4.1.0

What's Changed

• Feature: extend barcode collection search by @marcomoscasgr in #323
• Bump setuptools from 70.0.0 to 70.1.1 by @dependabot in #329
• Bump sqlalchemy from 2.0.30 to 2.0.31 by @dependabot in #327
• Bump setuptools from 70.1.1 to 70.2.0 by @dependabot in #330
• Bump setuptools from 70.2.0 to 70.3.0 by @dependabot in #331
• Bump setuptools from 70.3.0 to 71.0.0 by @dependabot in #339
• Bump setuptools from 71.0.0 to 71.1.0 by @dependabot in #343
• Bump pytest from 8.2.2 to 8.3.1 by @dependabot in #342
• Bump pytest from 8.3.1 to 8.3.2 by @dependabot in #345
• Bump cryptography from 42.0.8 to 43.0.0 by @dependabot in #344
• update container labels by @avnishsinghh in #346
• Bump setuptools from 71.1.0 to 72.1.0 by @dependabot in #347
• Bump black from 24.4.2 to 24.8.0 by @dependabot in #348
• Bump setuptools from 72.1.0 to 72.2.0 by @dependabot in #351
• Bump sqlalchemy from 2.0.31 to 2.0.32 by @dependabot in #349
• Bump setuptools from 72.2.0 to 73.0.0 by @dependabot in #352
• Bump yattag from 1.15.2 to 1.16.0 by @dependabot in #350
• Bump setuptools from 73.0.0 to 73.0.1 by @dependabot in #353
• Bump setuptools from 73.0.1 to 74.0.0 by @dependabot in #355
• Add missing database connection pool arguments by @kjsanger in #357

New Contributors

• @avnishsinghh made their first contribution in #346

Full Changelog: 4.0.2...4.1.0

4.0.2

What's Changed

• Bump partisan from 2.10.0 to 2.10.2 by @kjsanger in #326

Full Changelog: 4.0.1...4.0.2

4.0.1

What's Changed

• Set ACL zone for study/sample metadata updates by @kjsanger in #324

Full Changelog: 4.0.0...4.0.1

4.0.0

What's Changed

• Bump setuptools from 69.5.1 to 70.0.0 by @dependabot in #313
• Bump structlog from 24.1.0 to 24.2.0 by @dependabot in #316
• Bump cryptography from 42.0.7 to 42.0.8 by @dependabot in #319
• Bump pytest from 8.2.1 to 8.2.2 by @dependabot in #320
• Fix study/sample metadata updates not updating permissions by @kjsanger in #318
• Fix association of VFC files with related CRAM files by @kjsanger in #322

Full Changelog: 3.1.4...4.0.0

3.1.4

What's Changed

• Bump pytest from 8.2.0 to 8.2.1 by @dependabot in #311
• Bump pymysql from 1.1.0 to 1.1.1 by @dependabot in #314
• Fix performance issue where debug code was left in production by @kjsanger in #315

Full Changelog: 3.1.3...3.1.4

3.1.3

What's Changed

• Fix and simplify the Illumina split_name function by @kjsanger in #312

Full Changelog: 3.1.2...3.1.3

3.1.2

What's Changed

• Fix argument name missed when refactoring by @kjsanger in #310

Full Changelog: 3.1.1...3.1.2

3.1.1

What's Changed

• Bump pyenv from 2.3.12 to 2.4.1 by @kjsanger in #309

Full Changelog: 3.1.0...3.1.1

3.1.0

What's Changed

• Bump black from 24.4.0 to 24.4.1 by @dependabot in #294
• Bump black from 24.4.1 to 24.4.2 by @dependabot in #297
• Bump pytest from 8.1.1 to 8.2.0 by @dependabot in #296
• Add option to find legacy Infinium microarray data by @kjsanger in #295
• Refactoring by @kjsanger in #298
• Make db_config the primary name for database configurations by @kjsanger in #299
• Add support for updating Sequenom metadata in iRODS by @kjsanger in #300
• Bump cryptography from 42.0.5 to 42.0.7 by @dependabot in #304
• Bump sqlalchemy from 2.0.29 to 2.0.30 by @dependabot in #302
• Add iRODS 4.3.2, remove 4.3-nightly by @kjsanger in #305
• Fix handling of PendingRollbackError when processing large datasets by @kjsanger in #307
• Add ONT year runs meta-report by @kjsanger in #306
• Bump yattag from 1.14.0 to 1.15.2 by @dependabot in #308

Full Changelog: 3.0.1...3.1.0

3.0.1

What's Changed

• Fix skip-missing-runs argument type by @kjsanger in #293

Full Changelog: 3.0.0...3.0.1