v0.9.12

What's Changed

Changes and additions:

• MRG: switch to importlib.metadata from pkg_resources (into main) by @ctb in #547
• MRG: add --output-all-comparisons to manysearch, multisearch, and pairwise by @ctb in #544* MRG: update to (prospective) sourmash r0.18.0 by @ctb in #548
• MRG: add capacity for skipmer sketching and search by @bluegenes in #531
• MRG: integrate sketching utils from directsketch by @bluegenes in #516

Updates:

• Bump pyo3 from 0.22.6 to 0.23.1 by @dependabot in #530
• Bump serde from 1.0.214 to 1.0.215 by @dependabot in #528
• Bump serde_json from 1.0.132 to 1.0.133 by @dependabot in #529
• Bump pyo3 from 0.23.1 to 0.23.2 by @dependabot in #537
• Bump anyhow from 1.0.93 to 1.0.94 by @dependabot in #541
• Bump serde from 1.0.215 to 1.0.216 by @dependabot in #545
• Bump pyo3 from 0.23.2 to 0.23.3 by @dependabot in #540

Full Changelog: v0.9.11...v0.9.12

v0.9.11

What's Changed

• Add probability of overlap and weighted containment for Multisearch matches by @olgabot in #458
• MRG: fix a variety of small clippy issues by @ctb in #518
• MRG: update code after sourmash fix to Collection::sig_from_record() by @ctb in #514
• MRG: add --input-moltype to singlesketch by @ctb in #515
• MRG: bump to version 0.9.11 by @ctb in #522

Full Changelog: v0.9.10...v0.9.11

v0.9.10

What's Changed

• Bump pyo3 from 0.22.5 to 0.22.6 by @dependabot in #509
• Bump anyhow from 1.0.92 to 1.0.93 by @dependabot in #507
• Bump tempfile from 3.13.0 to 3.14.0 by @dependabot in #506
• Bump csv from 1.3.0 to 1.3.1 by @dependabot in #508
• MRG: fix sketch downsampling across the plugin, incl fastmultigather, manysearch, and multisearch by @ctb in #504
• MRG: bump version to 0.9.10 by @ctb in #511

Full Changelog: v0.9.9...v0.9.10

v0.9.9

What's Changed

• Add clang to environment yml by @olgabot in #465
• Bump anyhow from 1.0.89 to 1.0.90 by @dependabot in #486
• Bump serde_json from 1.0.128 to 1.0.132 by @dependabot in #485
• Bump pyo3 from 0.22.4 to 0.22.5 by @dependabot in #484
• Set up pixi for development environment by @luizirber in #470
• Bump serde from 1.0.210 to 1.0.213 by @dependabot in #490
• Bump anyhow from 1.0.90 to 1.0.91 by @dependabot in #489
• Python Black Formatting by @olgabot in #492
• MRG: choose default scaled for multiple collections based on first collection by @ctb in #488
• MRG: switch to using in_dir instead of try/finally for one last test by @ctb in #487
• MRG: rename internal file & functions to use 'rocksdb' by @ctb in #494
• MRG: update sourmash to r0.17.0 by @ctb in #500
• Bump anyhow from 1.0.91 to 1.0.92 by @dependabot in #496
• Update pytest-cov requirement from <6.0,>=2.12 to >=2.12,<7.0 by @dependabot in #495
• MRG: Fix scaled determination in fastgather and fastmultigather by @ctb in #498
• MRG: bump to v0.9.9 by @ctb in #502

New Contributors

• @luizirber made their first contribution in #470

Full Changelog: v0.9.8...v0.9.9

v0.9.8

What's Changed

• MRG: update function signatures to remove remaining warnings by @ctb in #422
• [MRG] Add --save-matches to fastmultigather by @mr-eyes in #397
• MRG: bump to in-dev version 0.9.8 by @ctb in #429
• Bump serde_json from 1.0.124 to 1.0.125 by @dependabot in #433
• Bump camino from 1.1.7 to 1.1.9 by @dependabot in #432
• Bump serde from 1.0.206 to 1.0.208 by @dependabot in #431
• MRG: bump sourmash to v0.15.1 by @ctb in #435
• Bump serde from 1.0.208 to 1.0.209 by @dependabot in #443
• Bump serde_json from 1.0.125 to 1.0.127 by @dependabot in #442
• MRG: misc cleanup by @ctb in #424
• MRG: optionally, create empty results files for in-memory fastmultigather by @bluegenes in #446
• MRG: add .PHONY targets to Makefile by @ctb in #449
• Bump serde_json from 1.0.127 to 1.0.128 by @dependabot in #453
• Bump anyhow from 1.0.86 to 1.0.87 by @dependabot in #454
• Bump serde from 1.0.209 to 1.0.210 by @dependabot in #452
• Bump pyo3 from 0.22.2 to 0.22.3 by @dependabot in #457
• Bump anyhow from 1.0.87 to 1.0.89 by @dependabot in #456
• Add hp, dayhoff options to manysketch by @olgabot in #345
• Bump tempfile from 3.12.0 to 3.13.0 by @dependabot in #461
• Bump sourmash from 0.15.1 to 0.15.2 by @dependabot in #460
• Add singlesketch command by @mr-eyes in #459
• MRG: fix performance regression in manysearch by removing unnecessary downsampling by @ctb in #464
• Bump pyo3 from 0.22.3 to 0.22.4 by @dependabot in #474
• MRG: update to code for forthcoming sourmash release by @ctb in #467
• MRG: add generic support for any type of sketch collection as query or database by @ctb in #430
• MRG: avoid clones by using new Signature::try_into() -> KmerMinHash by @ctb in #471
• MRG: update to v0.9.8 by @ctb in #475

Full Changelog: v0.9.7...v0.9.8

v0.9.7

What's Changed

• MRG: provide --internal-storage and --no-internal-storage for index by @ctb in #390
• MRG: add pretty printing option to manysearch command by @ctb in #408
• MRG: update documentation for RocksDB index and internal/external storage, + miscellaneous improvements by @ctb in #416
• MRG: bump version to 0.9.7 by @ctb in #419

Dependabot updates:

• Update pytest requirement from <8.3.0,>=6.2.4 to >=6.2.4,<8.4.0 by @dependabot in #396
• Bump pyo3 from 0.22.1 to 0.22.2 by @dependabot in #395
• Bump predicates from 3.1.0 to 3.1.2 by @dependabot in #403
• Bump tempfile from 3.10.1 to 3.11.0 by @dependabot in #405
• Bump serde_json from 1.0.120 to 1.0.122 by @dependabot in #404
• Bump assert_cmd from 2.0.14 to 2.0.15 by @dependabot in #402
• Bump sourmash from 0.14.1 to 0.15.0 by @dependabot in #399
• Bump env_logger from 0.11.3 to 0.11.5 by @dependabot in #401
• Bump tempfile from 3.11.0 to 3.12.0 by @dependabot in #414
• Bump assert_cmd from 2.0.15 to 2.0.16 by @dependabot in #412
• Bump serde from 1.0.204 to 1.0.206 by @dependabot in #413
• Bump serde_json from 1.0.122 to 1.0.124 by @dependabot in #411

Full Changelog: v0.9.6...v0.9.7

v0.9.6

What's Changed

• MRG: bump to v.0.9.6-dev by @ctb in #367
• MRG: write manysketch --singleton sketches incrementally to reduce memory usage by @bluegenes in #375
• MRG: add abund estimation to manysearch by @bluegenes in #302
• MRG: update zip crate to 2.0 by @bluegenes in #385
• MRG: fix deprecated method warning in lib.rs by @ctb in #391
• MRG: add error-exit in fastmultigather against rocksdb for failed gather by @ctb in #392
• MRG: add additional weighted information to manysearch output by @ctb in #388
• MRG: bump to v0.9.6 for release by @ctb in #393

Dependabot updates:

• Bump simple-error from 0.3.0 to 0.3.1 by @dependabot in #369
• Bump log from 0.4.21 to 0.4.22 by @dependabot in #373
• Bump rustworkx-core from 0.14.2 to 0.15.1 by @dependabot in #371
• Bump serde_json from 1.0.117 to 1.0.119 by @dependabot in #370
• Bump serde_json from 1.0.119 to 1.0.120 by @dependabot in #383
• Bump serde from 1.0.203 to 1.0.204 by @dependabot in #384
• Bump pyo3 from 0.21.2 to 0.22.1 by @dependabot in #382

Full Changelog: v0.9.5...v0.9.6

v0.9.5

What's Changed

• MRG: update ReportType string output by @ctb in #359
• MRG: fix fastgather query_bp and query_n_hashes to restore tax compatibility by @bluegenes in #353
• MRG: write self comparisons for all sketches with --write-all by @ctb in #360
• MRG: fix ANI from non-rocksdb gather output by @ctb in #361
• MRG: update docs and -h messages for v0.9.5 release by @ctb in #364

Full Changelog: v0.9.4...v0.9.5

v0.9.4

What's Changed

Changes:

• MRG: parallelize loading sketches into memory by @bluegenes in #292
• MRG: fix minor typo/improve pairwise docs by @ctb in #336
• MRG: update test name for github CI to tests_on_linux by @ctb in #344
• MRG: fixed RocksDB-based fastmultigather by @ctb in #348
• MRG: bump version to 0.9.4, upgrade sourmash req by @ctb in #351
• MRG: fix lint error, & processed sig reporting for rocksdb/fastmultigather by @ctb in #320
• MRG: fix CI build & tests by @ctb in #325
• MRG: write full gather result from fastgather and non-rocksdb fastmultigather by @bluegenes in #298

Dependabot updates:

• Bump rayon from 1.9.0 to 1.10.0 by @dependabot in #290
• Bump sourmash from 0.13.0 to 0.13.1 by @dependabot in #289
• Update pytest-cov requirement from <5.0,>=2.12 to >=2.12,<6.0 by @dependabot in #288
• Bump serde_json from 1.0.114 to 1.0.115 by @dependabot in #294
• Bump anyhow from 1.0.81 to 1.0.82 by @dependabot in #300
• Bump serde from 1.0.197 to 1.0.198 by @dependabot in #306
• Bump serde_json from 1.0.115 to 1.0.116 by @dependabot in #305
• Bump pyo3 from 0.20.3 to 0.21.2 by @dependabot in #307
• Bump conda-incubator/setup-miniconda from 3.0.3 to 3.0.4 by @dependabot in #317
• Bump serde from 1.0.198 to 1.0.199 by @dependabot in #315
• Update pytest requirement from <8.2.0,>=6.2.4 to >=6.2.4,<8.3.0 by @dependabot in #314
• Bump serde from 1.0.199 to 1.0.200 by @dependabot in #323
• Bump anyhow from 1.0.82 to 1.0.83 by @dependabot in #335
• Bump serde from 1.0.200 to 1.0.201 by @dependabot in #333
• Bump serde_json from 1.0.116 to 1.0.117 by @dependabot in #332
• Bump camino from 1.1.6 to 1.1.7 by @dependabot in #339
• Bump anyhow from 1.0.83 to 1.0.86 by @dependabot in #340
• Bump serde from 1.0.201 to 1.0.202 by @dependabot in #338
• Bump serde from 1.0.202 to 1.0.203 by @dependabot in #343

Full Changelog: v0.9.3...v0.9.4

v0.9.3

What's Changed

• MRG: bump version to v0.9.3-dev by @ctb in #278
• MRG: fix manysketch naming bug by @bluegenes in #284
• MRG: fail-exit when 0 signatures are loaded from a collection by @bluegenes in #282
• MRG: bump version to 0.9.3 by @ctb in #286

Full Changelog: v0.9.2...v0.9.3