"""Utils Module."""

from scphylo.ul._caller import get_samples_df, is_paired
from scphylo.ul._hclustering import (
    dist_cosine_ignore_na,
    dist_dendro,
    dist_l1_ignore_na,
    hclustering,
)
from scphylo.ul._packages import (
    import_graph_tool,
    import_graphviz,
    import_gurobi,
    import_mpi4py,
    import_rpy2,
)
from scphylo.ul._trees import (
    cells_rooted_at,
    is_leaf,
    muts_rooted_at,
    partition_cells,
    root_id,
    to_cfmatrix,
    to_mtree,
    to_tree,
)
from scphylo.ul._utils import (
    calc_nll_matrix,
    cleanup,
    count_flips,
    dir_base,
    dirbase,
    executable,
    get_file,
    infer_rates,
    is_conflict_free,
    is_conflict_free_gusfield,
    log_flip,
    log_input,
    log_output,
    mkdir,
    parse_log_file,
    parse_params_file,
    parse_score_file,
    remove,
    split_mut,
    stat,
    timeit,
    tmpdir,
    tmpdirsys,
    tmpfile,
    tqdm_joblib,
    with_timeout,
)

__all__ = (
    dist_cosine_ignore_na,
    dist_dendro,
    dist_l1_ignore_na,
    hclustering,
    import_graph_tool,
    import_graphviz,
    import_gurobi,
    import_mpi4py,
    import_rpy2,
    cells_rooted_at,
    muts_rooted_at,
    partition_cells,
    root_id,
    to_cfmatrix,
    to_mtree,
    to_tree,
    calc_nll_matrix,
    cleanup,
    dir_base,
    dirbase,
    get_file,
    parse_params_file,
    parse_log_file,
    parse_score_file,
    infer_rates,
    is_conflict_free,
    is_conflict_free_gusfield,
    log_flip,
    log_input,
    log_output,
    mkdir,
    remove,
    stat,
    timeit,
    tmpdir,
    tmpdirsys,
    tmpfile,
    tqdm_joblib,
    with_timeout,
    is_leaf,
    executable,
    split_mut,
    count_flips,
    is_paired,
    get_samples_df,
)
