MRG: 4.8.7 release branch

[ctb]

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 (MRG: 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 (MRG: 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 (MRG: enable loading lineages from annotated gather with match_name instead of name #3078)

Bug fixes:

• fix output for sketch ... --singleton (MRG: fix output for sketch ... --singleton #3066)
• fix calculate_gather_stats threshold=0 bug (MRG: fix calculate_gather_stats threshold=0 bug #3052)

Cleanup and documentation updates:

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

Developer updates:

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

Dependabot updates:

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

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 86.88%. Comparing base (cfe6a96) to head (459b7ff).

Additional details and impacted files

@@            Coverage Diff             @@
##           latest    #3090      +/-   ##
==========================================
+ Coverage   86.86%   86.88%   +0.02%     
==========================================
  Files         136      136              
  Lines       15552    15543       -9     
  Branches     2637     2637              
==========================================
- Hits        13509    13505       -4     
+ Misses       1741     1736       -5     
  Partials      302      302              

Flag	Coverage Δ
hypothesis-py	25.44% <ø> (ø)
python	92.87% <ø> (ø)
rust	61.45% <ø> (+0.05%)	⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

[ctb]

Release candidate testing:

• Command line tests pass for a release candidate
• All eight release candidate wheels are built

Releasing to PyPI:

• RC tag(s)s deleted on github
• Release tag cut
• Release notes written
• All eight release wheels built
• Release wheels uploaded to pypi
• tar.gz distribution uploaded to pypi

After release to PyPI and conda-forge/bioconda packages built:

• PyPI page updated
• Zenodo DOI successfully minted upon new github release - see search results
• pip install sourmash installs the correct version
• conda-forge sourmash-minimal-feedstock has updated sourmash-minimal to the correct version
• mamba create -n smash-release -y sourmash installs the correct version

Optional but recommended:

• PR submitted to update pyodide version
• PR submitted to update spack version