MRG: small docs fixes and updates #3681
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Ready for review & merge @sourmash-bio/devs |
doc/command-line.md
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| @@ -197,6 +205,7 @@ Optional arguments: | |||
| ``` | |||
| ### `sourmash compare` - compare many signatures | |||
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| **Note:** As of 2025, we have a much faster implementation of `compare` called `multisearch` available in [the branchwater plugin](https://github.com/sourmash-bio/sourmash_plugin_branchwater). It is multithreaded and should be (at worst) equivalent in memory usage, although it does accept a slightly more restricted set of inputs than `compare`. | |||
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Much lower in memory I think --will have to look at benchmarking in the issues. Compare is just not even feasible at large scale.
doc/command-line.md
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| Related commands: | ||
| * `sourmash compare` will compare many sketches to many sketches. | ||
| * `sourmash prefetch` is an upgraded version of `search` that returns more information in the output CSV file. | ||
| * `sourmash scripts multisearch` from [the branchwater plugin](https://github.com/sourmash-bio/sourmash_plugin_branchwater) will search multiple sketches against a database. |
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Did you mean manysearch here instead of multisearch? If yes, maybe add: ...and provides abundance-weighted results/information. If not, maybe worth mentioning here too?
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Hmm, it's possible I'm just thinking of the memory reductions from using pairwise, I can't seem to find multisearch vs compare benchmarking at the moment. |
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Both are good catches, thanks! I was being lazy on the memory statement - I think you're right, it's much lower memory. |
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@bluegenes see adc884e. |
Cleanup and documentation updates: * minor updates to release docs (#3695) * small docs fixes and updates (#3681) Developer updates: * release core 0.21.0 (#3712) Dependabot updates: * Build(deps): Bump camino from 1.1.9 to 1.1.10 (#3669) * Build(deps): Bump cfg-if from 1.0.0 to 1.0.1 (#3689) * Build(deps): Bump conda-incubator/setup-miniconda from 3.1.1 to 3.2.0 (#3676) * Build(deps): Bump getset from 0.1.5 to 0.1.6 (#3700) * Build(deps): Bump prefix-dev/setup-pixi from 0.8.8 to 0.8.10 (#3688) * Build(deps): Bump proptest from 1.6.0 to 1.7.0 (#3674) * Build(deps): Bump pypa/cibuildwheel from 2.23.3 to 3.0.0 (#3687) * Build(deps): Bump roaring from 0.10.12 to 0.11.0 (#3702) * Build(deps): Update maturin requirement from <1.9.0,>=1 to >=1,<1.10.0 (#3699) * Build(deps): Update pytest requirement from <8.4.0,>=6.2.4 to >=6.2.4,<8.5.0 (#3670) * EXP: Revert "Build(deps): Bump pypa/cibuildwheel from 2.23.3 to 3.0.0 (#3687) (#3691) * [pre-commit.ci] pre-commit autoupdate (#3668) * [pre-commit.ci] pre-commit autoupdate (#3673) * [pre-commit.ci] pre-commit autoupdate (#3698)
Many miscellaneous doc updates, fixes, and upgrades.
query=>matchinf_unique_to_querydescription (ref Application off_unique_to_queryandthreshold_bp#3154)sourmash-minimalconda-forge package to release checklist (add conda-forge & sourmash-minimal into release checklist #3112)fastgather,fastmultigather, andmultisearchto docs (ref deprecatesourmash multigatherfor 5.0 #1614 (comment), updatemultigatherdocumentation to be clearer, and to recommendfastmultigather#3069)betterplotplugin tosourmash plotdocs (build an ordination plot (NMDS? PCoA?) on top of sourmash compare distance matrices #2900)sigsubcommands (sig mergeincorrectly claims that it only outputs JSON sigs #2891)TODO:
Fixes #3112
Fixes #3069
Fixes #3055
Fixes #3004
Fixes #2900
Fixes #2891
Fixes #3653
Fixes #3543