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

Merged

TimoLassmann merged 29 commits into

mainfrom

extra

May 16, 2026

Merged

Prep extra for release: cleanup, security fixes, dep bumps#66
TimoLassmann merged 29 commits into
mainfrom
extra

Commits on Mar 9, 2026
- Sparse consistency bonus matrix, ensemble alignment, NSGA-III optimizer, and benchmark infrastructure
  
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  bfbf450
Commits on Mar 12, 2026
- Prior to parameter cleanup
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  f0cf213
- Clean 2-path architecture with per-run optimizer parameters
  
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  claude
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  ae4ce12
Commits on Mar 18, 2026
- POAR consistency merge, Kimura nucleotide matrices, NSGA-III optimized presets for protein/RNA/DNA
  
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  claude
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  32e555d
Commits on Mar 19, 2026
- Unified nucleotide presets: replace separate RNA/DNA with single preset_nucleotide()
  
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  claude
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  9208173
Commits on Mar 21, 2026
- Chase-Lev work-stealing thread pool with tests and benchmarks
  
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  claude
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  ccaa5a9
Commits on Mar 24, 2026
- Threadpool as default parallelization, unified CLI mode presets
  
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  claude
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  3e84b9a
- Add memcheck container, parallel optimizer, and stress tests
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  adb215a
Commits on Mar 25, 2026
- Consolidate entry points, parallelize alignment pipeline
  
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  8fd3daf
Commits on Mar 26, 2026
- Add confidence masking for ensemble alignment output
  
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  1002f0a
- Add sequences to existing alignment (--add mode)
  
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  53abded
Commits on Apr 1, 2026
- Fix _mm_malloc guards, update build.zig for zig 0.15, modernize benchmark runner
  
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  280a40e
Commits on Apr 17, 2026
- Fix benchmark corruption bugs: temp-file race, length-invariant check, defensive buffer init
  
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  claude
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  79f325b
Commits on May 15, 2026
- Bump locked dependencies to resolve Dependabot CVEs
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  67308a1
- Drop stale OMP_NUM_THREADS from cibuildwheel config
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  2db696c
- Remove deprecated 'precise' mode alias; align mode docs
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  1c9b47f
- Remove paper-side benchmarks, optimizers, and PRDs
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  dd01498
- Remove dead code
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  9c7a24d
- Tidy design-doc references; commit parameter-cleanup PRD
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  e7e55b3
- Clean up build warnings and stale libomp installs in CI
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  fb0d5c4
Commits on May 16, 2026
- Drop developer-only design docs from the source tree
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  eee0d93
- Harden POAR file parsing against integer overflow
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  d1ce73c
- Fix test_module_exports: add four missing symbols
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  afc18b5
- Fix Linux build: gate d2 declaration on HAVE_AVX2
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  f7b3dac
- Remove benchmark CI workflow
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  b09d43f
- Fix DSSIM matrix mismatch; harden finalise + comparison error paths
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  f5baaf3
- Add tests/check-local.sh — pre-push verification gate
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  90d3e74
- Apply black formatting to python-kalign/__init__.py
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  fe02b24
- Bump version to 3.5.2 and add ChangeLog entry
  TimoLassmann
  committed
  5bd7602

Commits

Commits on Mar 9, 2026

Commits on Mar 12, 2026

Commits on Mar 18, 2026

Commits on Mar 19, 2026

Commits on Mar 21, 2026

Commits on Mar 24, 2026

Commits on Mar 25, 2026

Commits on Mar 26, 2026

Commits on Apr 1, 2026

Commits on Apr 17, 2026

Commits on May 15, 2026

Commits on May 16, 2026