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Published February 17, 2021 | Version v4.0.0rc1
Software Open

dib-lab/sourmash: v4.0.0rc1

Creators

  • 1. University of California, Davis
  • 2. @dib-lab - @ucdavis
  • 3. @BlockSigner
  • 4. @czbiohub
  • 5. CZ BioHub
  • 6. @dib-lab
  • 7. @github
  • 8. @pqdev
  • 9. Profile picture credit goes to XKCD
  • 10. xmnlab
  • 11. @gitlabhq
  • 12. @10xgenomics
  • 13. @pyupio

Description

This is a pre-release version of sourmash v4.0.0. Draft release notes are below; comments appreciated!

Major changes for 4.0

4.0 is a major new version of sourmash, and it contains a number of new and breaking features.

Please see our migration guide for more information on how to migrate from v3.x to version 4.0!

New or changed behavior
  • default SBT storage is now .sbt.zip (#1174, #1170)
  • add sourmash sketch command for creating signatures (#1159)
  • protein ksizes in MinHash are now divided by 3, except in sourmash compute (#1277)
  • refactor MinHash API and implementation: add, iadd, merge, hashes, and max_hash (#1282, #1154, #1139, #1301)
  • add HyperLogLog implementation (#1223)
  • SourmashSignature.name is now a property (not a method): use str(sig) instead of name() (#1179, #1232)
  • lca summarize no longer merges all signatures, and uses hash abundance by default (#1175)
  • indexand lca index (#1186, #1222) now support --from-file and no longer require signature files on command line
  • --traverse-directory is now on by default for signature loading behavior (#1178)
Feature removal
  • remove Python 2.7 support (& end Python 2 compatibility) (#1145, #1144)
  • remove lca gather (#1307)
  • remove 10x support from sourmash compute (#1229)
  • remove 'dump' command (#1157)
Feature/function deprecations
  • deprecate sourmash compute (#1159)
  • deprecate load_signatures, sourmash.load_one_signature, create_sbt_index, and load_sbt_index (#1279, #1304)
  • deprecate import_csv in favor of new sourmash sig import --csv (#1281)
Refactoring, improvements, and minor bug fixes:
  • accept file list in sourmash sig cat (#1236)
  • add unique_intersect_bp and gather_result_rank to gather CSV output (#1219)
  • remove deprecated minhash functions (#1149)
  • fix Rust panic error in signature creation (#1172)
  • cache nodes in SBT during search (#1161)
  • fix two bugs in gather --output-unassigned (#1156)
  • Refactor the gather code so that it uses 'hashes' instead of 'mins' (#1329)
  • Update output from gather w/o abundances, so that abund output is empty instead of 0(#1328)
Documentation updates
  • substantial revisions and updates to the documentation (#1283)
  • add information about versioning, migrations, etc to the docs (#1153)
Infrastructure and CI changes:
  • update finch requirement from 0.3.0 to 0.4.1 (#1290)
  • update rand for test, and activate "js" feature for getrandom (#1275)
  • dev updates (configs and doc) (#1298)
  • move wheel building from Travis to GitHub Actions (#1295)
  • fix new clippy warnings from Rust 1.49 (#1267)
  • use tox for running tests locally (#696)
  • CI: small build fixes (#1252)
  • CI: Fix releases in GitHub Actions (#1250)
  • update build_wheel action paths
  • CI: moving python tests from travis to GH actions (#1249)
  • CI: move wheel building to GitHub actions (#1244)
  • remove last .rst file from docs (#1185)
  • update CI for latest branch name change (#1150)

Files

dib-lab/sourmash-v4.0.0rc1.zip

Files (19.0 MB)

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Additional details

Related works

Is supplement to
https://github.com/dib-lab/sourmash/tree/v4.0.0rc1 (URL)