.17.2 (2622)
* Bump once_cell from 1.17.2 to 1.18.0 (2635)
* Bump ouroboros from 0.15.6 to 0.17.0 (2654)
* Bump ouroboros from 0.17.0 to 0.17.2 (2687)
* Bump proptest from 1.1.0 to 1.2.0 (2627)
* Bump pypa/cibuildwheel from 2.12.1 to 2.12.3 (2590)
* Bump pypa/cibuildwheel from 2.12.3 to 2.13.0 (2624)
* Bump pypa/cibuildwheel from 2.13.0 to 2.13.1 (2642)
* Bump pypa/cibuildwheel from 2.13.1 to 2.14.0 (2673)
* Bump pypa/cibuildwheel from 2.14.0 to 2.14.1 (2681)
* Bump pypa/cibuildwheel from 2.14.1 to 2.15.0 (2716)
* Bump serde from 1.0.160 to 1.0.162 (2609)
* Bump serde from 1.0.162 to 1.0.163 (2612)
* Bump serde from 1.0.163 to 1.0.164 (2644)
* Bump serde from 1.0.164 to 1.0.166 (2666)
* Bump serde from 1.0.166 to 1.0.168 (2679)
* Bump serde_json from 1.0.100 to 1.0.103 (2682)
* Bump serde_json from 1.0.103 to 1.0.104 (2701)
* Bump serde_json from 1.0.96 to 1.0.97 (2653)
* Bump serde_json from 1.0.97 to 1.0.99 (2660)
* Bump serde_json from 1.0.99 to 1.0.100 (2675)
* Bump supercharge/redis-github-action from 1.5.0 to 1.6.0 (2700)
* Bump tempfile from 3.5.0 to 3.6.0 (2639)
* Bump tempfile from 3.6.0 to 3.7.0 (2686)
* Bump tempfile from 3.7.0 to 3.7.1 (2705)
* Bump thiserror from 1.0.40 to 1.0.43 (2674)
* Bump thiserror from 1.0.43 to 1.0.44 (2685)
* Bump wasm-bindgen from 0.2.84 to 0.2.86 (2615)
* Bump wasm-bindgen from 0.2.86 to 0.2.87 (2640)
* Bump wasm-bindgen-test from 0.3.34 to 0.3.36 (2620)
* Bump wasm-bindgen-test from 0.3.36 to 0.3.37 (2656)
* Bump web-sys from 0.3.61 to 0.3.63 (2619)
* Bump web-sys from 0.3.63 to 0.3.64 (2655)

This is a bugfix release for a `sourmash tax` bug - see 2579.

Minor new features:

* add optional reporting for duplicated names in sketch fromfile (2580)

Bug fixes:

* fix lineage_summary tax bug (2579)

Dependabot updates:

* Bump serde from 1.0.159 to 1.0.160 (2575)
* Bump serde_json from 1.0.95 to 1.0.96 (2574)

Minor new features:

* add --create-empty-results option to gather (2557)

Bug fixes:

* fix exception error when no arguments are provided to `sig intersect` (2555)

Cleanup and documentation updates:

* update `sourmash sketch` docs for building merged sketches (2563)
* fix broken crates.io badge (2556)
* add --csv to command-line docs for `compare` (2565)

Developer updates:

* Remove codecov from tox, use GH action instead (2568)

Dependabot updates:

* Update pytest requirement from <7.3.0,>=6.2.4 to >=6.2.4,<7.4.0 (2558)
* Bump tempfile from 3.4.0 to 3.5.0 (2561)
* Bump serde from 1.0.158 to 1.0.159 (2560)
* Bump getrandom from 0.2.8 to 0.2.9 (2559)