feat(seqopt): pure-Python EA operators + DEAP parity + SeqOptPlot (protein engineering)#271

Merged

breimanntools merged 13 commits into

feat/seqopt-deap-parity

Jun 25, 2026

Commits on Jun 25, 2026

feat(seqopt): complete pure-Python EA operator set + DEAP parity oracle

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test(seqopt): assert the precise DEAP-parity invariants
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feat(seqopt): visualization + external-predictor objectives + convergence history

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docs(seqopt): realistic GSEC example notebooks + impact-ref bug fix

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feat(seqopt): memory-bounded fast engine, cumulative Pareto archive, hero plots

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feat(seqopt): genealogy plot + DEAP mapping table in the class docstring
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refactor(seqopt): expose cmap as a parameter on SeqOptPlot (package consistency)
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docs(seqopt): protein-design tutorial (SeqOpt + SeqOptPlot)
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docs(seqopt): frame SeqOpt as protein ENGINEERING (not de novo design) + refs
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docs(seqopt): correct directed-evolution + de novo refs from the source reviews
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docs(seqopt): also cite Yang, Wu & Arnold (2019) for ML-guided directed evolution
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Merge remote-tracking branch 'origin/master' into feat/seqopt-deap-parity
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docs(adr): assign ADR-0045 to the SeqOpt DEAP-parity + pure-Python operators decision
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