├── .github └── workflows │ └── ci.yml ├── .gitignore ├── .pre-commit-config.yaml ├── LICENSE ├── README.md ├── README.rst ├── config ├── hydra │ ├── benchmark_optimizer.yaml │ ├── optimizer │ │ └── discrete_evolution.yaml │ └── test_function │ │ ├── dhfr.yaml │ │ ├── ehrlich.yaml │ │ ├── rough_mt_fuji.yaml │ │ ├── tfbind8.yaml │ │ └── trpb.yaml └── wandb │ ├── ehrlich_benchmark_sweep.yaml │ ├── lookup_benchmark_sweep.yaml │ ├── optimizer_hparam_sweep.yaml │ ├── reproduce_fig_4a.yaml │ ├── reproduce_fig_4b.yaml │ ├── reproduce_fig_4c.yaml │ ├── reproduce_fig_4d.yaml │ └── reproduce_fig_5.yaml ├── holo ├── __init__.py ├── logging │ ├── __init__.py │ └── _wandb_setup.py ├── optim │ ├── __init__.py │ └── _discrete_evolution.py └── test_functions │ ├── __init__.py │ ├── closed_form │ ├── __init__.py │ ├── _ehrlich.py │ └── _rough_mt_fuji.py │ ├── elemental │ ├── __init__.py │ ├── _discrete_markov_process.py │ ├── _hamming_dist.py │ └── _motif.py │ └── lookup │ ├── __init__.py │ ├── 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