from ._trees import (
    Subclone,
    TumorTree,
    TumorTreeCohort,
    VectorizedTrees,
    wrap_trees,
    save_cohort_to_json,
    load_cohort_from_json,
    save_vectorized_trees_npz,
    load_vectorized_trees_npz,
)
from ._simulation import generate_trees, generate_fmat
from ._plot import (
    plot_fmat,
    plot_fmat_posterior,
    plot_epistasis,
    plot_fmat_std,
    plot_tree,
)
from ._inference import (
    jlogp,
    update_params,
    compute_normalizing_constant,
    FiTreeJointLikelihood,
    prior_fitree,
    recoverable_entries,
    greedy_init_fmat,
    init_prior_rhs,
    init_prior_normal,
    prior_fitree_mixed,
)

__all__ = [
    "Subclone",
    "TumorTree",
    "TumorTreeCohort",
    "VectorizedTrees",
    "wrap_trees",
    "save_cohort_to_json",
    "load_cohort_from_json",
    "save_vectorized_trees_npz",
    "load_vectorized_trees_npz",
    "generate_trees",
    "generate_fmat",
    "plot_fmat",
    "plot_fmat_posterior",
    "plot_epistasis",
    "plot_fmat_std",
    "plot_tree",
    "jlogp",
    "update_params",
    "compute_normalizing_constant",
    "FiTreeJointLikelihood",
    "prior_fitree",
    "recoverable_entries",
    "greedy_init_fmat",
    "init_prior_rhs",
    "init_prior_normal",
    "prior_fitree_mixed",
]
