Prep extra for release: cleanup, security fixes, dep bumps#66

Merged

TimoLassmann merged 29 commits into

mainfrom

May 16, 2026

Commits on Mar 9, 2026

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

TimoLassmann
and
claude
committed

Commits on Mar 12, 2026

Commits on Mar 18, 2026

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

TimoLassmann
and
claude
committed

Commits on Mar 19, 2026

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

TimoLassmann
and
claude
committed

Commits on Mar 21, 2026

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

TimoLassmann
and
claude
committed

Commits on Mar 24, 2026

Commits on Mar 25, 2026

Consolidate entry points, parallelize alignment pipeline

TimoLassmann
and
claude
committed

Commits on Mar 26, 2026

Commits on Apr 1, 2026

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

TimoLassmann
and
claude
committed

Commits on Apr 17, 2026

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

TimoLassmann
and
claude
committed

Commits on May 15, 2026

Commits on May 16, 2026