PPanGGOLiN 2.1.1

Bug Fixes

• Added support for Python 3.11 and 3.12 by @JeanMainguy (issues #253 and #268, PR #255).
• Fixed handling of Aragorn genes that exceed contig length by @JeanMainguy (issue #254, PR #256).
• Fixed output configuration in workflow commands when set in the config file by @JeanMainguy (PR #261).
• Sort gene families in the TSV file by cluster size and alphabetically by gene to ensure consistent output across runs by @jpjarnoux (issue #263, PR #265).
• Fixed issue in projection when using a spotless pangenome by @JeanMainguy (issue #264, PR #266).
• Added a warning log for partition failures to improve error visibility, as a first step towards better handling of partitioning issues by @JeanMainguy (issue #262, PR #269).
• Minor code improvements and typo corrections in the documentation and source by @fchapoton (#257, #258, and #259).

New Contributors

• We thank @fchapoton for their first contributions in #257, #258, and #259.

Full Changelog: 2.1.0...2.1.1