PPanGGOLiN 2.3.2

Minor Changes

• Refactor and optimize RGP clustering by @tlemane and @JeanMainguy in #392
• Support Python 3.10–3.13 and drop Python 3.9 by @JeanMainguy in #399
• Replace custom GenBank parsing with gb-io by @mnsoln in #397
• Replace Aragorn subprocess with pyaragorn by @fathirramadhan-web in #402
• Automated release workflow by @JeanMainguy in #404

Bug Fixes

• Fix GEXF namespace so the pangenome graph can be parsed by @ggautreau in #388
• Improve parsing and error handling for malformed genome/file-path and FASTA inputs by @JeanMainguy in #405
• Partition reproducibility by @rsiminel in #408
• Open the pangenome read-only when only reading it by @ggautreau in #389

Documentation

• Move CONTRIBUTING doc for GitHub detection by @JeanMainguy in #385
• Add generated command-line reference documentation by @JeanMainguy in #386
• Refactor command line documentation and improve RGP clustering details by @jpjarnoux in #391
• Add example input files to align and projection documentation by @JeanMainguy in #393
• Display default values of arguments in help text by @JeanMainguy in #396
• Normalize CLI help by @JeanMainguy in #395
• Improve tab wording by @JeanMainguy in #406
• Regenerate and commit the generated command reference when CLI changes by @JeanMainguy in #407
• Add CITATION.cff by @goelakash in #398

New Contributors

A big thank you to our new contributors for their first contributions to PPanGGOLiN:

• @mnsoln for replacing the custom GenBank parser with gb-io in #397
• @goelakash for adding CITATION.cff in #398
• @fathirramadhan-web for replacing the Aragorn subprocess with pyaragorn in #402

Full Changelog: 2.3.1...2.3.2