Sourmash

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

Please see [our migration guide](https://sourmash.readthedocs.io/en/latest/support.html#migrating-from-sourmash-v3-x-to-sourmash-v4-x) for more information on how to migrate from v3.x to version 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](https://github.com/dib-lab/sourmash/issues) if your results change!

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)
* `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)
* 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)

Feature deprecations

* add deprecation warning for `sourmash compute --input-is-10x` (1326)
* add warnings about new `sourmash lca summarize` behavior (1326)
* add warning for new behavior of `MinHash.merge(...)` (1326)
* add deprecation warning for `TarStorage` (1165)

Infrastructure and CI changes:

* Backport github actions to stable branch (3.5.x) (1317)

This is the first of several minor releases (v3.5.x) from the new `stable` branch. These releases focus on preparing for sourmash v4.0 by introducing deprecations and warnings for features that will be removed in v4.0.

Refactoring and deprecations:
* `MinHash` class refactoring (1128, 1129); many deprecations for 4.0 and 5.0
* `sourmash dump` deprecated, for removal in 4.0 (1147)
* `import sourmash_lib` deprecated, for removal in 4.0 (1143)

Cleanup:
* remove mentions of ijson and khmer (no longer needed dependencies) 1140

Documentation:
* Simplify and clean up README (1124)
* Add sourmash logo to docs and README (1127)
* update release process and release notes (1125)

Rust:
* Update typed-builder requirement from 0.6.0 to 0.7.0 (1121)

Major new features:
* Document `sourmash.fig` usage and behavior; enable output of `compare` clustering with labels (859)
* Adds --majority option to `lca classify` using majority vote algorithm (1113)

Minor improvements:
* MinHash compatibility check to sourmash sig intersect (1116)

Bugs fixed:
* add ksize selectors back into sourmash sig functions (1105)

Documentation updates:
* Minor updates to release procedure (1102)
* Update DB links in docs (1084)

Major new features:
* enable seamless loading of signatures from indexed databases (1059, 1083, 1090)
* add `signature cat` and `signature split` commands to combine/split signature files (1044, 1074)
* add compute-optimized MinHash (for small scaled or large cardinalities) in Rust (1045)
* optionally weight lca summarize output by hashval abundance. (1022)
* enable moltypes other than DNA in LCA databases (1013)

Minor improvements:
* add --num-results/-n to gather (1047)
* improve lca index error message when inserting num signature (1076)
* autodetect FASTA/FASTQ files if given as signatures (1078)
* add is_lineage_match, pop_to_rank, make_lineage to lca_utils (1081)
* use stricter niffler versions and add new gz feature to it (1070)
* added `MinHash.clear()` and `MinHash.add_hash_with_abundance` to Python API (1046)

Bugs fixed:
* investigations and fixes around new gather behavior. (1001)

Refactoring:
* move tests from `test_lca` into `test_lca_functions` (1035)
* remove unused run_shell_cmd function (1032)
* refactor some tests in test_sourmash.py to use utils.in_tempdir decorators (1020)
* use install scripts from py-ipfs-http-client (1068)

Documentation:
* Improve documentation around abundance projection (1073)
* Replace recommonmark with myst (docs) (1021)
* Fix doctest filename error (1040)

Thanks to luizirber ctb bluegenes erikyoung85 for their contributions!