1.0.0

Main improvements

• Significantly improved consensus calling accuracy around small deletions
• Significantly improved consensus calling accuracy around large clip-dominant deletions in --realign mode for some alignments
• Fixed issue with difflib.SequenceMatcher where identifying overlaps in clip-dominant regions could fail unexpectedly
  • Fixes related TypeError with --realign enabled (reported by @sivico26)
• Faster installation and consensus generation

Other changes

• Added support for Python versions up to 3.13, offering significant performance improvements
• Minimum Python version increased from 3.6 to 3.8
• Replaced Biopython with dnaio for sequence IO
• Testing improvements:
  • Expected consensus sequences now are validated by the test suite, guarding against regressions
  • Added clip-dominant test case helpfully shared by @sivico26 (#23)
  • Test suite now runs in CI with both newest and oldest supported Python versions
• Moved to pyproject.toml with Flit build backend
• Added Ruff pre-commit

Breaking changes

• Removed:
  • kindel variants
  • Plotting functions other than kindel plot-clips (renamed in this release to kindel plot)

Please open an issue if this release causes problems or breaks your workflow.