chore(deps): update dependency sourmash to v4.8.12 #306
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This PR contains the following updates:
==4.8.4->==4.8.12Release Notes
sourmash-bio/sourmash (sourmash)
v4.8.12Compare Source
Developer updates:
Manifest::intersect_manifestto Rust core (#3305)sig_from_recordto use scaled fromRecordto downsample (#3387)HashFunctions(#3344)CollectionSet(#3397)KmerMinHash; fixRevIndex::gatherbug aroundscaled. (#3342)FSStorage::load_sigencounters more than oneSignaturein a JSON record (#3333)RocksDB::openon bad directory (#3306)calculate_gather_statsto disallow repeated downsampling (#3352)ScaledType(#3364)csv_summary(#3311)Dependabot and pre-commit CI updates:
v4.8.11Compare Source
Minor new features:
Bug fixes:
Cleanup and documentation updates:
Developer updates:
Dependabot updates:
v4.8.10Compare Source
This release is accompanied by the publication of a JOSS paper: “sourmash v4: A multitool to quickly search, compare, and analyze genomic and metagenomic data sets”, our new citation handle!
Minor new features:
selectparameters; enforce types when building manifests (#3212)sig extractto no longer create empty zips (#3214)Bug fixes:
Cleanup and documentation updates:
Developer updates:
Dependabot updates:
v4.8.9Compare Source
Minor new features:
--set-nametosig intersectandsig subtract(#3162)sig overlapandsig subtractto load more than JSON signatures (#3153)tax genomeclassification errors (#3100)Bug fixes:
remaining_bpoutput from sourmash gather (#3195)Cleanup and documentation updates:
f_unique_weighted(#3164)Developer updates:
test_distance_utpy(#3126)sourmash computefor sourmash v5.0 (#3103).cargo/configtoconfig.toml(#3147)Dependabot updates:
v4.8.8Compare Source
We are proud to report that sourmash v4.8.8 has been accepted after peer review by pyOpenSci! See the review here!
Major new features:
Dependabot updates:
v4.8.7Compare Source
Note: This release changes the way
sourmash multigathernames output files in some situations. Please see https://github.com/sourmash-bio/sourmash/pull/2722 for details.Minor new features:
--relpathforsig checkandsig collect(#3054)multigatheroutput by adding md5sum along with-U/--output-add-query-md5sum(#2722)Bug fixes:
sketch ... --singleton(#3066)calculate_gather_statsthreshold=0bug (#3052)Cleanup and documentation updates:
sourmash gather --helpissue (#3032)Developer updates:
byteorder,chrono,once_cell, andwasm-bindgen(#3065)Dependabot updates:
v4.8.6Compare Source
Minor new features:
taxgather reading flexibility (#2986)KmerMinHash::mergein core (#2973)compareandplot, for better customization (#2598)sourmash tax(#2608)Bug fixes:
tax metagenometo work on gather output created with--estimate-ani-ci(#2952)GatherResult(#2962)search --containmentandprefetch(#2971)Documentation updates:
gatherandprefetchoutput (#2954)Developer updates:
Dependabot updates:
v4.8.5Compare Source
This release drops support for Python < 3.10, and also reorganizes and expands the documentation substantially!
Major new features:
taxoverlcafor taxonomic analysis (#2777)Bug fixes:
sourmash plotlabels/indices arguments make sense (#2790)Cleanup and documentation updates:
*add usage docs for
sig import/ingest(#2785)Developer updates:
PYTHONDEVMODE=1(#2849)__all__tosig/__main__.py(#2778)Dependabot updates:
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