release notes for sourmash v4.8.5

[ctb]

editing here: https://hackmd.io/jlTSEgzlR6GO9_X9dmZgGQ?view

sourmash release notes v4.8.5

This release drops support for Python < 3.10, and also reorganizes and expands the documentation substantially!

Major new features:

• Drop Python 3.8 and 3.9, default to Python 3.10 for most CI tasks (Drop 3.8 and 3.9, default to 3.10 for most CI tasks #2848)
• Revise documentation structure; add internals page. (MRG: revise documentation structure; add internals page. #2184)
• Adjust documentation to recommend tax over lca for taxonomic analysis (MRG: adjust documentation to recommend tax over lca for taxonomic analysis #2777)

Bug fixes:

• make sourmash plot labels/indices arguments make sense (MRG: make sourmash plot labels/indices arguments make sense #2790)

Cleanup and documentation updates:

• Various minor updates to docs (MRG: Various minor updates to docs #2854)
• Deps: update typed-builder and histogram, bump MSRV to 1.65 (Deps: update typed-builder and histogram, bump MSRV to 1.65 #2858)
• Fix wheel building and semver checks post r0.12.0 (CI: Fix wheel building and semver checks post r0.12.0 #2857)
• Added seed to parameter strings add seed to param string docs #1732 (Added seed to parameter strings #1732 #2836)
• Add link for developer documentation to sidebar (add link for developer documentation to sidebar #2847)
• add explicit install tutorial (MRG: add explicit install tutorial #2826)
• fix many minor documentation nits (MRG: fix many minor documentation nits #2814)
• update docs for tax grep: only searches tax (MRG: update docs for tax grep: only searches tax #2789)
  *add usage docs for sig import/ingest (MRG: add usage docs for sig import/ingest #2785)

Developer updates:

• Feat: on-disk RevIndex based on RocksDB (Feat: on-disk RevIndex based on RocksDB #2230)
• Fix many warnings from PYTHONDEVMODE=1 (Fix many warning from PYTHONDEVMODE=1 #2849)
• Build: Fix Rust 1.75 beta lints; flake update (Build: Fix Rust 1.75 beta lints; flake update #2841)
• try pinning maturin to <1.3.0 to fix dev build CI (EXP: try pinning maturin to <1.3.0 to fix dev build CI #2799)
• minor updates to release procedure after 4.8.4 (MRG: minor updates to release procedure after 4.8.4 #2783)
• run rust checks always (MRG: run rust checks always #2787)
• add __all__ to sig/__main__.py (MRG: add __all__ to sig/__main__.py #2778)
• bump version to 4.8.5-dev (MRG: bump version to 4.8.5-dev #2766)

Dependabot updates:

• Bump ouroboros from 0.18.0 to 0.18.1 (Bump ouroboros from 0.18.0 to 0.18.1 #2875)
• Bump once_cell from 1.18.0 to 1.19.0 (Bump once_cell from 1.18.0 to 1.19.0 #2874)
• Bump actions/setup-python from 4 to 5 (Bump actions/setup-python from 4 to 5 #2873)
• Bump cachix/cachix-action from 12 to 13 (Bump cachix/cachix-action from 12 to 13 #2861)
• Bump conda-incubator/setup-miniconda from 3.0.0 to 3.0.1 (Bump conda-incubator/setup-miniconda from 3.0.0 to 3.0.1 #2860)
• Bump cachix/install-nix-action from 23 to 24 (Bump cachix/install-nix-action from 23 to 24 #2859)
• Bump rkyv from 0.7.40 to 0.7.42 (Bump rkyv from 0.7.40 to 0.7.42 #2863)
• Bump csv from 1.2.0 to 1.3.0 (Bump csv from 1.2.0 to 1.3.0 #2862)
• Bump roaring from 0.10.1 to 0.10.2 (Bump roaring from 0.10.1 to 0.10.2 #2865)
• Bump web-sys from 0.3.65 to 0.3.66 (Bump web-sys from 0.3.65 to 0.3.66 #2864)
• Bump byteorder from 1.4.3 to 1.5.0 (Bump byteorder from 1.4.3 to 1.5.0 #2866)
• Bump proptest from 1.3.1 to 1.4.0 (Bump proptest from 1.3.1 to 1.4.0 #2837)
• Bump getrandom from 0.2.10 to 0.2.11 (Bump getrandom from 0.2.10 to 0.2.11 #2839)
• Bump web-sys from 0.3.64 to 0.3.65 (Bump web-sys from 0.3.64 to 0.3.65 #2838)
• Bump wasm-bindgen-test from 0.3.37 to 0.3.39 (Bump wasm-bindgen-test from 0.3.37 to 0.3.39 #2853)
• Bump wasm-bindgen from 0.2.88 to 0.2.89 (Bump wasm-bindgen from 0.2.88 to 0.2.89 #2850)
• Bump mymindstorm/setup-emsdk from 12 to 13 (Bump mymindstorm/setup-emsdk from 12 to 13 #2851)
• Bump conda-incubator/setup-miniconda from 2.2.0 to 3.0.0 (Bump conda-incubator/setup-miniconda from 2.2.0 to 3.0.0 #2852)
• Bump wasm-bindgen from 0.2.87 to 0.2.88 (Bump wasm-bindgen from 0.2.87 to 0.2.88 #2834)
• Bump serde_json from 1.0.107 to 1.0.108 (Bump serde_json from 1.0.107 to 1.0.108 #2829)
• Bump tempfile from 3.8.0 to 3.8.1 (Bump tempfile from 3.8.0 to 3.8.1 #2828)
• Bump bytecount from 0.6.5 to 0.6.7 (Bump bytecount from 0.6.5 to 0.6.7 #2830)
• Bump bytecount from 0.6.4 to 0.6.5 (Bump bytecount from 0.6.4 to 0.6.5 #2822)
• Bump thiserror from 1.0.49 to 1.0.50 (Bump thiserror from 1.0.49 to 1.0.50 #2823)
• Bump actions/setup-node from 3 to 4 (Bump actions/setup-node from 3 to 4 #2821)
• Bump rustix from 0.37.20 to 0.37.25 (Bump rustix from 0.37.20 to 0.37.25 #2817)
• Bump pypa/cibuildwheel from 2.16.1 to 2.16.2 (Bump pypa/cibuildwheel from 2.16.1 to 2.16.2 #2808)
• Bump memmap2 from 0.8.0 to 0.9.0 (Bump memmap2 from 0.8.0 to 0.9.0 #2807)
• Bump byteorder from 1.4.3 to 1.5.0 (Bump byteorder from 1.4.3 to 1.5.0 #2806)
• Bump pypa/cibuildwheel from 2.16.0 to 2.16.1 (Bump pypa/cibuildwheel from 2.16.0 to 2.16.1 #2797)
• Bump thiserror from 1.0.48 to 1.0.49 (Bump thiserror from 1.0.48 to 1.0.49 #2796)
• Bump proptest from 1.2.0 to 1.3.1 (Bump proptest from 1.2.0 to 1.3.1 #2795)
• Bump bytecount from 0.6.3 to 0.6.4 (Bump bytecount from 0.6.3 to 0.6.4 #2794)
• Bump memmap2 from 0.7.1 to 0.8.0 (Bump memmap2 from 0.7.1 to 0.8.0 #2780)
• Bump rayon from 1.7.0 to 1.8.0 (Bump rayon from 1.7.0 to 1.8.0 #2782)
• Bump docker/setup-qemu-action from 2 to 3 (Bump docker/setup-qemu-action from 2 to 3 #2767)
• Bump pypa/cibuildwheel from 2.15.0 to 2.16.0 (Bump pypa/cibuildwheel from 2.15.0 to 2.16.0 #2768)
• Bump serde_json from 1.0.106 to 1.0.107 (Bump serde_json from 1.0.106 to 1.0.107 #2769)
• Bump chrono from 0.4.30 to 0.4.31 (Bump chrono from 0.4.30 to 0.4.31 #2771)

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checklists

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

[ctb]

sourmash-minimal-feedstock is broken, of course, presumably by the same thing that is preventing branchwater from compiling.

[ctb]

yep - on OSX, error: aligned deallocation function of type 'void (void *, std::align_val_t) noexcept' is only available on macOS 10.13 or newer - link to log

[ctb]

linux has succeeded tho! 🎉

[ctb]

conda-forge/sourmash-minimal-feedstock#55 fixed the sourmash-minimal build, and #2879 updated sourmash itself.

[ctb]

closing since a more recent release will catch the undone things. #2991