from phylogenie.generators import (
    AliSimDatasetGenerator,
    BDEITreeDatasetGenerator,
    BDSSTreeDatasetGenerator,
    BDTreeDatasetGenerator,
    CanonicalTreeDatasetGenerator,
    DatasetGenerator,
    DatasetGeneratorConfig,
    EpidemiologicalTreeDatasetGenerator,
    FBDTreeDatasetGenerator,
    TreeDatasetGeneratorConfig,
)
from phylogenie.io import load_fasta, load_newick
from phylogenie.msa import MSA
from phylogenie.skyline import (
    SkylineMatrix,
    SkylineMatrixCoercible,
    SkylineParameter,
    SkylineParameterLike,
    SkylineVector,
    SkylineVectorCoercible,
    SkylineVectorLike,
    skyline_matrix,
    skyline_parameter,
    skyline_vector,
)
from phylogenie.tree import Tree
from phylogenie.treesimulator import (
    Event,
    get_BD_events,
    get_BDEI_events,
    get_BDSS_events,
    get_canonical_events,
    get_epidemiological_events,
    get_FBD_events,
    simulate_tree,
)

__all__ = [
    "AliSimDatasetGenerator",
    "BDEITreeDatasetGenerator",
    "BDSSTreeDatasetGenerator",
    "BDTreeDatasetGenerator",
    "CanonicalTreeDatasetGenerator",
    "DatasetGenerator",
    "DatasetGeneratorConfig",
    "EpidemiologicalTreeDatasetGenerator",
    "FBDTreeDatasetGenerator",
    "SkylineMatrix",
    "SkylineMatrixCoercible",
    "skyline_matrix",
    "SkylineParameter",
    "SkylineParameterLike",
    "skyline_parameter",
    "SkylineVector",
    "SkylineVectorCoercible",
    "SkylineVectorLike",
    "skyline_vector",
    "Tree",
    "TreeDatasetGeneratorConfig",
    "Event",
    "get_BD_events",
    "get_BDEI_events",
    "get_BDSS_events",
    "get_canonical_events",
    "get_epidemiological_events",
    "get_FBD_events",
    "simulate_tree",
    "load_fasta",
    "load_newick",
    "MSA",
]
