MRG: rework the manifest documentation; do misc cleanup #3027
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…urmash into manifest_relpath
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This was referenced Mar 5, 2024
…o update_sig_collect
…o update_sig_collect
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Ready for review & merge, @sourmash-bio/devs ! |
bluegenes
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Co-authored-by: Tessa Pierce Ward <bluegenes@users.noreply.github.com>
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# 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)
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This PR:
sourmash sig collectoutput where it said "loaded 0 signatures"TODO:
sig manifestdocs to point out that they do not generate standalone manifestssig checkandsig collectto tell people to expand their paths refsig collectshould resolve to individual files when loading a pathlist or a directory #3039MultiIndex#3040Related issues:
sourmash sig manifeston zip files yields unusable standalone manifest CSVs #3009 by recommendingsig collectandsig checkinstead ofsig manifestfor making standalone manifestssig collectshould resolve to individual files when loading a pathlist or a directory #3039MultiIndex#3040