├── .bumpversion.cfg ├── .editorconfig ├── .github └── workflows │ └── CI.yml ├── .gitignore ├── .gitmodules ├── .readthedocs.yml ├── AUTHORS.md ├── CITATION.cff ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── Dockerfile ├── LICENSE ├── Makefile ├── README.md ├── binder ├── README.md ├── bucket=prq49 │ ├── a=all_stints_all_series_profiles+endeavor=16 │ │ ├── case_study_16005.ipynb │ │ ├── catalog_dataset.ipynb │ │ ├── clear_notebooks.sh │ │ ├── clear_outplots.sh │ │ ├── differentiation_complexity.ipynb │ │ ├── dishpylib │ │ ├── execute_notebooks.sh │ │ ├── fitness.ipynb │ │ ├── fitness_complexity.ipynb │ │ ├── genome_robustness.ipynb │ │ ├── index.ipynb │ │ ├── interface_complexity.ipynb │ │ ├── mutation_accumulation.ipynb │ │ ├── phenotype_characteristics.ipynb │ │ ├── phenotype_complexity.ipynb │ │ ├── x=complexity-fitness.ipynb │ │ ├── x=complexity-robustness.ipynb │ │ ├── x=fitness_complexity-phenotypic_complexity.ipynb │ │ └── x=mutation_accumulation-robustness.ipynb │ ├── a=all_stints_all_thread_profiles+endeavor=16 │ │ ├── catalog_dataset.ipynb │ │ ├── clear_notebooks.sh │ │ ├── clear_outplots.sh │ │ ├── dishpylib │ │ ├── elapsed_updates.ipynb │ │ ├── execute_notebooks.sh │ │ └── phylogenetic_roots.ipynb │ ├── a=noncritical-phenotypeneutral-nopinterpolation-competitions+endeavor=16 │ │ ├── clear_notebooks.sh │ │ ├── clear_outplots.sh │ │ ├── dishpylib │ │ ├── execute_notebooks.sh │ │ └── interpolation_complexity.ipynb │ ├── clear_notebooks.sh │ ├── clear_outplots.sh │ └── execute_notebooks.sh ├── clear_notebooks.sh ├── clear_outplots.sh ├── execute_notebooks.sh ├── index.ipynb ├── requirements.txt └── runtime.txt ├── ci ├── alphabetize_imports.sh ├── alphabetize_includes.sh ├── deploy_assets.sh ├── deploy_gh_pages.sh ├── ensure_end_of_file_newlines.sh ├── generate_headerguards.sh ├── grep_dotos.sh ├── modernize_filename_suffixes.sh ├── parse_documentation_coverage.py ├── parse_dotos.py ├── parse_version.py ├── partition_includes.sh ├── replace_tabs.sh ├── strip_trailing_whitespace.sh ├── test_2space_indentation.sh ├── test_alphabetize_imports.sh ├── test_alphabetize_includes.sh ├── test_end_of_file_newlines.sh ├── test_filename_whitespace.sh ├── test_headerguards.sh ├── test_make_clean.sh ├── test_merge_conflict_markers.sh ├── test_modern_suffixes.sh ├── test_notebooks_clear.sh ├── test_partition_includes.sh ├── test_readme_snippets.py ├── test_tabs.sh ├── test_tidy.sh └── test_trailing_whitespace.sh ├── configpacks ├── README.md ├── bucket=dnh2v+mutation_rate=0.10 │ ├── build_native.sh │ ├── build_web.sh │ ├── competitionjob │ │ └── .gitkeep │ ├── doubling-timejob │ │ └── .gitkeep │ ├── evolvejob │ │ └── dishtiny.cfg │ ├── monoculturejob │ │ └── .gitkeep │ ├── nopoutjob │ │ └── .gitkeep │ └── phenotype-differentiationjob │ │ └── .gitkeep ├── bucket=dnh2v+mutation_rate=0.33 │ ├── build_native.sh │ ├── build_web.sh │ ├── competitionjob │ │ └── .gitkeep │ ├── doubling-timejob │ │ └── .gitkeep │ ├── evolvejob │ │ └── dishtiny.cfg │ ├── monoculturejob │ │ └── .gitkeep │ ├── nopoutjob │ │ └── .gitkeep │ └── phenotype-differentiationjob │ │ └── .gitkeep ├── bucket=dnh2v+mutation_rate=1.00 │ ├── build_native.sh │ ├── build_web.sh │ ├── competitionjob │ │ └── .gitkeep │ ├── doubling-timejob │ │ └── .gitkeep │ ├── evolvejob │ │ └── dishtiny.cfg │ ├── monoculturejob │ │ └── .gitkeep │ ├── nopoutjob │ │ └── .gitkeep │ └── phenotype-differentiationjob │ │ └── .gitkeep ├── bucket=dnh2v+mutation_rate=2.00 │ ├── build_native.sh │ ├── build_web.sh │ ├── competitionjob │ │ └── .gitkeep │ ├── doubling-timejob │ │ └── .gitkeep │ ├── evolvejob │ │ └── dishtiny.cfg │ ├── monoculturejob │ │ └── .gitkeep │ ├── nopoutjob │ │ └── .gitkeep │ └── phenotype-differentiationjob │ │ └── .gitkeep ├── bucket=prq49+diversity=0.25_series+mut_freq=1.00+mut_sever=1.00 │ ├── build_native.sh │ ├── build_web.sh │ ├── competitionjob │ │ └── dishtiny.cfg │ ├── doubling-timejob │ │ └── dishtiny.cfg │ ├── evolvejob │ │ └── dishtiny.cfg │ ├── monoculturejob │ │ └── dishtiny.cfg │ ├── nopoutjob │ │ └── dishtiny.cfg │ ├── phenotype-differentiationjob │ │ └── dishtiny.cfg │ └── polyculturejob │ │ └── dishtiny.cfg ├── bucket=prq49+diversity=0.50_series+mut_freq=1.00+mut_sever=1.00 │ ├── build_native.sh │ ├── build_web.sh │ ├── competitionjob │ │ └── dishtiny.cfg │ ├── doubling-timejob │ │ └── dishtiny.cfg │ ├── evolvejob │ │ └── dishtiny.cfg │ ├── monoculturejob │ │ └── dishtiny.cfg │ ├── nopoutjob │ │ └── dishtiny.cfg │ ├── phenotype-differentiationjob │ │ └── dishtiny.cfg │ └── polyculturejob │ │ └── dishtiny.cfg └── default │ ├── build_native.sh │ ├── build_web.sh │ ├── competitionjob │ └── .gitkeep │ ├── doubling-timejob │ └── .gitkeep │ ├── evolvejob │ └── .gitkeep │ ├── monoculturejob │ └── .gitkeep │ ├── nopoutjob │ └── .gitkeep │ └── phenotype-differentiationjob │ └── .gitkeep ├── container ├── ccache.conf └── policy.xml ├── dishpylib ├── README.md ├── __init__.py ├── pyanalysis │ ├── __init__.py │ ├── calc_loglikelihoods_by_num_sets.py │ ├── calc_loglikelihoods_over_set_sizes.py │ ├── count_hands_with_k_or_more_sets.py │ ├── count_hands_without_k_or_more_sets.py │ ├── estimate_credible_interval.py │ └── estimate_interpolation_complexity.py ├── pyassemblers │ ├── __init__.py │ ├── _validate_assembled_dataframe.py │ ├── assemble_config_records.py │ ├── assemble_deletion_mutant_competitions.py │ ├── assemble_deletion_mutant_phenotype_differentiation.py │ ├── assemble_evolve_dpp_metrics.py │ ├── assemble_evolve_dpp_metrics_threadfirst.py │ ├── assemble_evolve_dpp_metrics_threadmean.py │ ├── assemble_evolve_kin_conflict_statistics.py │ ├── assemble_insertion_mutant_competitions.py │ ├── assemble_insertion_mutant_phenotype_differentiation.py │ ├── assemble_lowestroot_immediatepredecessor_battles.py │ ├── assemble_monoculture_birth_log_statistics.py │ ├── assemble_monoculture_dpp_metrics_threadfirst.py │ ├── assemble_monoculture_dpp_metrics_threadmean.py │ ├── assemble_monoculture_kin_conflict_by_replev_statistics.py │ ├── assemble_monoculture_kin_conflict_statistics.py │ ├── assemble_mutant_competitions.py │ ├── assemble_mutant_phenotype_differentiation.py │ ├── assemble_mutating_competitions.py │ ├── assemble_noncritical_nopout_fitness_competitions.py │ ├── assemble_noncritical_phenotypeequivalent_nopinterpolation_competitions.py │ ├── assemble_phenotype_neutral_nopout_fitness_competitions.py │ ├── assemble_phenotype_neutral_nopout_phenotype_differentiation.py │ ├── assemble_phenotype_neutral_nopouts.py │ ├── assemble_point_mutant_competitions.py │ ├── assemble_point_mutant_phenotype_differentiation.py │ ├── assemble_predecessor_battles.py │ ├── assemble_predecessor_competitions.py │ ├── assemble_progenitor_competitions.py │ ├── assemble_strain_competitions.py │ ├── assemble_variant_competitions.py │ ├── assemble_wildtype_doubling_time.py │ ├── either_perturbation_competitions_assembler_factory.py │ ├── messaging_selfsend_competitions_assembler_factory.py │ └── perturbation_competitions_assembler_factory.py ├── pydecorators │ ├── __init__.py │ ├── announce_job_decorator_factory.py │ ├── only_every_nth_stint_decorator_factory.py │ └── try_except_missing_data_decorator_factory.py ├── pyhelpers │ ├── NumpyEncoder.py │ ├── __init__.py │ ├── auto_tqdm.py │ ├── fit_control_t_distns.py │ ├── get_control_t_distns.py │ ├── get_env_context.py │ ├── get_git_revision_hash.py │ ├── get_notebook_cell_execution_count.py │ ├── get_notebook_name.py │ ├── get_notebook_path.py │ ├── in_ipynb.py │ ├── make_outattr_metadata.py │ ├── make_timestamp.py │ ├── preprocess_competition_fitnesses.py │ └── print_runtime.py ├── pyloaders │ ├── __init__.py │ ├── genome_local_autoload.py │ └── genome_s3_autoload.py ├── pytabulators │ ├── __init__.py │ ├── filter_for_phenotype_neutral_nopout.py │ ├── reshape_birth_log.py │ ├── reshape_dpp.py │ ├── reshape_dpp_threadfirst.py │ ├── reshape_dpp_threadmean.py │ ├── reshape_kin_conflict.py │ ├── reshape_kin_conflict_by_replev.py │ ├── tabulate_either_perturbation_fitness.py │ ├── tabulate_fitness_complexity.py │ ├── tabulate_interpolation_complexity.py │ ├── tabulate_mutant_fitness.py │ ├── tabulate_mutant_phenotype_differentiation.py │ ├── tabulate_noncritical_nopout_fitness.py │ ├── tabulate_perturbation_fitness.py │ ├── tabulate_phenotype_equivalent_nopout_fitness.py │ ├── tabulate_phenotype_neutral_nopout_phenotype_differentiation.py │ ├── tabulate_predecessor_battle_fitness.py │ ├── tabulate_predecessor_fitness.py │ ├── tabulate_progenitor_fitness.py │ ├── tabulate_selfsend_fitness.py │ ├── tabulate_strain_fitness.py │ └── tabulate_wildtype_doubling_time.py └── test │ ├── __init__.py │ ├── run_tests.sh │ └── test_pyanalysis │ ├── __init__.py │ ├── dishpylib │ └── test_count_hands_with_k_or_more_sets.py ├── docs ├── Makefile ├── acknowledgements.md ├── assets │ ├── classdiagram.pdf │ ├── classdiagram.png │ ├── classdiagram.svg │ ├── cookie.gif │ ├── cpu_detail.pdf │ ├── hardware.png │ ├── moreno.jpg │ ├── oee4-03.pdf │ ├── oee4-03.png │ ├── oee4-03.svg │ ├── oee4-10.pdf │ ├── oee4-10.png │ ├── oee4-10.svg │ ├── oee4-cpu.pdf │ ├── oee4-cpu.svg │ ├── oee4-wse.pdf │ ├── oee4-wse.svg │ ├── oee4.ai │ ├── ofria.jpg │ ├── overview.pdf │ ├── population.png │ └── undergrads.jpg ├── citing.md ├── code_of_conduct.md ├── conf.py ├── contributing.md ├── data.md ├── development.md ├── emojicodes.json ├── glossary.md ├── index.md ├── installation.md ├── publications.md ├── simulation.md ├── usage.md └── workflow.md ├── fuzzing ├── Makefile └── update.cpp ├── include ├── README.md └── dish2 │ ├── algorithm │ ├── README.md │ ├── assess_instructions_for_phenotypic_divergence.hpp │ ├── assess_module_for_phenotypic_divergence.hpp │ ├── battleship_nop_out_phenotypically_neutral_instructions.hpp │ ├── battleship_nop_out_phenotypically_neutral_modules.hpp │ ├── detect_phenotypic_divergence.hpp │ ├── exhaustive_jenga_nop_out_phenotypically_neutral_instructions.hpp │ ├── get_lowest_root.hpp │ ├── jenga_nop_out_phenotypically_neutral_instructions.hpp │ ├── make_battleship_phenotype_equivalent_nopout.hpp │ ├── make_jenga_phenotype_equivalent_nopout.hpp │ ├── run_until_phenotypic_divergence.hpp │ └── seed_genomes_into.hpp │ ├── cell │ ├── Cardinal.hpp │ ├── Cell.hpp │ ├── README.md │ ├── cardinal_iterators │ │ ├── ApoptosisRequestWrapper.hpp │ │ ├── CardinalQuorumStateWrapper.hpp │ │ ├── CellAgeWrapper.hpp │ │ ├── ControllerMappedStateWrapper.hpp │ │ ├── CpuWrapper.hpp │ │ ├── EntireElapsedInstructionCyclesWrapper.hpp │ │ ├── EpochWrapper.hpp │ │ ├── ExtrospectiveStateIndexedSwapWrapper.hpp │ │ ├── ExtrospectiveStateWrapper.hpp │ │ ├── GenomeNodeInputWrapper.hpp │ │ ├── GenomeNodeOutputWrapper.hpp │ │ ├── HeirRequestWrapper.hpp │ │ ├── IdentityWrapper.hpp │ │ ├── IncomingInterMessageCounterWrapper.hpp │ │ ├── IncomingIntraMessageCounterWrapper.hpp │ │ ├── IntraMessageNodeWrapper.hpp │ │ ├── IntrospectiveStateIndexedSwapWrapper.hpp │ │ ├── IntrospectiveStateWrapper.hpp │ │ ├── IsAliveWrapper.hpp │ │ ├── IsChildCellOfWrapper.hpp │ │ ├── IsChildGroupOfWrapper.hpp │ │ ├── IsNewbornWrapper.hpp │ │ ├── IsParentCellOfWrapper.hpp │ │ ├── IsParentGroupOfWrapper.hpp │ │ ├── KinGroupAgeWrapper.hpp │ │ ├── KinGroupIDAncestorViewWrapper.hpp │ │ ├── KinGroupIDViewWrapper.hpp │ │ ├── KinGroupWillExpireWrapper.hpp │ │ ├── KinMatchWrapper.hpp │ │ ├── MessageNodeInputWrapper.hpp │ │ ├── MostRecentCauseOfDeathWrapper.hpp │ │ ├── NeighborApoptosisWrapper.hpp │ │ ├── NeighborCellAgeWrapper.hpp │ │ ├── NeighborEpochWrapper.hpp │ │ ├── NeighborFragmentedWrapper.hpp │ │ ├── NeighborIsAliveWrapper.hpp │ │ ├── NeighborIsNewbornWrapper.hpp │ │ ├── NeighborKinGroupAgeWrapper.hpp │ │ ├── NeighborKinGroupIDAncestorViewWrapper.hpp │ │ ├── NeighborKinGroupIDViewWrapper.hpp │ │ ├── NeighborKinGroupWillExpireWrapper.hpp │ │ ├── NeighborMostRecentCauseOfDeathWrapper.hpp │ │ ├── NeighborNumKnownQuorumBitsWrapper.hpp │ │ ├── NeighborOptimumQuorumExceededWrapper.hpp │ │ ├── NeighborPhylogeneticRootViewWrapper.hpp │ │ ├── NeighborResourceReceiveResistanceWrapper.hpp │ │ ├── NeighborResourceStockpileWrapper.hpp │ │ ├── NeighborSpawnedFromWrapper.hpp │ │ ├── NumBusyCoresWrapper.hpp │ │ ├── NumKnownQuorumBitsWrapper.hpp │ │ ├── OptimumQuorumExceededWrapper.hpp │ │ ├── ParentFragmentedWrapper.hpp │ │ ├── PeripheralWrapper.hpp │ │ ├── PhylogeneticRootMatchWrapper.hpp │ │ ├── PhylogeneticRootViewWrapper.hpp │ │ ├── PushNodeInputWrapper.hpp │ │ ├── PushNodeOutputWrapper.hpp │ │ ├── ReadableStateWrapper.hpp │ │ ├── ReceivedResourceFromWrapper.hpp │ │ ├── ResourceInputPeekWrapper.hpp │ │ ├── ResourceNodeInputWrapper.hpp │ │ ├── ResourceNodeOutputWrapper.hpp │ │ ├── ResourceReceiveResistanceWrapper.hpp │ │ ├── ResourceReserveRequestWrapper.hpp │ │ ├── ResourceSendLimitWrapper.hpp │ │ ├── ResourceSendRequestWrapper.hpp │ │ ├── ResourceStockpileWrapper.hpp │ │ ├── RicherThanNeighborWrapper.hpp │ │ ├── SpawnArrestWrapper.hpp │ │ ├── SpawnCountWrapper.hpp │ │ ├── SpawnRequestWrapper.hpp │ │ ├── SpawnedFromWrapper.hpp │ │ ├── StateNodeInputWrapper.hpp │ │ ├── StateNodeOutputWrapper.hpp │ │ ├── StockpileDepletedWrapper.hpp │ │ ├── StockpileFecundWrapper.hpp │ │ ├── TransientNopStateWrapper.hpp │ │ ├── WritableStateIndexedSwapWrapper.hpp │ │ ├── WritableStateWrapper.hpp │ │ ├── _IntrospectiveStateIndexedSwapper.hpp │ │ ├── _ReadableStateIndexedSwapper.hpp │ │ └── _WritableStateIndexedSwapper.hpp │ └── routine_impls │ │ ├── DeathRoutine.hpp │ │ ├── FragmentationRoutine.hpp │ │ ├── HeirPayoutRoutine.hpp │ │ ├── MakeAliveRoutine.hpp │ │ └── _index.hpp │ ├── config │ ├── ConfigBase.hpp │ ├── README.md │ ├── TemporaryConfigOverride.hpp │ ├── TemporaryThreadIdxOverride.hpp │ ├── calc_rng_preseed.hpp │ ├── cfg.hpp │ ├── dump_config.hpp │ ├── dump_config_csv.hpp │ ├── get_endeavor.hpp │ ├── get_repro.hpp │ ├── get_slurm_job_id.hpp │ ├── has_replicate.hpp │ ├── has_rng_preseed.hpp │ ├── has_series.hpp │ ├── has_stint.hpp │ ├── make_arg_specs.hpp │ ├── num_cells_global.hpp │ ├── num_cells_local.hpp │ ├── print_assets.hpp │ ├── print_config.hpp │ ├── print_extrospective_states.hpp │ ├── print_introspective_states.hpp │ ├── print_pwd.hpp │ ├── print_readable_states.hpp │ ├── print_writable_states.hpp │ ├── running_log_duration_in_updates.hpp │ ├── setup.hpp │ ├── setup_assets.hpp │ ├── setup_config.hpp │ └── thread_idx.hpp │ ├── configbyroot │ ├── README.md │ ├── RootMutationConfig.hpp │ ├── RootMutationConfigs.hpp │ ├── RootPerturbationConfig.hpp │ ├── RootPerturbationConfigs.hpp │ ├── root_mutation_configs.hpp │ ├── root_perturbation_configs.hpp │ └── summarize_root_config.hpp │ ├── debug │ ├── LogEntry.hpp │ ├── LogEntryType.hpp │ ├── LogLevelGuard.hpp │ ├── LogScope.hpp │ ├── LogStackFrame.hpp │ ├── LogTee.hpp │ ├── PopulationExtinctionException.hpp │ ├── README.md │ ├── backtrace_enable.hpp │ ├── enable.hpp │ ├── entry_types.hpp │ ├── log_event.hpp │ ├── log_event_dispatcher.hpp │ ├── log_level.hpp │ ├── log_msg.hpp │ ├── log_msg_emscripten.hpp │ ├── log_msg_native.hpp │ ├── log_stack.hpp │ ├── log_stack_dispatcher.hpp │ ├── log_tee.hpp │ └── make_log_entry_boilerplate.hpp │ ├── enum │ ├── CauseOfDeath.hpp │ └── README.md │ ├── events │ ├── AlwaysEvent.hpp │ ├── EventManager.hpp │ ├── EventSeries.hpp │ ├── IsChildCellOfEvent.hpp │ ├── IsChildGroupOfEvent.hpp │ ├── IsNewbornEvent.hpp │ ├── IsParentCellOfEvent.hpp │ ├── KinGroupMatchEvent.hpp │ ├── KinGroupMismatchEvent.hpp │ ├── KinGroupWillExpireEvent.hpp │ ├── KinGroupWillNotExpireEvent.hpp │ ├── NeighborApoptosisEvent.hpp │ ├── NeighborFragmentedEvent.hpp │ ├── NeighborIsAliveEvent.hpp │ ├── NeighborIsNewbornEvent.hpp │ ├── NeighborIsNotAliveEvent.hpp │ ├── NeighborKinGroupWillExpireEvent.hpp │ ├── NeighborOptimumQuorumExceededEvent.hpp │ ├── OptimumQuorumExceededEvent.hpp │ ├── OptimumQuorumNotExceededEvent.hpp │ ├── ParentFragmentedEvent.hpp │ ├── PhylogeneticRootMatchEvent.hpp │ ├── PhylogeneticRootMismatchEvent.hpp │ ├── PoorerThanNeighborEvent.hpp │ ├── README.md │ ├── ReceivedResourceFromEvent.hpp │ ├── RicherThanNeighborEvent.hpp │ ├── StockpileDepletedEvent.hpp │ ├── StockpileFecundEvent.hpp │ └── _index.hpp │ ├── genome │ ├── EventTags.hpp │ ├── GenerationCounter.hpp │ ├── Genome.hpp │ ├── KinGroupEpochStamps.hpp │ ├── KinGroupID.hpp │ ├── MutationCounter.hpp │ ├── README.md │ └── RootID.hpp │ ├── introspection │ ├── README.md │ ├── any_live_cells.hpp │ ├── compare_resource_stockpiles.hpp │ ├── count_birth_events.hpp │ ├── count_cardinals.hpp │ ├── count_dead_cells.hpp │ ├── count_death_events.hpp │ ├── count_kin_neighbors.hpp │ ├── count_live_cardinals.hpp │ ├── count_live_cells.hpp │ ├── count_spawn_events.hpp │ ├── count_unique_coding_genotypes.hpp │ ├── count_unique_module_expression_profiles.hpp │ ├── count_unique_module_regulation_profiles.hpp │ ├── count_unique_root_ids.hpp │ ├── count_unique_stint_root_ids.hpp │ ├── get_fraction_cardinals_apoptosis_request.hpp │ ├── get_fraction_cardinals_incoming_inter_message.hpp │ ├── get_fraction_cardinals_incoming_intra_message.hpp │ ├── get_fraction_cardinals_receiving_resource.hpp │ ├── get_fraction_cardinals_resource_receive_resistance.hpp │ ├── get_fraction_cardinals_resource_reserve_request.hpp │ ├── get_fraction_cardinals_resource_send_request.hpp │ ├── get_fraction_cardinals_spawn_arrest.hpp │ ├── get_fraction_cardinals_spawn_request.hpp │ ├── get_fraction_cells_apoptosis_request.hpp │ ├── get_fraction_cells_incoming_inter_message.hpp │ ├── get_fraction_cells_incoming_intra_message.hpp │ ├── get_fraction_cells_kin_group_loners.hpp │ ├── get_fraction_cells_receiving_resource.hpp │ ├── get_fraction_cells_resource_receive_resistance.hpp │ ├── get_fraction_cells_resource_reserve_request.hpp │ ├── get_fraction_cells_resource_send_request.hpp │ ├── get_fraction_cells_spawn_arrest.hpp │ ├── get_fraction_cells_spawn_request.hpp │ ├── get_fraction_fecund_resource_stockpile.hpp │ ├── get_fraction_live_cells.hpp │ ├── get_fraction_nulliparous.hpp │ ├── get_kin_group_sizes.hpp │ ├── get_lowest_root_id.hpp │ ├── get_lowest_root_prevalent_coding_genotype.hpp │ ├── get_lowest_root_prevalent_coding_genotype_genome.hpp │ ├── get_maximum_kin_group_size.hpp │ ├── get_maximum_module_count.hpp │ ├── get_maximum_program_length.hpp │ ├── get_mean_cell_age.hpp │ ├── get_mean_elapsed_insertions_deletions.hpp │ ├── get_mean_elapsed_mutation_occurences.hpp │ ├── get_mean_elapsed_point_mutations.hpp │ ├── get_mean_epoch.hpp │ ├── get_mean_generation.hpp │ ├── get_mean_genome_compression_ratio.hpp │ ├── get_mean_incoming_inter_message_count_per_cardinal.hpp │ ├── get_mean_incoming_inter_message_count_per_cell.hpp │ ├── get_mean_incoming_intra_message_count_per_cardinal.hpp │ ├── get_mean_incoming_intra_message_count_per_cell.hpp │ ├── get_mean_kin_group_age.hpp │ ├── get_mean_kin_group_size.hpp │ ├── get_mean_module_count.hpp │ ├── get_mean_program_length.hpp │ ├── get_mean_resource_received_per_cardinal.hpp │ ├── get_mean_resource_received_per_cell.hpp │ ├── get_mean_resource_stockpile.hpp │ ├── get_mean_spawn_count.hpp │ ├── get_median_kin_group_size.hpp │ ├── get_num_kin_group_loners.hpp │ ├── get_num_running_log_cardinal_updates.hpp │ ├── get_num_running_log_cell_updates.hpp │ ├── get_num_running_log_live_cardinal_updates.hpp │ ├── get_num_running_log_live_cell_updates.hpp │ ├── get_num_running_log_updates.hpp │ ├── get_population_compression_ratio.hpp │ ├── get_prevalent_coding_genotype.hpp │ ├── get_prevalent_coding_genotype_genome.hpp │ ├── get_root_id_abundance.hpp │ ├── get_root_id_count.hpp │ ├── get_root_id_counts.hpp │ ├── get_root_id_prevalence.hpp │ ├── get_stint_root_id_counts.hpp │ ├── get_total_spawn_event_kin_eliminated.hpp │ ├── get_total_spawn_event_kin_neighbors.hpp │ ├── get_total_spawn_event_neighbors.hpp │ ├── get_unique_root_ids.hpp │ ├── get_unique_stint_root_ids.hpp │ ├── has_coalesced.hpp │ ├── is_extinct.hpp │ ├── make_cardi_coord_to_live_cardi_idx_translator.hpp │ ├── make_causes_of_death_string_histogram.hpp │ ├── no_live_cells.hpp │ ├── sum_entire_elapsed_instruction_cycles.hpp │ ├── sum_entire_elapsed_instruction_cycles_for_live_cells.hpp │ ├── sum_state_mesh_intra_attempted_puts.hpp │ ├── sum_state_mesh_intra_blocked_puts.hpp │ ├── sum_state_mesh_intra_dropped_puts.hpp │ ├── sum_state_mesh_intra_net_flux.hpp │ ├── sum_state_mesh_intra_read_count.hpp │ ├── sum_state_mesh_intra_revision_count.hpp │ ├── sum_state_mesh_proc_attempted_puts.hpp │ ├── sum_state_mesh_proc_blocked_puts.hpp │ ├── sum_state_mesh_proc_dropped_puts.hpp │ ├── sum_state_mesh_proc_net_flux.hpp │ ├── sum_state_mesh_proc_read_count.hpp │ ├── sum_state_mesh_proc_revision_count.hpp │ ├── sum_state_mesh_thread_attempted_puts.hpp │ ├── sum_state_mesh_thread_blocked_puts.hpp │ ├── sum_state_mesh_thread_dropped_puts.hpp │ ├── sum_state_mesh_thread_net_flux.hpp │ ├── sum_state_mesh_thread_read_count.hpp │ ├── sum_state_mesh_thread_revision_count.hpp │ ├── summarize_causes_of_death.hpp │ ├── summarize_module_expression.hpp │ └── summarize_module_regulation.hpp │ ├── load │ ├── README.md │ ├── apply_population_filters.hpp │ ├── count_root_ids.hpp │ ├── get_innoculum_filename.hpp │ ├── get_innoculum_filenames.hpp │ ├── get_innoculum_slug.hpp │ ├── get_innoculum_slugs.hpp │ ├── get_root_ids.hpp │ ├── innoculate_population.hpp │ ├── innoculum_attr_handlers │ │ ├── _index.hpp │ │ ├── apply_deletion_mutate_on_load.hpp │ │ ├── apply_insertion_mutate_on_load.hpp │ │ ├── apply_mutate_on_load.hpp │ │ ├── apply_point_mutate_on_load.hpp │ │ ├── set_extrospective_state_target_idx.hpp │ │ ├── set_inter_message_selfsend_filter_mod.hpp │ │ ├── set_inter_message_selfsend_filter_target.hpp │ │ ├── set_intermittent_extrospective_state_exchange_probability.hpp │ │ ├── set_intermittent_extrospective_state_rotate_probability.hpp │ │ ├── set_intermittent_introspective_state_exchange_probability.hpp │ │ ├── set_intermittent_introspective_state_rotate_probability.hpp │ │ ├── set_intermittent_writable_state_exchange_probability.hpp │ │ ├── set_intermittent_writable_state_rotate_probability.hpp │ │ ├── set_intra_message_selfsend_filter_mod.hpp │ │ ├── set_intra_message_selfsend_filter_target.hpp │ │ ├── set_introspective_state_target_idx.hpp │ │ ├── set_mutation_occurence_rate_multiplicand.hpp │ │ ├── set_program_max_size_override.hpp │ │ └── set_writable_state_target_idx.hpp │ ├── load_innoculum.hpp │ ├── load_innoculum_genome.hpp │ ├── load_innoculum_population.hpp │ ├── load_world.hpp │ ├── make_genome_slug.hpp │ ├── monoculture_population.hpp │ ├── reconstitute_population.hpp │ └── reconstitute_population_load.hpp │ ├── operations │ ├── AddToOwnState.hpp │ ├── BcstIntraMessageIf.hpp │ ├── MultiplyOwnState.hpp │ ├── README.md │ ├── ReadNeighborState.hpp │ ├── ReadOwnState.hpp │ ├── SendInterMessageIf.hpp │ ├── SendIntraMessageIf.hpp │ ├── WriteOwnStateIf.hpp │ └── _index.hpp │ ├── peripheral │ ├── Peripheral.hpp │ ├── README.md │ └── readable_state │ │ ├── ReadableState.hpp │ │ ├── introspective_state │ │ ├── IntrospectiveState.hpp │ │ ├── interpreted_introspective_state │ │ │ ├── InterpretedIntrospectiveState.hpp │ │ │ ├── IsChildCellOf.hpp │ │ │ ├── IsChildGroupOf.hpp │ │ │ ├── IsNewborn.hpp │ │ │ ├── IsParentCellOf.hpp │ │ │ ├── IsParentGroupOf.hpp │ │ │ ├── KinGroupMatch.hpp │ │ │ ├── KinGroupWillExpire.hpp │ │ │ ├── NeighborApoptosis.hpp │ │ │ ├── NeighborFragmented.hpp │ │ │ ├── NeighborIsNewborn.hpp │ │ │ ├── NeighborKinGroupWillExpire.hpp │ │ │ ├── NeighborOptimumQuorumExceeded.hpp │ │ │ ├── OptimumQuorumExceeded.hpp │ │ │ ├── ParentFragmented.hpp │ │ │ ├── PhylogeneticRootMatch.hpp │ │ │ ├── RicherThanNeighbor.hpp │ │ │ ├── StockpileDepleted.hpp │ │ │ └── StockpileFecund.hpp │ │ └── raw_introspective_state │ │ │ ├── CellAge.hpp │ │ │ ├── Epoch.hpp │ │ │ ├── IncomingInterMessageCounter.hpp │ │ │ ├── IncomingIntraMessageCounter.hpp │ │ │ ├── IsAlive.hpp │ │ │ ├── KinGroupAge.hpp │ │ │ ├── KinGroupIDAncestorView.hpp │ │ │ ├── KinGroupIDView.hpp │ │ │ ├── MostRecentCauseOfDeath.hpp │ │ │ ├── NumKnownQuorumBits.hpp │ │ │ ├── PhylogeneticRootView.hpp │ │ │ ├── RawIntrospectiveState.hpp │ │ │ ├── ReceivedResourceFrom.hpp │ │ │ ├── ResourceStockpile.hpp │ │ │ ├── SpawnCount.hpp │ │ │ └── SpawnedFrom.hpp │ │ └── writable_state │ │ ├── NopState.hpp │ │ ├── TransientNopState.hpp │ │ ├── WritableState.hpp │ │ └── controller_mapped_state │ │ ├── ApoptosisRequest.hpp │ │ ├── ControllerMappedState.hpp │ │ ├── HeirRequest.hpp │ │ ├── RepLevRequest.hpp │ │ ├── ResourceReceiveResistance.hpp │ │ ├── ResourceReserveRequest.hpp │ │ ├── ResourceSendLimit.hpp │ │ ├── ResourceSendRequest.hpp │ │ ├── SpawnArrest.hpp │ │ └── SpawnRequest.hpp │ ├── prefab │ ├── LogEventReadout.hpp │ ├── LogReadout.hpp │ ├── LogStackReadout.hpp │ ├── ModalGuard.hpp │ ├── ModalLogReadout.hpp │ └── README.md │ ├── push │ ├── DistanceToGraphCenterCellState.hpp │ ├── DistanceToGraphCenterMessage.hpp │ ├── PushCellState.hpp │ ├── PushMessage.hpp │ └── README.md │ ├── py │ ├── README.md │ ├── dump_animate_frames_script.hpp │ ├── dump_concat_csvs_script.hpp │ └── strip_pyinclude_artifacts.hpp │ ├── quorum │ ├── CardinalQuorumState.hpp │ ├── CellQuorumState.hpp │ ├── QuorumMessage.hpp │ └── README.md │ ├── record │ ├── README.md │ ├── StintRootIDChangeoverRecorder.hpp │ ├── cell_census │ │ ├── write_cell_age.hpp │ │ ├── write_kin_group_age.hpp │ │ ├── write_kin_group_id.hpp │ │ ├── write_peripheral_count.hpp │ │ ├── write_resource_stockpile.hpp │ │ └── write_spawn_count.hpp │ ├── drawings │ │ ├── DrawerCollection.hpp │ │ ├── DrawerManager.hpp │ │ ├── GridDrawer.hpp │ │ ├── PolymorphicDrawer.hpp │ │ └── SeriesDrawer.hpp │ ├── dump_abundance_genome.hpp │ ├── dump_abundance_over_all_roots_genome.hpp │ ├── dump_arbitrary_genome.hpp │ ├── dump_arbitrary_over_all_roots_genome.hpp │ ├── dump_benchmark_results.hpp │ ├── dump_birth_log.hpp │ ├── dump_coalescence_result.hpp │ ├── dump_death_log.hpp │ ├── dump_genome.hpp │ ├── dump_genome_statistics.hpp │ ├── dump_in_progress_jenga_nopout_genome.hpp │ ├── dump_interroot_phenotype_differentiation.hpp │ ├── dump_kin_conflict_by_replev_statistics.hpp │ ├── dump_kin_conflict_statistics.hpp │ ├── dump_population.hpp │ ├── dump_spawn_log.hpp │ ├── finalize │ │ ├── animate_frames.hpp │ │ ├── create_deduplicated_drawing_archive.hpp │ │ ├── create_montage.hpp │ │ ├── finalize_artifacts.hpp │ │ ├── finalize_benchmarks.hpp │ │ ├── finalize_data.hpp │ │ ├── finalize_drawings.hpp │ │ ├── finalize_videos.hpp │ │ ├── finalize_zips.hpp │ │ ├── try_animate_frames.hpp │ │ └── try_create_montage.hpp │ ├── global_records_finalize.hpp │ ├── global_records_initialize.hpp │ ├── make_filename │ │ ├── make_artifact_path.hpp │ │ ├── make_battleship_divergence_updates_filename.hpp │ │ ├── make_benchmark_path.hpp │ │ ├── make_benchmark_results_filename.hpp │ │ ├── make_birth_log_filename.hpp │ │ ├── make_cell_census_filename.hpp │ │ ├── make_coalescence_result_filename.hpp │ │ ├── make_data_path.hpp │ │ ├── make_death_log_filename.hpp │ │ ├── make_demographic_phenotypic_phylogenetic_metrics_filename.hpp │ │ ├── make_drawing_archive_filename.hpp │ │ ├── make_drawing_filename.hpp │ │ ├── make_drawing_path.hpp │ │ ├── make_dump_abundance_genome_filename.hpp │ │ ├── make_dump_abundance_over_all_roots_genome_filename.hpp │ │ ├── make_dump_arbitrary_genome_filename.hpp │ │ ├── make_dump_arbitrary_over_all_roots_genome_filename.hpp │ │ ├── make_dump_population_filename.hpp │ │ ├── make_elapsed_updates_filename.hpp │ │ ├── make_frame_path.hpp │ │ ├── make_genome_statistics_filename.hpp │ │ ├── make_in_progress_jenga_nopout_genome_filename.hpp │ │ ├── make_interroot_phenotype_differentiation_filename.hpp │ │ ├── make_jenga_divergence_updates_filename.hpp │ │ ├── make_kin_conflict_by_replev_statistics_filename.hpp │ │ ├── make_kin_conflict_statistics_filename.hpp │ │ ├── make_log_filename.hpp │ │ ├── make_meta_path.hpp │ │ ├── make_montage_filename.hpp │ │ ├── make_phylogenetic_root_abundances_filename.hpp │ │ ├── make_spawn_log_filename.hpp │ │ ├── make_stint_root_id_changeover_filename.hpp │ │ └── make_zip_path.hpp │ ├── try_write_all_drawings.hpp │ ├── write_all_drawings.hpp │ ├── write_cell_census.hpp │ ├── write_demographic_phenotypic_phylogenetic_metrics.hpp │ ├── write_phylogenetic_root_abundances.hpp │ ├── write_selected_drawings.hpp │ └── write_selected_frames.hpp │ ├── run │ ├── README.md │ ├── print_progress.hpp │ ├── setup_thread_local_random.hpp │ ├── thread_artifacts_dump.hpp │ ├── thread_benchmarks_dump.hpp │ ├── thread_data_dump.hpp │ ├── thread_data_write.hpp │ ├── thread_end_snapshot.hpp │ ├── thread_evolve.hpp │ ├── thread_job.hpp │ ├── thread_should_continue.hpp │ ├── thread_step.hpp │ └── thread_try_end_snapshot.hpp │ ├── runninglog │ ├── BirthEvent.hpp │ ├── DeathEvent.hpp │ ├── README.md │ ├── RunningLog.hpp │ ├── RunningLogs.hpp │ └── SpawnEvent.hpp │ ├── services │ ├── ApoptosisService.hpp │ ├── BirthSetupService.hpp │ ├── CellAgeService.hpp │ ├── CellDeathService.hpp │ ├── CollectiveHarvestingService.hpp │ ├── CollectiveResourceDecayService.hpp │ ├── ConduitFlushService.hpp │ ├── ControllerMappedStateNoiseService.hpp │ ├── CpuExecutionService.hpp │ ├── DecayToBaselineService.hpp │ ├── EpochAdvanceService.hpp │ ├── EventLaunchingService.hpp │ ├── GroupExpirationService.hpp │ ├── InterMessageLaunchingService.hpp │ ├── InterMessagePurgingService.hpp │ ├── IntermittentExtrospectiveStateExchangeRestoreService.hpp │ ├── IntermittentExtrospectiveStateExchangeService.hpp │ ├── IntermittentExtrospectiveStateRotateRestoreService.hpp │ ├── IntermittentExtrospectiveStateRotateService.hpp │ ├── IntermittentIntrospectiveStateExchangeRestoreService.hpp │ ├── IntermittentIntrospectiveStateExchangeService.hpp │ ├── IntermittentIntrospectiveStateRotateRestoreService.hpp │ ├── IntermittentIntrospectiveStateRotateService.hpp │ ├── IntermittentWritableStateExchangeRestoreService.hpp │ ├── IntermittentWritableStateExchangeService.hpp │ ├── IntermittentWritableStateRotateRestoreService.hpp │ ├── IntermittentWritableStateRotateService.hpp │ ├── InterpretedIntrospectiveStateRefreshService.hpp │ ├── IntraMessageLaunchingService.hpp │ ├── MessageCounterClearService.hpp │ ├── PushService.hpp │ ├── QuorumCapService.hpp │ ├── QuorumService.hpp │ ├── README.md │ ├── ResourceDecayService.hpp │ ├── ResourceHarvestingService.hpp │ ├── ResourceReceivingService.hpp │ ├── ResourceSendingService.hpp │ ├── RunningLogPurgeService.hpp │ ├── ServiceManager.hpp │ ├── SpawnSendingService.hpp │ ├── StateInputJumpService.hpp │ ├── StateOutputPutService.hpp │ └── _index.hpp │ ├── services_threadlocal │ ├── CellUpdateService.hpp │ ├── DiversityMaintenanceService.hpp │ ├── README.md │ ├── StintDiversityMaintenanceService.hpp │ ├── ThreadLocalServiceManager.hpp │ └── _index.hpp │ ├── spec │ ├── GenomeMeshSpec.hpp │ ├── IntraMessageMeshSpec.hpp │ ├── MessageMeshSpec.hpp │ ├── PushMeshSpec.hpp │ ├── QuorumMeshSpec.hpp │ ├── README.md │ ├── ResourceMeshSpec.hpp │ ├── Spec.hpp │ ├── StateMeshSpec.hpp │ ├── _NLEV.hpp │ ├── prefab │ │ ├── Spec_default.hpp │ │ ├── Spec_dnh2v.hpp │ │ ├── Spec_prq49.hpp │ │ └── _index.hpp │ └── print_spec.hpp │ ├── utility │ ├── BytewiseIterator.hpp │ ├── IndexShuffler.hpp │ ├── IterShuffler.hpp │ ├── README.md │ ├── autoload.hpp │ ├── calc_fitness_differential.hpp │ ├── get_hostname.hpp │ ├── is_native.hpp │ ├── is_web.hpp │ ├── make_histogram.hpp │ ├── make_mask.hpp │ ├── make_targeted_mask.hpp │ ├── measure_compression_ratio.hpp │ ├── mkdir_exists_ok.hpp │ ├── nop_nth_op.hpp │ ├── pare_keyname_filename.hpp │ ├── pare_keyname_filename_impl.hpp │ ├── path_exists.hpp │ ├── print_js_stacktrace.hpp │ ├── sha256_file.hpp │ ├── sha256_reduce.hpp │ ├── static_coarse_timer.hpp │ ├── strlen.hpp │ ├── to_alnum.hpp │ └── try_with_timeout.hpp │ ├── viz │ ├── README.md │ ├── artists │ │ ├── ApoptosisRequestArtist.hpp │ │ ├── Artist.hpp │ │ ├── CardinalOrderArtist.hpp │ │ ├── CellBirthArtist.hpp │ │ ├── DistanceToGraphCenterArtist.hpp │ │ ├── DummyArtist.hpp │ │ ├── EpochArtist.hpp │ │ ├── ExpressionByModuleArtist.hpp │ │ ├── HeirRequestArtist.hpp │ │ ├── IncomingInterMessageCounterArtist.hpp │ │ ├── IncomingIntraMessageCounterArtist.hpp │ │ ├── IsAliveArtist.hpp │ │ ├── KinGroupAgeArtist.hpp │ │ ├── KinGroupIDArtist.hpp │ │ ├── KinGroupIDLevArtist.hpp │ │ ├── KinGroupIDViewArtist.hpp │ │ ├── KinMatchArtist.hpp │ │ ├── LearnedQuorumBitArtist.hpp │ │ ├── LearnedQuorumBitsArtist.hpp │ │ ├── MostRecentCauseOfDeathArtist.hpp │ │ ├── NeighborKinGroupIDViewArtist.hpp │ │ ├── NeighborPosArtist.hpp │ │ ├── NumBusyCoresArtist.hpp │ │ ├── NumModulesArtist.hpp │ │ ├── PcaBinaryExpressionArtist.hpp │ │ ├── PcaExpressionArtist.hpp │ │ ├── PcaRegulationArtist.hpp │ │ ├── PcaTrinaryRegulationArtist.hpp │ │ ├── PeripheralityLevArtist.hpp │ │ ├── PhylogeneticRootArtist.hpp │ │ ├── QuorumBitArtist.hpp │ │ ├── QuorumBitOwnArtist.hpp │ │ ├── QuorumBitsArtist.hpp │ │ ├── QuorumCapArtist.hpp │ │ ├── RegulationByModuleArtist.hpp │ │ ├── RegulationExposedByModuleArtist.hpp │ │ ├── ResourceInputPeekArtist.hpp │ │ ├── ResourceStockpileArtist.hpp │ │ ├── SpawnArrestArtist.hpp │ │ ├── SpawnRequestArtist.hpp │ │ ├── SpawnedFromArtist.hpp │ │ ├── TaxaArtist.hpp │ │ └── _index.hpp │ ├── border_colormaps │ │ ├── DummyBorderColorMap.hpp │ │ ├── KinGroupIDBorderColorMap.hpp │ │ ├── KinGroupIDBorderGrayColorMap.hpp │ │ ├── KinGroupIDBorderInvertColorMap.hpp │ │ ├── MatchBorderColorMap.hpp │ │ └── TaxaBorderColorMap.hpp │ ├── fill_colormaps │ │ ├── BooleanColorMap.hpp │ │ ├── CauseOfDeathColorMap.hpp │ │ ├── CellBirthColorMap.hpp │ │ ├── DistanceToGraphCenterColorMap.hpp │ │ ├── DummyFillColorMap.hpp │ │ ├── EpochColorMap.hpp │ │ ├── IncomingInterMessageCounterColorMap.hpp │ │ ├── IsAliveColorMap.hpp │ │ ├── KinGroupAgeColorMap.hpp │ │ ├── KinGroupIDFillColorMap.hpp │ │ ├── KinGroupIDGrayscaleFillColorMap.hpp │ │ ├── KinGroupIDLevFillColorMap.hpp │ │ ├── KinMatchColorMap.hpp │ │ ├── NumBusyCoresColorMap.hpp │ │ ├── PcaBinaryExpressionColorMap.hpp │ │ ├── PcaExpressionColorMap.hpp │ │ ├── PcaRegulationColorMap.hpp │ │ ├── PcaTrinaryRegulationColorMap.hpp │ │ ├── PhylogeneticRootColorMap.hpp │ │ ├── QuorumBitsColorMap.hpp │ │ ├── RegulationColorMap.hpp │ │ ├── RegulationExposedColorMap.hpp │ │ ├── ResourceInputPeekColorMap.hpp │ │ └── ResourceStockpileColorMap.hpp │ ├── getters │ │ ├── ApoptosisRequestGetter.hpp │ │ ├── CardiCoordGetter.hpp │ │ ├── CardinalIteratorAdapter.hpp │ │ ├── CardinalOrderGetter.hpp │ │ ├── CellAgeGetter.hpp │ │ ├── DistanceToGraphCenterGetter.hpp │ │ ├── DummyGetter.hpp │ │ ├── EpochGetter.hpp │ │ ├── ExpressionByModuleGetter.hpp │ │ ├── GenomeGetter.hpp │ │ ├── HeirRequestGetter.hpp │ │ ├── IncomingInterMessageCounterGetter.hpp │ │ ├── IncomingIntraMessageCounterGetter.hpp │ │ ├── IsAliveGetter.hpp │ │ ├── KinGroupAgeGetter.hpp │ │ ├── KinGroupIDGetter.hpp │ │ ├── KinGroupIDLevGetter.hpp │ │ ├── KinGroupIDViewGetter.hpp │ │ ├── KinMatchGetter.hpp │ │ ├── LearnedQuorumBitGetter.hpp │ │ ├── LearnedQuorumBitsGetter.hpp │ │ ├── MostRecentCauseOfDeathGetter.hpp │ │ ├── NeighborKinGroupIDViewGetter.hpp │ │ ├── NeighborPosGetter.hpp │ │ ├── NumBusyCoresGetter.hpp │ │ ├── NumModulesGetter.hpp │ │ ├── PeripheralityLevGetter.hpp │ │ ├── PhylogeneticRootGetter.hpp │ │ ├── QuorumBitGetter.hpp │ │ ├── QuorumBitOwnGetter.hpp │ │ ├── QuorumBitsGetter.hpp │ │ ├── QuorumCapGetter.hpp │ │ ├── RegulationByModuleGetter.hpp │ │ ├── RegulationExposedByModuleGetter.hpp │ │ ├── ResourceInputPeekGetter.hpp │ │ ├── ResourceStockpileGetter.hpp │ │ ├── SpawnArrestGetter.hpp │ │ ├── SpawnRequestGetter.hpp │ │ └── SpawnedFromGetter.hpp │ ├── renderers │ │ ├── CardinalFillRenderer.hpp │ │ ├── CellBorderRenderer.hpp │ │ └── CellFillRenderer.hpp │ └── util │ │ └── CanvasMathHelper.hpp │ ├── web │ ├── Animator.hpp │ ├── ControlPanel.hpp │ ├── DataPill.hpp │ ├── DataPillCollection.hpp │ ├── DocumentHandles.hpp │ ├── ExecutionLogPanel.hpp │ ├── GridViewer.hpp │ ├── InstructionListDetailItem.hpp │ ├── InstructionListEntryItem.hpp │ ├── InstructionListNopOutItem.hpp │ ├── InstructionListRefreshItem.hpp │ ├── ModalLogReadoutPanel.hpp │ ├── PrevalentGenotypePanel.hpp │ ├── README.md │ ├── SeriesViewer.hpp │ ├── SystematicsPanel.hpp │ ├── ViewerCollection.hpp │ ├── ViewerManager.hpp │ ├── ViewerPanel.hpp │ ├── WebInterface.hpp │ ├── data_pills │ │ ├── ElapsedGenerationsPill.hpp │ │ ├── MaximumModuleCountPill.hpp │ │ ├── MaximumProgramLengthPill.hpp │ │ ├── MeanElapsedInsertionsDeletionsPill.hpp │ │ ├── MeanElapsedMutationOccurencesPill.hpp │ │ ├── MeanElapsedPointMutationsPill.hpp │ │ ├── MeanEpochPill.hpp │ │ ├── MeanModuleCountPill.hpp │ │ ├── MeanProgramLengthPill.hpp │ │ ├── NumLiveCellsPill.hpp │ │ ├── NumPhylogeneticRootsPill.hpp │ │ ├── NumUniqueGenotypesPill.hpp │ │ ├── NumUniqueModuleExpressionProfilesPill.hpp │ │ ├── NumUniqueModuleRegulationProfilesPill.hpp │ │ ├── PrevalentGenotypeCountPill.hpp │ │ └── _index.hpp │ └── viewer_categories │ │ ├── ApoptosisCategory.hpp │ │ ├── DemographicsCategory.hpp │ │ ├── GroupStructureCategory.hpp │ │ ├── MessagingCategory.hpp │ │ ├── RegulationCategory.hpp │ │ ├── ReproductionCategory.hpp │ │ ├── ResourceCollectionCategory.hpp │ │ ├── SharingCategory.hpp │ │ └── _index.hpp │ └── world │ ├── ProcWorld.hpp │ ├── README.md │ ├── ThreadWorld.hpp │ └── iterators │ ├── CodingGenotypeConstWrapper.hpp │ ├── ElapsedInsertionsDeletionsConstWrapper.hpp │ ├── ElapsedMutationOccurencesConstWrapper.hpp │ ├── ElapsedPointMutationsConstWrapper.hpp │ ├── GenerationCounterConstWrapper.hpp │ ├── GenotypeConstWrapper.hpp │ ├── LiveCellIdxIterator.hpp │ ├── LiveCellIterator.hpp │ ├── LogIteratorAdapter.hpp │ ├── PeripheralityLevWrapper.hpp │ ├── RootIDConstWrapper.hpp │ ├── RootIDValWrapper.hpp │ ├── StintRootIDValWrapper.hpp │ ├── WorldIteratorAbridger.hpp │ ├── WorldIteratorAdapter.hpp │ ├── WorldIteratorAnyOfer.hpp │ ├── WorldIteratorAverager.hpp │ └── WorldIteratorValueAdapter.hpp ├── microbenchmarks ├── Makefile ├── MaketemplateForwarding ├── MaketemplateRunning ├── README.md ├── dish2 │ ├── Makefile │ ├── generic_work.cpp │ ├── nop.cpp │ └── update.cpp ├── script │ ├── consolidate.py │ ├── fixup_and_validate.sh │ ├── graph.py │ ├── headtail.sh │ └── upload.sh └── slurm │ ├── README.md │ ├── job.sh │ ├── nnode=1+nproc=8+ext=.slurm.sh │ └── nnode=8+nproc=1+ext=.slurm.sh ├── package.json ├── postprocessing ├── README.md ├── collate.py ├── collate_helpers │ ├── README.md │ ├── collate_control_competition_series.sh │ ├── collate_evolve_config_records_series.sh │ ├── collate_evolve_statistics_series.sh │ ├── collate_genome_statistics_series.sh │ ├── collate_lowestroot_immediatepredecessor_battle_series.sh │ ├── collate_monoculture_runninglogs_series.sh │ ├── collate_monoculture_statistics_series.sh │ ├── collate_mutant_competition_series.sh │ ├── collate_mutant_deletion_competition_series.sh │ ├── collate_mutant_deletion_phenotype_differentiation_series.sh │ ├── collate_mutant_insertion_competition_series.sh │ ├── collate_mutant_insertion_phenotype_differentiation_series.sh │ ├── collate_mutant_phenotype_differentiation_series.sh │ ├── collate_mutant_point_competition_series.sh │ ├── collate_mutant_point_phenotype_differentiation_series.sh │ ├── collate_mutating_competition_series.sh │ ├── collate_noncritical_nopout_competition_series.sh │ ├── collate_noncritical_phenotypeequivalent_nopinterpolation_competition_series.sh │ ├── collate_perturbation_competition_series.sh │ ├── collate_phenotype_neutral_nopout_competition_series.sh │ ├── collate_phenotype_neutral_nopout_phenotype_differentiation_series.sh │ ├── collate_predecessor_battle_series.sh │ ├── collate_selfsend_competition_series.sh │ ├── collate_strain_competition_series.sh │ ├── collate_variant_competition_series.sh │ └── collate_wildtype_doubling_time_series.sh ├── collate_one_stint_across_series.sh ├── collate_series_profiles_across_stints.sh ├── collate_thread_profiles_across_stints.sh ├── dishpylib ├── elaborate_all_stints_all_series_profiles.py ├── elaborate_all_stints_all_thread_profiles.py ├── postprocess_all_stints.sh ├── postprocess_one_stint.sh ├── tabulate_and_stitch_stint_series_profiles.py └── tabulate_and_stitch_stint_thread_profiles.py ├── script ├── README.md ├── animate_frames.py ├── check_progress.sh ├── check_quota.sh ├── concat_csvs.py ├── consolidate_benchmarking_dumps.sh ├── dishpylib ├── gitget.sh ├── host_sbatch.sh ├── host_squeue.sh ├── layout_interstrain_tournament.py ├── make_noncritical_nopouts.py ├── make_nop_interpolated_variants.py ├── make_nopped_op_variants.py ├── purge_logs.sh ├── repro_runner.sh ├── setup_cloudshell.sh ├── slurm_stoker.slurm.sh.jinja ├── slurm_stoker_containerized_kickoff.sh └── slurm_stoker_kickoff.sh ├── slurm ├── README.md ├── collate │ ├── collatecronkickoff.sh │ ├── competitions_collatecronjob.slurm.sh.jinja │ ├── evolve_collatecronjob.slurm.sh.jinja │ ├── genomes_collatecronjob.slurm.sh.jinja │ └── monocultures_collatecronjob.slurm.sh.jinja ├── competition │ ├── competitionjob.slurm.sh.jinja │ ├── controlcompetitionkickoff.sh │ ├── lowestroot-immediatepredecessorbattlekickoff.sh │ ├── mutantcompetitionkickoff.sh │ ├── mutantdeletioncompetitionkickoff.sh │ ├── mutantinsertioncompetitionkickoff.sh │ ├── mutantpointcompetitionkickoff.sh │ ├── mutatingcompetitionkickoff.sh │ ├── noncritical-nopoutcompetitionkickoff.sh │ ├── noncritical-phenotypeequivalent-nopinterpolation-competitionkickoff.sh │ ├── perturbationcompetitionkickoff.sh │ ├── phenotype-neutral-nopoutcompetitionkickoff.sh │ ├── predecessorbattlekickoff.sh │ ├── selfsendcompetitionkickoff.sh │ ├── straincompetitioncronjob.slurm.sh.jinja │ ├── straincompetitioncronkickoff.sh │ └── straincompetitionkickoff.sh ├── doubling-time │ ├── doubling-timejob.slurm.sh.jinja │ └── wildtypedoubling-timekickoff.sh ├── evolve │ ├── evolvefollowupsjob.slurm.sh.jinja │ ├── evolvefollowupskickoff.sh │ ├── evolvejob.slurm.sh.jinja │ └── evolvekickoff.sh ├── genomes │ ├── nopoutjob.slurm.sh.jinja │ └── nopoutkickoff.sh ├── monocultures │ ├── monoculturejob.slurm.sh.jinja │ └── monoculturekickoff.sh ├── phenotype-differentiation │ ├── mutantdeletionphenotype-differentiationkickoff.sh │ ├── mutantinsertionphenotype-differentiationkickoff.sh │ ├── mutantphenotype-differentiationkickoff.sh │ ├── mutantpointphenotype-differentiationkickoff.sh │ ├── phenotype-differentiationjob.slurm.sh.jinja │ └── phenotype-neutral-nopoutphenotype-differentiationkickoff.sh └── polycultures │ ├── polyculturejob.slurm.sh.jinja │ └── polyculturekickoff.sh ├── source ├── README.md ├── native.cpp └── web.cpp ├── tests ├── Makefile ├── MaketemplateForwarding ├── MaketemplateRunning ├── MaketemplateWebRunning ├── convert_for_tests.sh ├── dish2 │ ├── Makefile │ ├── cell │ │ ├── Makefile │ │ ├── cardinal_iterators │ │ │ ├── ApoptosisRequestWrapper.cpp │ │ │ ├── CardinalQuorumStateWrapper.cpp │ │ │ ├── CpuWrapper.cpp │ │ │ ├── GenomeNodeInputWrapper.cpp │ │ │ ├── GenomeNodeOutputWrapper.cpp │ │ │ ├── IdentityWrapper.cpp │ │ │ ├── IsAliveWrapper.cpp │ │ │ ├── KinMatchWrapper.cpp │ │ │ ├── Makefile │ │ │ ├── NeighborResourceReceiveResistanceWrapper.cpp │ │ │ ├── PeripheralWrapper.cpp │ │ │ ├── ResourceNodeInputWrapper.cpp │ │ │ ├── ResourceNodeOutputWrapper.cpp │ │ │ ├── ResourceReserveRequestWrapper.cpp │ │ │ ├── ResourceSendLimitWrapper.cpp │ │ │ ├── ResourceSendRequestWrapper.cpp │ │ │ ├── ResourceStockpileWrapper.cpp │ │ │ ├── SpawnArrestWrapper.cpp │ │ │ ├── SpawnRequestWrapper.cpp │ │ │ └── StateNodeInputWrapper.cpp │ │ └── cell │ │ │ ├── Cardinal.cpp │ │ │ ├── Cell.cpp │ │ │ └── Makefile │ ├── config │ │ ├── Makefile │ │ └── calc_rng_preseed.cpp │ ├── genome │ │ ├── EventTags.cpp │ │ ├── GenerationCounter.cpp │ │ ├── Genome.cpp │ │ ├── KinGroupID.cpp │ │ ├── Makefile │ │ ├── MutationCounter.cpp │ │ └── RootID.cpp │ ├── operations │ │ ├── AddToOwnState.cpp │ │ ├── Makefile │ │ ├── MultiplyOwnState.cpp │ │ ├── ReadNeighborState.cpp │ │ ├── ReadOwnState.cpp │ │ ├── SendInterMessageIf.cpp │ │ └── WriteOwnStateIf.cpp │ ├── peripheral │ │ ├── Makefile │ │ ├── peripheral │ │ │ ├── Makefile │ │ │ └── Peripheral.cpp │ │ └── readable_state │ │ │ ├── Makefile │ │ │ ├── introspective_state │ │ │ ├── Makefile │ │ │ ├── interpreted_introspective_state │ │ │ │ └── Makefile │ │ │ ├── introspective_state │ │ │ │ ├── IntrospectiveState.cpp │ │ │ │ └── Makefile │ │ │ └── raw_introspective_state │ │ │ │ ├── IsAlive.cpp │ │ │ │ ├── Makefile │ │ │ │ └── ResourceStockpile.cpp │ │ │ ├── readable_state │ │ │ ├── Makefile │ │ │ └── ReadableState.cpp │ │ │ └── writable_state │ │ │ ├── Makefile │ │ │ ├── controller_mapped_state │ │ │ ├── ApoptosisRequest.cpp │ │ │ ├── ControllerMappedState.cpp │ │ │ ├── Makefile │ │ │ ├── ResourceReceiveResistance.cpp │ │ │ ├── ResourceReserveRequest.cpp │ │ │ ├── ResourceSendLimit.cpp │ │ │ ├── ResourceSendRequest.cpp │ │ │ ├── SpawnArrest.cpp │ │ │ └── SpawnRequest.cpp │ │ │ └── writable_state │ │ │ ├── Makefile │ │ │ ├── NopState.cpp │ │ │ └── WritableState.cpp │ ├── quorum │ │ ├── CardinalQuorumState.cpp │ │ ├── CellQuorumState.cpp │ │ ├── Makefile │ │ └── QuorumMessage.cpp │ ├── record │ │ ├── GridDrawer.cpp │ │ └── Makefile │ ├── runninglog │ │ ├── Makefile │ │ └── RunningLog.cpp │ ├── services │ │ ├── Makefile │ │ └── QuorumService.cpp │ ├── spec │ │ ├── GenomeMeshSpec.cpp │ │ ├── Makefile │ │ ├── MessageMeshSpec.cpp │ │ ├── QuorumMeshSpec.cpp │ │ ├── ResourceMeshSpec.cpp │ │ ├── Spec.cpp │ │ └── StateMeshSpec.cpp │ ├── utility │ │ ├── Makefile │ │ ├── pare_keyname_filename.cpp │ │ ├── sha256_reduce.cpp │ │ ├── static_coarse_timer.cpp │ │ └── try_with_timeout.cpp │ ├── viz │ │ ├── Makefile │ │ ├── artists │ │ │ ├── Artist.cpp │ │ │ ├── DummyArtist.cpp │ │ │ ├── IsAliveArtist.cpp │ │ │ ├── KinGroupIDArtist.cpp │ │ │ ├── Makefile │ │ │ ├── PhylogeneticRootArtist.cpp │ │ │ ├── QuorumBitsArtist.cpp │ │ │ ├── ResourceStockpileArtist.cpp │ │ │ ├── assets │ │ │ │ ├── Artist.png │ │ │ │ ├── DummyArtist.png │ │ │ │ ├── IsAliveArtist.png │ │ │ │ ├── KinGroupIDArtist.png │ │ │ │ ├── PhylogeneticRootArtist.png │ │ │ │ └── ResourceStockpileArtist.png │ │ │ └── package.json │ │ ├── border_colormaps │ │ │ ├── DummyBorderColorMap.cpp │ │ │ ├── KinGroupIDBorderColorMap.cpp │ │ │ └── Makefile │ │ ├── fill_colormaps │ │ │ ├── DummyFillColorMap.cpp │ │ │ ├── IsAliveColorMap.cpp │ │ │ ├── KinGroupIDFillColorMap.cpp │ │ │ ├── Makefile │ │ │ ├── PhylogeneticRootColorMap.cpp │ │ │ ├── QuorumBitsColorMap.cpp │ │ │ └── ResourceStockpileColorMap.cpp │ │ ├── getters │ │ │ ├── CardinalIteratorAdapter.cpp │ │ │ ├── DummyGetter.cpp │ │ │ ├── IsAliveGetter.cpp │ │ │ ├── KinGroupIDGetter.cpp │ │ │ ├── Makefile │ │ │ ├── PhylogeneticRootGetter.cpp │ │ │ ├── QuorumBitsGetter.cpp │ │ │ └── ResourceStockpileGetter.cpp │ │ ├── renderers │ │ │ ├── CardinalFillRenderer.cpp │ │ │ ├── CellBorderRenderer.cpp │ │ │ ├── CellFillRenderer.cpp │ │ │ ├── Makefile │ │ │ ├── assets │ │ │ │ ├── CardinalFillRenderer.png │ │ │ │ ├── CellBorderRenderer.png │ │ │ │ └── CellFillRenderer.png │ │ │ └── package.json │ │ └── util │ │ │ ├── CanvasMathHelper.cpp │ │ │ └── Makefile │ ├── web │ │ ├── Animator.cpp │ │ ├── ControlPanel.cpp │ │ ├── GridViewer.cpp │ │ ├── Makefile │ │ ├── ViewerCollection.cpp │ │ ├── ViewerPanel.cpp │ │ ├── WebInterface.cpp │ │ └── package.json │ └── world │ │ ├── Makefile │ │ ├── ProcWorld.cpp │ │ └── ThreadWorld.cpp └── source │ ├── Makefile │ ├── native.bats │ └── native_opt.bats ├── third-party ├── Catch ├── Empirical ├── cereal ├── conduit ├── force-cover ├── install_dependencies.sh ├── install_emsdk.sh ├── install_force-cover.sh ├── requirements.in └── requirements.txt ├── twitterbot ├── watch_me_evolve.py ├── wme_competitionjob.py ├── wme_doubling-timejob.py ├── wme_evolvejob.py ├── wme_monoculturejob.py ├── wme_nopoutjob.py └── wme_phenotype-differentiationjob.py └── web ├── README.md ├── binoculars.jpg ├── cpus.jpg ├── custom.css ├── desk.jpg ├── football.jpg ├── includes ├── acknowledgements.html ├── config.html ├── controls.html ├── dominant-viewer.html ├── execution-log-panel.html ├── header.html ├── jumbotron.html ├── population-loader.html ├── readme.html ├── references-body.html ├── social.html ├── source-body.html ├── spinner.html ├── status-console.html ├── systematics.html ├── view-key.html.jinja ├── view-selector.html └── viewer.html ├── jquery-1.11.2.min.js ├── keys.toml ├── lightbulb.jpg ├── make_html.py ├── mirror.jpg ├── moreno.jpg ├── ofria.jpg ├── perry.jpg ├── rodriguez.png ├── stork.jpg └── template.html.jinja /.bumpversion.cfg: -------------------------------------------------------------------------------- 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