refactor(seqopt): single NSGA-II kernel (drop engine knob) + rename tutorial to protein engineering#272
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…protein engineering (1) Engine simplification: exact/fast were byte-identical, so the dual-engine knob was pure redundancy. Collapse to a single memory-bounded chunked-vectorized non-dominated sort: fast_non_dominated_sort now uses the chunked dominance matrix; remove fast_non_dominated_sort_vec / select_nsga2_engine / the engine-branch in rank_and_crowding; drop the engine run() param + LIST_SEQOPT_ENGINE + validation + the engine tests. The DEAP parity tests, comparison script (ours vs DEAP), ADR-0045 D2/D4, release note and CONTEXT.md are updated to the single kernel. Output unchanged (464-test gate green). (2) Rename tutorial7_protein_design -> tutorial7_protein_engineering (+ toctree) so the filename matches the protein-engineering framing. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Codecov Report❌ Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## master #272 +/- ##
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Coverage 96.13% 96.14%
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Files 176 176
Lines 16733 16739 +6
Branches 2863 2856 -7
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+ Hits 16087 16093 +6
- Misses 363 364 +1
+ Partials 283 282 -1
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Summary
Two follow-ups to PR #271 (both requested):
Drop the redundant
engineknob.engine="exact"and"fast"produced byte-identical fronts, so the dual-engine parameter was pure redundancy. Collapsed to a single memory-bounded chunked-vectorized non-dominated sort:fast_non_dominated_sortnow uses the chunked dominance matrix; removedfast_non_dominated_sort_vec/select_nsga2_engine/ the engine branch inrank_and_crowding; dropped theenginerun()param +LIST_SEQOPT_ENGINE+ validation + the engine-specific tests. DEAP parity tests, the comparison script (nowoursvsdeap), ADR-0045 (D2/D4), the release note and CONTEXT.md updated. Output unchanged.Rename the tutorial
tutorial7_protein_design→tutorial7_protein_engineering(+ toctree), so the filename matches the protein-engineering framing.Verification
464-test broad gate green locally;
engineremoved from the public API; docstrings clean; comparison script runs (ours faster than DEAP). Merged current with master.🤖 Generated with Claude Code