from dataframe import surface_postprocess_trie, surface_unpack_reconstruct
from frozen_instrumentation import (
    HereditaryStratigraphicAssemblage,
    HereditaryStratigraphicAssemblageSpecimen,
    HereditaryStratigraphicSpecimen,
)
from genome_instrumentation import (
    HereditaryStratigraphicColumn,
    HereditaryStratigraphicColumnBundle,
    HereditaryStratum,
    HereditaryStratumOrderedStoreDict,
    HereditaryStratumOrderedStoreList,
    HereditaryStratumOrderedStoreTree,
    provided_stratum_ordered_stores,
    stratum_ordered_stores,
)
from juxtaposition import (
    calc_definitive_max_rank_of_first_retained_disparity_between,
    calc_definitive_max_rank_of_last_retained_commonality_between,
    calc_definitive_min_ranks_since_first_retained_disparity_with,
    calc_definitive_min_ranks_since_last_retained_commonality_with,
    calc_min_implausible_spurious_consecutive_differentia_collisions_between,
    calc_probability_differentia_collision_between,
    calc_rank_of_first_retained_disparity_between,
    calc_rank_of_last_retained_commonality_between,
    calc_ranks_since_first_retained_disparity_with,
    calc_ranks_since_last_retained_commonality_with,
    diff_retained_ranks,
    get_last_common_stratum_between,
    get_nth_common_rank_between,
)
from phylogenetic_inference import (
    ArbitraryPrior,
    AssignDestructionTimeYoungestPlusOneTriePostprocessor,
    AssignOriginTimeExpectedValueTriePostprocessor,
    AssignOriginTimeNaiveTriePostprocessor,
    AssignOriginTimeNodeRankTriePostprocessor,
    AssignOriginTimeSampleNaiveTriePostprocessor,
    CompoundTriePostprocessor,
    ExponentialPrior,
    GeometricPrior,
    NopTriePostprocessor,
    PeelBackConjoinedLeavesTriePostprocessor,
    SampleAncestralRollbacksTriePostprocessor,
    UniformPrior,
    ballpark_patristic_distance_between,
    ballpark_rank_of_mrca_between,
    ballpark_ranks_since_mrca_with,
    build_distance_matrix_biopython,
    build_distance_matrix_numpy,
    build_tree,
    build_tree_nj,
    build_tree_searchtable,
    build_tree_trie,
    build_tree_trie_ensemble,
    build_tree_upgma,
    calc_patristic_distance_bounds_between,
    calc_rank_of_earliest_detectable_mrca_among,
    calc_rank_of_earliest_detectable_mrca_between,
    calc_rank_of_mrca_bounds_among,
    calc_rank_of_mrca_bounds_between,
    calc_rank_of_mrca_bounds_provided_confidence_level,
    calc_rank_of_mrca_uncertainty_among,
    calc_rank_of_mrca_uncertainty_between,
    calc_ranks_since_earliest_detectable_mrca_with,
    calc_ranks_since_mrca_bounds_provided_confidence_level,
    calc_ranks_since_mrca_bounds_with,
    calc_ranks_since_mrca_uncertainty_with,
    does_definitively_have_no_common_ancestor,
    does_definitively_share_no_common_ancestor,
    does_have_any_common_ancestor,
    does_share_any_common_ancestor,
    estimate_patristic_distance_between,
    estimate_rank_of_mrca_between,
    estimate_rank_of_mrca_maximum_likelihood,
    estimate_rank_of_mrca_naive,
    estimate_rank_of_mrca_unbiased,
    estimate_ranks_since_mrca_with,
    estimators,
    pairwise,
    population,
    priors,
    tree,
    trie_postprocess,
)
from serialization import (
    assemblage_from_records,
    col_from_int,
    col_from_packet,
    col_from_packet_buffer,
    col_from_records,
    col_to_dataframe,
    col_to_int,
    col_to_packet,
    col_to_records,
    col_to_specimen,
    pack_differentiae,
    pack_differentiae_bytes,
    pack_differentiae_str,
    policy_from_records,
    policy_to_records,
    pop_from_records,
    pop_to_assemblage,
    pop_to_dataframe,
    pop_to_records,
    specimen_from_records,
    unassemblage_from_records,
    unpack_differentiae,
    unpack_differentiae_bytes,
    unpack_differentiae_str,
)
from stratum_retention_strategy import (
    MrcaUncertaintyAbsExactEvaluator,
    MrcaUncertaintyAbsUpperBoundEvaluator,
    MrcaUncertaintyRelExactEvaluator,
    MrcaUncertaintyRelUpperBoundEvaluator,
    NumStrataRetainedExactEvaluator,
    NumStrataRetainedUpperBoundEvaluator,
    PropertyAtLeastParameterizer,
    PropertyAtMostParameterizer,
    PropertyExactlyParameterizer,
    UnsatisfiableParameterizationRequestError,
    depth_proportional_resolution_algo,
    depth_proportional_resolution_tapered_algo,
    fixed_resolution_algo,
    geom_seq_nth_root_algo,
    geom_seq_nth_root_tapered_algo,
    nominal_resolution_algo,
    perfect_resolution_algo,
    provided_stratum_retention_algorithms,
    pseudostochastic_algo,
    recency_proportional_resolution_algo,
    recency_proportional_resolution_curbed_algo,
    stochastic_algo,
    stratum_retention_algorithms,
    stratum_retention_policy_evaluators,
    stratum_retention_policy_parameterizers,
)
from stratum_retention_viz import (
    animate,
    ascii,
    col_to_ascii,
    mrca_uncertainty_absolute_barplot,
    mrca_uncertainty_relative_barplot,
    plot,
    policy_panel_animate,
    policy_panel_plot,
    strata_retained_frac_lineplot,
    strata_retained_num_lineplot,
    stratum_retention_animate,
    stratum_retention_dripplot,
)
from test_drive import (
    DecantingPhyloTracker,
    GarbageCollectingPhyloTracker,
    PerfectBacktrackHandle,
    compile_perfect_backtrack_phylogeny,
    compile_phylogeny_from_lineage_iters,
    descend_template_phylogeny,
    descend_template_phylogeny_,
    descend_template_phylogeny_alifestd,
    descend_template_phylogeny_biopython,
    descend_template_phylogeny_dendropy,
    descend_template_phylogeny_naive,
    descend_template_phylogeny_networkx,
    descend_template_phylogeny_posthoc,
    evolve_fitness_trait_population,
    generate_template_phylogeny,
    iter_perfect_backtrack_lineage,
    perfect_tracking,
)

__all__ = [
    # dataframe
    "surface_postprocess_trie",
    "surface_unpack_reconstruct",
    # frozen_instrumentation
    "HereditaryStratigraphicAssemblage",
    "HereditaryStratigraphicAssemblageSpecimen",
    "HereditaryStratigraphicSpecimen",
    # genome_instrumentation
    "stratum_ordered_stores",
    "HereditaryStratum",
    "HereditaryStratigraphicColumn",
    "HereditaryStratigraphicColumnBundle",
    "HereditaryStratumOrderedStoreDict",
    "HereditaryStratumOrderedStoreList",
    "HereditaryStratumOrderedStoreTree",
    "provided_stratum_ordered_stores",
    # juxtaposition
    "calc_definitive_max_rank_of_first_retained_disparity_between",
    "calc_definitive_max_rank_of_last_retained_commonality_between",
    "calc_definitive_min_ranks_since_first_retained_disparity_with",
    "calc_definitive_min_ranks_since_last_retained_commonality_with",
    "calc_min_implausible_spurious_consecutive_differentia_collisions_between",
    "calc_probability_differentia_collision_between",
    "calc_rank_of_first_retained_disparity_between",
    "calc_rank_of_last_retained_commonality_between",
    "calc_ranks_since_first_retained_disparity_with",
    "calc_ranks_since_last_retained_commonality_with",
    "diff_retained_ranks",
    "get_last_common_stratum_between",
    "get_nth_common_rank_between",
    # phylogenetic_inference
    "estimators",
    "pairwise",
    "population",
    "priors",
    "tree",
    "estimate_rank_of_mrca_maximum_likelihood",
    "estimate_rank_of_mrca_naive",
    "estimate_rank_of_mrca_unbiased",
    "ballpark_patristic_distance_between",
    "ballpark_rank_of_mrca_between",
    "ballpark_ranks_since_mrca_with",
    "calc_patristic_distance_bounds_between",
    "calc_rank_of_earliest_detectable_mrca_between",
    "calc_rank_of_mrca_bounds_between",
    "calc_rank_of_mrca_bounds_provided_confidence_level",
    "calc_rank_of_mrca_uncertainty_between",
    "calc_ranks_since_earliest_detectable_mrca_with",
    "calc_ranks_since_mrca_bounds_with",
    "calc_ranks_since_mrca_bounds_provided_confidence_level",
    "calc_ranks_since_mrca_uncertainty_with",
    "does_definitively_have_no_common_ancestor",
    "does_have_any_common_ancestor",
    "estimate_patristic_distance_between",
    "estimate_rank_of_mrca_between",
    "estimate_ranks_since_mrca_with",
    "build_distance_matrix_biopython",
    "build_distance_matrix_numpy",
    "calc_rank_of_earliest_detectable_mrca_among",
    "calc_rank_of_mrca_bounds_among",
    "calc_rank_of_mrca_uncertainty_among",
    "does_definitively_share_no_common_ancestor",
    "does_share_any_common_ancestor",
    "ArbitraryPrior",
    "GeometricPrior",
    "ExponentialPrior",
    "UniformPrior",
    "build_tree_nj",
    "build_tree_searchtable",
    "build_tree_trie",
    "build_tree_trie_ensemble",
    "build_tree_upgma",
    "build_tree",
    "trie_postprocess",
    "AssignDestructionTimeYoungestPlusOneTriePostprocessor",
    "AssignOriginTimeExpectedValueTriePostprocessor",
    "AssignOriginTimeNaiveTriePostprocessor",
    "AssignOriginTimeNodeRankTriePostprocessor",
    "AssignOriginTimeSampleNaiveTriePostprocessor",
    "CompoundTriePostprocessor",
    "NopTriePostprocessor",
    "PeelBackConjoinedLeavesTriePostprocessor",
    "SampleAncestralRollbacksTriePostprocessor",
    # serialization
    "assemblage_from_records",
    "col_from_int",
    "col_from_packet",
    "col_from_packet_buffer",
    "col_from_records",
    "col_to_dataframe",
    "col_to_int",
    "col_to_packet",
    "col_to_records",
    "col_to_specimen",
    "pack_differentiae",
    "pack_differentiae_bytes",
    "pack_differentiae_str",
    "policy_from_records",
    "policy_to_records",
    "pop_from_records",
    "pop_to_assemblage",
    "pop_to_dataframe",
    "pop_to_records",
    "specimen_from_records",
    "unassemblage_from_records",
    "unpack_differentiae",
    "unpack_differentiae_bytes",
    "unpack_differentiae_str",
    # stratum_retention_strategy
    "stratum_retention_policy_parameterizers",
    "stratum_retention_algorithms",
    "stratum_retention_policy_evaluators",
    "MrcaUncertaintyAbsExactEvaluator",
    "MrcaUncertaintyAbsUpperBoundEvaluator",
    "MrcaUncertaintyRelExactEvaluator",
    "MrcaUncertaintyRelUpperBoundEvaluator",
    "NumStrataRetainedExactEvaluator",
    "NumStrataRetainedUpperBoundEvaluator",
    "UnsatisfiableParameterizationRequestError",
    "depth_proportional_resolution_algo",
    "depth_proportional_resolution_tapered_algo",
    "fixed_resolution_algo",
    "geom_seq_nth_root_algo",
    "geom_seq_nth_root_tapered_algo",
    "nominal_resolution_algo",
    "perfect_resolution_algo",
    "provided_stratum_retention_algorithms",
    "pseudostochastic_algo",
    "recency_proportional_resolution_algo",
    "recency_proportional_resolution_curbed_algo",
    "stochastic_algo",
    "PropertyAtLeastParameterizer",
    "PropertyAtMostParameterizer",
    "PropertyExactlyParameterizer",
    # stratum_retention_viz
    "animate",
    "ascii",
    "plot",
    "col_to_ascii",
    "stratum_retention_animate",
    "policy_panel_animate",
    "mrca_uncertainty_absolute_barplot",
    "mrca_uncertainty_relative_barplot",
    "policy_panel_plot",
    "strata_retained_frac_lineplot",
    "strata_retained_num_lineplot",
    "stratum_retention_dripplot",
    # test_drive
    "descend_template_phylogeny_",
    "generate_template_phylogeny",
    "perfect_tracking",
    "descend_template_phylogeny",
    "descend_template_phylogeny_alifestd",
    "descend_template_phylogeny_biopython",
    "descend_template_phylogeny_dendropy",
    "descend_template_phylogeny_naive",
    "descend_template_phylogeny_networkx",
    "descend_template_phylogeny_posthoc",
    "evolve_fitness_trait_population",
    "compile_perfect_backtrack_phylogeny",
    "compile_phylogeny_from_lineage_iters",
    "DecantingPhyloTracker",
    "GarbageCollectingPhyloTracker",
    "iter_perfect_backtrack_lineage",
    "PerfectBacktrackHandle",
]
