v0.9.2

What's Changed

Features and improvements:

• MRG: add conda-forge shield by @bluegenes in #255
• MRG: add ANI to manysearch by @bluegenes in #256
• MRG: support prefix csv input for manysketch by @bluegenes in #243
• MRG: bump to v0.9.1-dev by @ctb in #260
• MRG: avoid printing out 0s by @ctb in #265
• MRG: index should error out if no sigs to index by @bluegenes in #267
• MRG: bump version to v0.9.2 by @ctb in #277

Dependency updates:

• Update pytest requirement from <8.1.0,>=6.2.4 to >=6.2.4,<8.2.0 by @dependabot in #270
• Bump env_logger from 0.11.2 to 0.11.3 by @dependabot in #271
• Bump anyhow from 1.0.80 to 1.0.81 by @dependabot in #275
• Bump rustworkx-core from 0.14.1 to 0.14.2 by @dependabot in #274
• Bump conda-incubator/setup-miniconda from 3.0.2 to 3.0.3 by @dependabot in #261

Full Changelog: v0.9.1...v0.9.2

v0.9.1

Updates and features:

• Add graph-based clustering with cluster (#234)
• Enable singleton sketching, facilitate reads-based sketching in manysketch (#184)
• Use updated core GatherResult to enable full results from fastmultigather(#205)
• Add ANI output to pairwise, multisearch (#236)
• Use core manifest utils (#217)

Dependency updates:

• Bump conda-incubator/setup-miniconda from 3.0.1 to 3.0.2 (#242)
• Bump env_logger from 0.10.2 to 0.11.2 (#240)
• Bump pyo3 from 0.20.2 to 0.20.3 (#241)
• bump to v0.9.1-dev (#230)
• Bump anyhow from 1.0.79 to 1.0.80 (#227)
• Bump assert_cmd from 2.0.13 to 2.0.14 (#229)

v0.9.0

What's Changed

This release significantly refactors Zip file loading and improves its performance; it is now the suggested way to work with large collections of small sketches. Support for standalone manifest CSVs has also been added.

Major and minor updates:

• MRG: use updated rocksdb-integrated sourmash core by @bluegenes in #134
• MRG: use core Collection and Select for sig loading by @bluegenes in #197
• MRG: enable loading manifest files by @bluegenes in #211
• MRG: remove eprintln from manifest loading by @ctb in #218
• MRG: parallelize collection_from_pathlist by @ctb in #221
• MRG: fix manifest protein k-mer sizes by @bluegenes in #224
• MRG: update docs for v0.9.0 by @ctb in #213

Miscellany:

• Bump predicates from 3.0.4 to 3.1.0 by @dependabot in #191
• Bump env_logger from 0.10.1 to 0.10.2 by @dependabot in #193
• Bump rayon from 1.8.0 to 1.8.1 by @dependabot in #192
• Bump actions/cache from 3 to 4 by @dependabot in #194
• MRG: bump version to 0.8.7-dev by @ctb in #195
• Bump serde from 1.0.195 to 1.0.196 by @dependabot in #200
• Bump serde_json from 1.0.111 to 1.0.113 by @dependabot in #199
• Update pytest requirement from <7.5.0,>=6.2.4 to >=6.2.4,<8.1.0 by @dependabot in #201
• Bump env_logger from 0.10.2 to 0.11.1 by @dependabot in #209
• Bump tempfile from 3.9.0 to 3.10.0 by @dependabot in #208

Full Changelog: v0.8.6...v0.9.0

v0.8.6

What's Changed

• MRG: update osx install instructions for new conda-forge install by @ctb in #168
• Bump anyhow from 1.0.75 to 1.0.76 by @dependabot in #170
• Bump serde_json from 1.0.108 to 1.0.109 by @dependabot in #172
• Bump tempfile from 3.8.1 to 3.9.0 by @dependabot in #173
• Bump pyo3 from 0.20.0 to 0.20.1 by @dependabot in #175
• Bump anyhow from 1.0.76 to 1.0.79 by @dependabot in #176
• MRG: minor doc updates by @ctb in #177
• MRG: bump to dev version 0.8.6-dev by @ctb in #179
• Bump pyo3 from 0.20.1 to 0.20.2 by @dependabot in #183
• Bump serde from 1.0.193 to 1.0.195 by @dependabot in #182
• Bump serde_json from 1.0.109 to 1.0.111 by @dependabot in #186
• Bump assert_cmd from 2.0.12 to 2.0.13 by @dependabot in #185
• MRG: Add the pairwise subcommand by @mr-eyes in #181
• MRG: bump version to 0.8.6 by @ctb in #189

Full Changelog: v0.8.5...v0.8.6

v0.8.5

What's Changed

• Bump conda-incubator/setup-miniconda from 3.0.0 to 3.0.1 by @dependabot in #159
• MRG: update docs by @ctb in #161
• MRG: update MacOS builds in support of conda-forge releases. by @ctb in #165
• MRG: bump version to 0.8.5 for release by @ctb in #166
• MRG: fix a minor typo in README by @ctb in #162

Full Changelog: v0.8.4...v0.8.5

v0.8.4

What's Changed

• Bump serde from 1.0.192 to 1.0.193 by @dependabot in #155
• Bump conda-incubator/setup-miniconda from 2.2.0 to 3.0.0 by @dependabot in #154
• MRG: fix error for large manysketch zips (> 4G) by @bluegenes in #157
• MRG: rename pyo3_branchwater to sourmash_plugin_branchwater by @ctb in #156
• MRG: bump version to 0.8.4 by @ctb in #158

Full Changelog: v0.8.3...v0.8.4

v0.8.3

What's Changed

• Bump tempfile from 3.8.0 to 3.8.1 by @dependabot in #143
• Bump serde from 1.0.189 to 1.0.190 by @dependabot in #144
• Bump serde_json from 1.0.107 to 1.0.108 by @dependabot in #145
• MRG: set authors in pyproject.toml by @ctb in #146
• Bump serde from 1.0.190 to 1.0.192 by @dependabot in #150
• Bump env_logger from 0.10.0 to 0.10.1 by @dependabot in #149
• Add "compilers" to environment.yml by @olgabot in #151
• MRG: update version to 0.8.3 by @ctb in #153

New Contributors

• @olgabot made their first contribution in #151

Full Changelog: v0.8.2...v0.8.3

v0.8.2

What's Changed

• MRG: fix reporting bug introduced in #123 by @bluegenes in #126
• Bump rayon from 1.7.0 to 1.8.0 by @dependabot in #128
• MRG: only load zip paths with compatible sketches by @bluegenes in #130
• MRG: allow search/gather with protein moltypes by @bluegenes in #132
• Bump csv from 1.2.2 to 1.3.0 by @dependabot in #137
• MRG: read sig.gz_{n} sigs from zipfiles by @bluegenes in #136
• MRG: update documentation for manysketch and index by @ctb in #138
• Bump pyo3 from 0.19.2 to 0.20.0 by @dependabot in #140
• Bump serde from 1.0.188 to 1.0.189 by @dependabot in #139
• MRG: bump to v0.8.2 by @ctb in #142

Full Changelog: v0.8.1...v0.8.2

v0.8.1

What's Changed

• MRG: add dependabot config by @ctb in #117
• Bump serde_json from 1.0.105 to 1.0.107 by @dependabot in #119
• Bump actions/checkout from 3 to 4 by @dependabot in #118
• Bump predicates from 3.0.3 to 3.0.4 by @dependabot in #120
• MRG: clearer message for manysketch by @bluegenes in #121
• MRG: actually iterate through reads by @bluegenes in #123
• MRG: fix clippy stuff; bump to v0.8.1 by @ctb in #124

New Contributors

• @dependabot made their first contribution in #119

Full Changelog: v0.8.0...v0.8.1

v0.8.0

What's Changed

• MRG: replace info with eprintln by @ctb in #90
• MRG: rename rust functions to match CLI. by @ctb in #93
• MRG: add query_name and query_md5 to gather & prefetch output by @ctb in #94
• MRG: report load sketch errors by @ctb in #97
• MRG: enable multithreaded sketching to zip file (manysketch) by @bluegenes in #88
• MRG: break up lib.rs into many different files by @ctb in #101
• MRG: clean lib.rs for new structure by @bluegenes in #104
• MRG: add utility functions for zip reading; use in index, multisearch by @bluegenes in #105
• MRG: enable zipfile loading for manysearch by @bluegenes in #99
• MRG: add zip reading to fastmultigather by @bluegenes in #106
• MRG: add zip loading for fastgather by @bluegenes in #112
• MRG: run cargo fmt --all on the entire codebase by @ctb in #116
• RELEASE: update docs for new zipfile support! by @ctb in #110

Full Changelog: v0.7.1...v0.8.0