sourmash v4.0 release notes

We are pleased to announce release 4.0 of sourmash! This release contains many feature improvements and new functionality, as well as many breaking changes with sourmash 2.x and 3.x.

Please see our migration guide for guidance on updating to sourmash v4, and post questions about migrating to sourmash 4.0 in the sourmash issue tracker.

Major changes for 4.0

Numerical output and search results are unchanged

There are no changes to numerical output or search results in this release; you should get the same results with v4 as you get with v3, except where command-line parameters need to be adjusted as noted below (see: protein ksize #1277, lca summarize changes #1175, sourmash gather on signatures without abundance #1328). Please file an issue if your results change!

New or changed behavior

  • default SBT storage is now (#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)

  • 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)

  • index and 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)

  • sourmash sketch and sourmash compute no longer create empty signatures from empty files and stdin (#1347)

  • sourmash sketch and sourmash compute set sig.filename to empty string when filename is - (#1347)

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)

Documentation updates

  • major update and cleanup of docs given new functionality; add sourmash sketch documentation (#1283)

  • add information about versioning, migrations, etc to the docs (#1153, #1283)

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)