v5.2.2

Rolling back most of the newly implemented logging features because they don't seem to play nice with distributed executors. Addition of better slurm testing.

What's Changed

• Rollback logging by @Ulthran in #559

Full Changelog: v5.2.1...v5.2.2

v5.2.1

Add versioneer for automated version updates

Full Changelog: v5.1.3...v5.2.1

v5.2.0

Cluster executors were running into issues with the Sunbeam logger initialized by sunbeam run not maintaining its handlers through to the Snakefile. This release moves away from the timestamped per-run log file in favor of a configurable, static location in the project root.

What's Changed

• Bump actions/download-artifact from 4 to 5 in /.github/workflows by @dependabot[bot] in #556
• Update Conda lockfiles by @github-actions[bot] in #555
• Use config-defined log file by @Ulthran in #557

Full Changelog: v5.1.2...v5.1.3

v5.1.2

Fix versioning bug for PyPi release, fix ruleorder bug with latest snakemake release.

What's Changed

• Bump snakemake from 9.8.2 to 9.9.0 by @dependabot[bot] in #551
• Update Conda lockfiles by @github-actions[bot] in #550
• Handle ruleorder for single-end reads by @Ulthran in #554

Full Changelog: v5.1.1...v5.1.2

v5.1.1

Fix sunbeam init bug that was putting relative paths in config files.

What's Changed

• Update Conda lockfiles by @github-actions[bot] in #537
• Bump pytest from 8.4.0 to 8.4.1 by @dependabot[bot] in #538
• Bump snakemake from 9.5.1 to 9.6.1 by @dependabot[bot] in #539
• Add debug logs to project config objects by @Ulthran in #540
• Bump snakemake from 9.6.1 to 9.6.2 by @dependabot[bot] in #542
• Update Conda lockfiles by @github-actions[bot] in #541
• Bump snakemake from 9.6.2 to 9.7.1 by @dependabot[bot] in #544
• Bump pandas from 2.3.0 to 2.3.1 by @dependabot[bot] in #546
• Bump snakemake from 9.7.1 to 9.8.2 by @dependabot[bot] in #547
• Fix absolute paths in generated samples.csv by @Ulthran in #549
• Update Conda lockfiles by @github-actions[bot] in #543

Full Changelog: v5.1.0...v5.1.1

v5.1.0

Fix some oddities with --exclude/--include eating positional arguments after them. There are still certain snakemake args that will behave this way but that's unavoidable. This release also includes the new unified sunbeam logger! It uses python's logging module to keep everything neat and outputs a new file with more detailed logs for post-mortems.

What's Changed

• Add FAQ by @Ulthran in #524
• Handle empty file paths in sunbeam_config gracefully by @Ulthran in #526
• Test for target after --exclude by @Ulthran in #528
• Bump pandas from 2.2.3 to 2.3.0 by @dependabot in #530
• Bump pytest from 8.3.5 to 8.4.0 by @dependabot in #531
• Update Conda lockfiles by @github-actions in #529
• Fix integration test command by @Ulthran in #534
• Update Conda lockfiles by @github-actions in #536
• 459 improve logging consistency by @Ulthran in #532

Full Changelog: v5.0.5...v5.1.0

v5.0.5

• Fix sporadic bug with filter_reads not being able to import sunbeam lib
• Fix some doc rendering bugs
• Update pin files

What's Changed

• Update Conda lockfiles by @github-actions in #519
• No conda env for filter_reads by @Ulthran in #522

Full Changelog: v5.0.4...v5.0.5

v5.0.4

Update release workflow to work with PyPi trusted publishing

Full Changelog: v5.0.3...v5.0.4

v5.0.3

Add get_ext_version as universally available amongst extensions to find themselves

What's Changed

• Update Conda lockfiles by @github-actions in #515
• Add central get_ext_version function by @Ulthran in #518

New Contributors

• @github-actions made their first contribution in #515

Full Changelog: v5.0.2...v5.0.3

v5.0.2

What's Changed

• Bump docker/build-push-action from 5 to 6 in /.github/workflows by @dependabot in #505
• Improved release flow testing by @Ulthran in #507
• Bump docker/build-push-action from 5 to 6 in /.github/workflows by @dependabot in #508
• Bump snakemake from 9.3.3 to 9.3.4 by @dependabot in #509
• Bump snakemake from 9.3.4 to 9.4.0 by @dependabot in #510
• Bump snakemake from 9.4.0 to 9.5.1 by @dependabot in #511
• Config modify doesn't overwrite more than it should by @Ulthran in #513

New Contributors

• @dependabot made their first contribution in #505

Full Changelog: v5.0.1...v5.0.2