MRG: 4.8.9 release branch (#3200)

Minor new features:

* add `--set-name` to `sig intersect` and `sig subtract` (#3162)
* upgrade `sig overlap` and `sig subtract` to load more than JSON
signatures (#3153)
* force continue past `tax genome` classification errors (#3100)

Bug fixes:

* fix `remaining_bp` output from sourmash gather (#3195)
* fix RocksDB-based gather & other rust-based infelicities revealed by
plugins (#3193, #3197)
* use correct denominator in f_unique_to_query (#3138)

Cleanup and documentation updates:

* update JOSS for sourmash v4 (#3114, #3203, #3209)
* fix links to taxonomy spreadsheets (#3119)
* fix description of `f_unique_weighted` (#3164)

Developer updates:

* transition internal signature loading functions (#3161)
* allow get/set record.filename (#3121)
* round a number that is losing precision in 15th place in
`test_distance_utpy` (#3126)
* disable ppc64le wheel building (#3127)
* prepare to remove `sourmash compute` for sourmash v5.0 (#3103)
* add rustup target x86_64-apple-darwin (#3148)
* mv `.cargo/config` to `config.toml` (#3147)
* fix clippy warnings about max_value (#3146)
* bump to v4.8.9-dev (#3135)
* update src/core/CHANGELOG.md for sourmash-rs core release r0.14.0
(#3199)

Dependabot updates:

* Bump DeterminateSystems/nix-installer-action from 11 to 12 (#3184)
* Bump DeterminateSystems/magic-nix-cache-action from 6 to 7 (#3185)
* Bump statrs from 0.16.0 to 0.16.1 (#3186)
* Bump serde from 1.0.202 to 1.0.203 (#3175)
* Bump ouroboros from 0.18.3 to 0.18.4 (#3176)
* Bump itertools from 0.12.1 to 0.13.0 (#3166)
* Bump camino from 1.1.6 to 1.1.7 (#3169)
* Bump serde from 1.0.201 to 1.0.202 (#3168)
* Bump thiserror from 1.0.60 to 1.0.61 (#3167)
* Bump pypa/cibuildwheel from 2.18.0 to 2.18.1 (#3165)
* Bump DeterminateSystems/magic-nix-cache-action from 4 to 6 (#3157)
* Bump DeterminateSystems/nix-installer-action from 10 to 11 (#3156)
* Bump pypa/cibuildwheel from 2.17.0 to 2.18.0 (#3155)
* Bump serde_json from 1.0.116 to 1.0.117 (#3159)
* Bump thiserror from 1.0.59 to 1.0.60 (#3158)
* Bump serde from 1.0.200 to 1.0.201 (#3160)
* Bump roaring from 0.10.3 to 0.10.4 (#3142)
* Bump histogram from 0.10.0 to 0.10.1 (#3141)
* Bump getrandom from 0.2.14 to 0.2.15 (#3143)
* Bump num-iter from 0.1.44 to 0.1.45 (#3140)
* Bump jinja2 from 3.1.3 to 3.1.4 (#3145)
* Bump serde from 1.0.199 to 1.0.200 (#3144)
* Bump serde from 1.0.198 to 1.0.199 (#3130)
* Bump conda-incubator/setup-miniconda from 3.0.3 to 3.0.4 (#3131)
* Update pytest requirement from <8.2.0,>=6.2.4 to >=6.2.4,<8.3.0
(#3132)
* Bump myst-parser from 2.0.0 to 3.0.1 (#3133)
* Bump thiserror from 1.0.58 to 1.0.59 (#3123)
* Bump serde_json from 1.0.115 to 1.0.116 (#3124)
* Bump serde from 1.0.197 to 1.0.198 (#3122)
* Update docutils requirement from <0.21,>=0.17.1 to >=0.17.1,<0.22
(#3116)

flake.nix

@@ -68,7 +68,7 @@
 
           sourmash = python.buildPythonPackage ( commonArgs // rec {
             pname = "sourmash";
-            version = "4.8.8";
+            version = "4.8.9";
             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 = "4.8.9-dev"
+version = "4.8.9"
 
 authors = [
   { name="Luiz Irber", orcid="0000-0003-4371-9659" },