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1. Commits on Jul 22, 2026

   • Refresh uv.lock: patched Pillow 12.3.0, cryptography 49.0.0 (dev deps only)

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2. Commits on May 16, 2026

   • Drop Python 3.9 and 3.10; bump to v3.6.0

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   • Bump GitHub Actions to Node.js 24 successor versions

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   • Bump version to 3.5.2 and add ChangeLog entry

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   • Apply black formatting to python-kalign/__init__.py

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   • Add tests/check-local.sh — pre-push verification gate

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   • Fix DSSIM matrix mismatch; harden finalise + comparison error paths

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   • Remove benchmark CI workflow

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   • Fix Linux build: gate d2 declaration on HAVE_AVX2

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   • Fix test_module_exports: add four missing symbols

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   • Harden POAR file parsing against integer overflow

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   • Drop developer-only design docs from the source tree

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3. Commits on May 15, 2026

   • Clean up build warnings and stale libomp installs in CI

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   • Tidy design-doc references; commit parameter-cleanup PRD

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   • Remove dead code

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   • Remove paper-side benchmarks, optimizers, and PRDs

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   • Remove deprecated 'precise' mode alias; align mode docs

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   • Drop stale OMP_NUM_THREADS from cibuildwheel config

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   • Bump locked dependencies to resolve Dependabot CVEs

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4. Commits on Apr 17, 2026

   • Fix benchmark corruption bugs: temp-file race, length-invariant check, defensive buffer init

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5. Commits on Apr 1, 2026

   • Fix _mm_malloc guards, update build.zig for zig 0.15, modernize benchmark runner

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6. Commits on Mar 26, 2026

   • Add sequences to existing alignment (--add mode)

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   • Add confidence masking for ensemble alignment output

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7. Commits on Mar 25, 2026

   • Consolidate entry points, parallelize alignment pipeline

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8. Commits on Mar 24, 2026

   • Add memcheck container, parallel optimizer, and stress tests

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   • Threadpool as default parallelization, unified CLI mode presets

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9. Commits on Mar 21, 2026

   • Chase-Lev work-stealing thread pool with tests and benchmarks

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     claude

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10. Commits on Mar 19, 2026

    • Unified nucleotide presets: replace separate RNA/DNA with single preset_nucleotide()

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11. Commits on Mar 18, 2026

    • POAR consistency merge, Kimura nucleotide matrices, NSGA-III optimized presets for protein/RNA/DNA

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12. Commits on Mar 12, 2026

    • Clean 2-path architecture with per-run optimizer parameters

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    • Prior to parameter cleanup

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13. Commits on Mar 9, 2026

    • Sparse consistency bonus matrix, ensemble alignment, NSGA-III optimizer, and benchmark infrastructure

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      TimoLassmann

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      claude

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14. Commits on Feb 27, 2026

    • Bump version to 3.5.1 for PyPI re-release

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    • Fixed more github action issues

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    • Fixed some github action failures

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