MRG: 4.8.6 release branch (#2963)

release notes: https://hackmd.io/SCoVcWS1RhCH-ndQNWF-1A?view

# sourmash release v4.8.6 - release notes

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)

flake.nix

@@ -68,7 +68,7 @@
 
           sourmash = python.buildPythonPackage ( commonArgs // rec {
             pname = "sourmash";
-            version = "4.8.6-dev";
+            version = "4.8.6";
             format = "pyproject";
 
             cargoDeps = rustPlatform.importCargoLock {

pyproject.toml

@@ -9,7 +9,7 @@ build-backend = 'maturin'
 name = "sourmash"
 description = "tools for comparing biological sequences with k-mer sketches"
 readme = "README.md"
-version = "4.8.6-dev"
+version = "4.8.6"
 
 authors = [
   { name="Luiz Irber", orcid="0000-0003-4371-9659" },