v0.11.7

What's Changed

• Bump actions/checkout from 4 to 5 by @dependabot[bot] in #336
• MRG: remove genbank_genomes; bump get-some-ncbi-genomes; rm lxml by @ctb in #341
• MRG: upgrade get-some-ncbi-genomes -> handle empty display names by @ctb in #342

Full Changelog: v0.11.6...v0.11.7

v0.11.6

What's Changed

• MRG: fix asserts; bump version by @ctb in #333

Full Changelog: v0.11.5...v0.11.6

To upgrade, try the following:

genome-grist run conf.yml gather_reads --touch
genome-grist run conf.yml gather_reads
genome-grist run conf.yml summarize_gather --touch
genome-grist run conf.yml summarize_mapping —touch

v0.11.5

What's Changed

• MRG: minor updates, performance improvements, and fixes by @ctb in #327

Full Changelog: v0.11.4...v0.11.5

Updating to version 0.11.5 from early version of 0.11.x.

This release adds some significant performance improvements by switching to polars and parquet. By default, genome-grist will rerun all of the mapping to genomes. However, there is no need to do this; you can run the following commands after updating:

genome-grist run conf.yml gather_reads --touch
genome-grist run conf.yml summarize_gather --touch
genome-grist run conf.yml summarize_mapping —touch

v0.11.4

What's Changed

• MRG: include Snakefile in pkg again by @bluegenes in #324

Full Changelog: v0.11.3...v0.11.4

v0.11.3

What's Changed

• MRG: fix version info & quickstart; update links. Bump to v0.11.3. by @ctb in #323

Full Changelog: v0.11.2...v0.11.3

v0.11.2

What's Changed

New features:

• MRG: add script to remove idents from manifest before search by @ctb in #321

Automated updates:

• Update pytest requirement from <7.5.0,>=5.1.2 to >=5.1.2,<8.1.0 by @dependabot in #310
• Bump conda-incubator/setup-miniconda from 2 to 3 by @dependabot in #302
• Bump actions/setup-python from 4 to 5 by @dependabot in #303
• Bump pytest-dependency from 0.5.1 to 0.6.0 by @dependabot in #305
• Bump actions/cache from 3 to 4 by @dependabot in #309

Full Changelog: v0.11.1...v0.11.2

v0.11.1

What's Changed

• MRG: simplify Snakefile by using new singlesketch output format; add retries to download genomes; bump ver by @ctb in #319

Full Changelog: v0.11.0...v0.11.1

v0.11.0

What's Changed

• Bump snakemake from 7.18.2 to 7.19.1 by @dependabot in #261
• Bump lxml from 4.9.1 to 4.9.2 by @dependabot in #260
• Bump snakemake from 7.19.1 to 7.20.0 by @dependabot in #264
• MRG: Ignore DeprecationWarning from sourmash in tests. by @ctb in #270
• Bump snakemake from 7.20.0 to 7.24.0 by @dependabot in #269
• Bump snakemake from 7.24.0 to 7.24.2 by @dependabot in #272
• Bump snakemake from 7.24.2 to 7.25.0 by @dependabot in #274
• Update pandas, pytest, and sourmash requirements. by @dependabot in #275
• Update pytest requirement from <7.4.0,>=5.1.2 to >=5.1.2,<7.5.0 by @dependabot in #289
• Bump lxml from 4.9.2 to 4.9.3 by @dependabot in #292
• MRG: fix sketch command in configuring doc by @ctb in #299
• MRG: fix list in output doc by @ctb in #300
• Bump actions/checkout from 3 to 4 by @dependabot in #298
• WIP: update genome-grist to modern days (May 2025) by @ctb in #313

Full Changelog: v0.9.3...v0.11.0

v0.9.3

What's Changed

• [MRG] update ignore_ident code for later use too by @ctb in #259

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

v0.9.2

What's Changed

• [MRG] add code to support skipping genomes by ident by @ctb in #255
• [MRG] update snakemake version in environment.yml, & other minor fixes by @ctb in #253
• [MRG] add gh-pages deploy action by @ctb in #252
• [MRG] add pip check to GitHub actions by @ctb in #254
• [MRG] update github actions to use modern conda/caching by @ctb in #256
• [MRG] update actions to make sure right version(s) are being used by @ctb in #258

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