MRG: 4.8.9 release branch

[ctb]

Minor new features:

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

Bug fixes:

• fix remaining_bp output from sourmash gather (MRG: fix remaining_bp output from sourmash gather #3195)
• fix RocksDB-based gather & other rust-based infelicities revealed by plugins (MRG: fix RocksDB-based gather & other rust-based infelicities revealed by plugins #3193, MRG: fix cargo fmt for updated disk_revindex.rs code #3197)
• use correct denominator in f_unique_to_query (MRG: use correct denominator in f_unique_to_query #3138)

Cleanup and documentation updates:

• update JOSS for sourmash v4 (MRG: update JOSS for sourmash v4 #3114, upd JOSS title capitalization #3203, MRG: add pyproject->zenodo script and file #3209)
• fix links to taxonomy spreadsheets (MRG: fix links to taxonomy spreadsheets #3119)
• fix description of f_unique_weighted (MRG: fix description of f_unique_weighted #3164)

Developer updates:

• transition internal signature loading functions (MRG: transition internal signature loading functions #3161)
• allow get/set record.filename (MRG: allow get/set record.filename #3121)
• round a number that is losing precision in 15th place in test_distance_utpy (MRG: round a number that is losing precision in 15th place in test_distance_utils.py #3126)
• disable ppc64le wheel building (MRG: disable ppc64le wheel building #3127)
• prepare to remove sourmash compute for sourmash v5.0 (MRG: prepare to remove sourmash compute for sourmash v5.0 #3103)
• add rustup target x86_64-apple-darwin (MRG: add rustup target x86_64-apple-darwin #3148)
• mv .cargo/config to config.toml (MRG: mv .cargo/config to config.toml #3147)
• fix clippy warnings about max_value (MRG: fix clippy warnings about max_value #3146)
• bump to v4.8.9-dev (MRG: bump to v4.8.9-dev #3135)
• update src/core/CHANGELOG.md for sourmash-rs core release r0.14.0 (MRG: 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 (Bump DeterminateSystems/nix-installer-action from 11 to 12 #3184)
• Bump DeterminateSystems/magic-nix-cache-action from 6 to 7 (Bump DeterminateSystems/magic-nix-cache-action from 6 to 7 #3185)
• Bump statrs from 0.16.0 to 0.16.1 (Bump statrs from 0.16.0 to 0.16.1 #3186)
• Bump serde from 1.0.202 to 1.0.203 (Bump serde from 1.0.202 to 1.0.203 #3175)
• Bump ouroboros from 0.18.3 to 0.18.4 (Bump ouroboros from 0.18.3 to 0.18.4 #3176)
• Bump itertools from 0.12.1 to 0.13.0 (Bump itertools from 0.12.1 to 0.13.0 #3166)
• Bump camino from 1.1.6 to 1.1.7 (Bump camino from 1.1.6 to 1.1.7 #3169)
• Bump serde from 1.0.201 to 1.0.202 (Bump serde from 1.0.201 to 1.0.202 #3168)
• Bump thiserror from 1.0.60 to 1.0.61 (Bump thiserror from 1.0.60 to 1.0.61 #3167)
• Bump pypa/cibuildwheel from 2.18.0 to 2.18.1 (Bump pypa/cibuildwheel from 2.18.0 to 2.18.1 #3165)
• Bump DeterminateSystems/magic-nix-cache-action from 4 to 6 (Bump DeterminateSystems/magic-nix-cache-action from 4 to 6 #3157)
• Bump DeterminateSystems/nix-installer-action from 10 to 11 (Bump DeterminateSystems/nix-installer-action from 10 to 11 #3156)
• Bump pypa/cibuildwheel from 2.17.0 to 2.18.0 (Bump pypa/cibuildwheel from 2.17.0 to 2.18.0 #3155)
• Bump serde_json from 1.0.116 to 1.0.117 (Bump serde_json from 1.0.116 to 1.0.117 #3159)
• Bump thiserror from 1.0.59 to 1.0.60 (Bump thiserror from 1.0.59 to 1.0.60 #3158)
• Bump serde from 1.0.200 to 1.0.201 (Bump serde from 1.0.200 to 1.0.201 #3160)
• Bump roaring from 0.10.3 to 0.10.4 (Bump roaring from 0.10.3 to 0.10.4 #3142)
• Bump histogram from 0.10.0 to 0.10.1 (Bump histogram from 0.10.0 to 0.10.1 #3141)
• Bump getrandom from 0.2.14 to 0.2.15 (Bump getrandom from 0.2.14 to 0.2.15 #3143)
• Bump num-iter from 0.1.44 to 0.1.45 (Bump num-iter from 0.1.44 to 0.1.45 #3140)
• Bump jinja2 from 3.1.3 to 3.1.4 (Bump jinja2 from 3.1.3 to 3.1.4 #3145)
• Bump serde from 1.0.199 to 1.0.200 (Bump serde from 1.0.199 to 1.0.200 #3144)
• Bump serde from 1.0.198 to 1.0.199 (Bump serde from 1.0.198 to 1.0.199 #3130)
• Bump conda-incubator/setup-miniconda from 3.0.3 to 3.0.4 (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 (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 (Bump myst-parser from 2.0.0 to 3.0.1 #3133)
• Bump thiserror from 1.0.58 to 1.0.59 (Bump thiserror from 1.0.58 to 1.0.59 #3123)
• Bump serde_json from 1.0.115 to 1.0.116 (Bump serde_json from 1.0.115 to 1.0.116 #3124)
• Bump serde from 1.0.197 to 1.0.198 (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 (Update docutils requirement from <0.21,>=0.17.1 to >=0.17.1,<0.22 #3116)

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 86.69%. Comparing base (d7ea4b9) to head (e1d49e3).
Report is 72 commits behind head on latest.

Additional details and impacted files

@@           Coverage Diff           @@
##           latest    #3200   +/-   ##
=======================================
  Coverage   86.69%   86.69%           
=======================================
  Files         136      136           
  Lines       15841    15841           
  Branches     2716     2716           
=======================================
  Hits        13734    13734           
  Misses       1797     1797           
  Partials      310      310           

Flag	Coverage Δ
hypothesis-py	25.35% <ø> (ø)
python	92.33% <ø> (ø)
rust	62.29% <ø> (ø)

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