MRG: 4.8.7 release branch (#3090)

# Release notes for sourmash v4.8.7

Note: This release changes the way `sourmash multigather` names output
files in some situations. Please see
#2722 for details.

Minor new features:

* support proper manifest creation with `--relpath` for `sig check` and
`sig collect` (#3054)
* fix `multigather` output by adding md5sum along with
`-U/--output-add-query-md5sum` (#2722)
* enable loading lineages from annotated gather with match_name instead
of name (#3078)

Bug fixes:

* fix output for `sketch ... --singleton` (#3066)
* fix `calculate_gather_stats` `threshold=0` bug (#3052)

Cleanup and documentation updates:

* adjust protein ksize for record/manifest (#3019)
* Resolve `sourmash gather --help` issue (#3032)
* rework the manifest documentation; do misc cleanup (#3027)
* add branchwater web to docs (#3018)

Developer updates:

* make core Manifest booleans python compatible (core) (#3007)
* safer ksize selection while still accommodating k=k*3 (#3028)
* fix clippy beta issues (#3088)
* tell dependabot to ignore upgrades to `byteorder`, `chrono`,
`once_cell`, and `wasm-bindgen` (#3065)
* update rust changelog for r0.13.0 in preparation for release (#3033)
* Allow changing storage location for a collection in RevIndex (#3015)
* Fix tox and nix configs so all tox tests execute correctly (#2992)
* Calculate all gather stats in rust; use for rocksdb gather (#2943)
* bump screed req to 1.1.3 (#3067)
* bump to v4.8.7-dev (#2989)

Dependabot updates:

* Bump DeterminateSystems/magic-nix-cache-action from 1 to 3 (#2994)
* Bump DeterminateSystems/magic-nix-cache-action from 3 to 4 (#3085)
* Bump DeterminateSystems/nix-installer-action from 4 to 9 (#2995)
* Bump DeterminateSystems/nix-installer-action from 9 to 10 (#3083)
* Bump chrono from 0.4.33 to 0.4.34 (#3000)
* Bump conda-incubator/setup-miniconda from 3.0.1 to 3.0.2 (#3046)
* Bump conda-incubator/setup-miniconda from 3.0.2 to 3.0.3 (#3057)
* Bump histogram from 0.9.0 to 0.9.1 (#3002)
* Bump itertools from 0.12.0 to 0.12.1 (#3043)
* Bump log from 0.4.20 to 0.4.21 (#3062)
* Bump num-iter from 0.1.43 to 0.1.44 (#2997)
* Bump pypa/cibuildwheel from 2.16.5 to 2.17.0 (#3084)
* Bump rayon from 1.8.1 to 1.9.0 (#3058)
* Bump roaring from 0.10.2 to 0.10.3 (#3014)
* Bump serde from 1.0.196 to 1.0.197 (#3045)
* Bump serde_json from 1.0.113 to 1.0.114 (#3044)
* Bump tempfile from 3.10.0 to 3.10.1 (#3059)
* Bump thiserror from 1.0.56 to 1.0.57 (#2999)
* Bump thiserror from 1.0.57 to 1.0.58 (#3082)
* Bump wasm-bindgen from 0.2.91 to 0.2.92 (#3060)
* Bump wasm-bindgen-test from 0.3.40 to 0.3.41 (#2996)
* Bump wasm-bindgen-test from 0.3.41 to 0.3.42 (#3063)
* Bump web-sys from 0.3.67 to 0.3.68 (#2998)
* Bump web-sys from 0.3.68 to 0.3.69 (#3061)
* Revert "Bump wasm-bindgen from 0.2.91 to 0.2.92 (#3060)" (#3064)
* Update asv to 0.6.2 (#3025)
* Update pytest requirement from <8.1.0,>=6.2.4 to >=6.2.4,<8.2.0
(#3075)

flake.nix

@@ -68,7 +68,7 @@
 
           sourmash = python.buildPythonPackage ( commonArgs // rec {
             pname = "sourmash";
-            version = "4.8.6";
+            version = "4.8.7";
             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 = "4.8.7-dev"
+version = "4.8.7"
 
 authors = [
   { name="Luiz Irber", orcid="0000-0003-4371-9659" },