"""Utility Module

This module provides a collection of helper functions for data preprocessing,
feature selection, statistical data exploration, graph network pruning, and reproducibility.
"""

from .logger import get_logger
from .reproducibility import set_seed

from .data import (
    variance_summary,
    zero_summary,
    expression_summary,
    correlation_summary,
    nan_summary,
    sparse_filter,
    data_stats,
)

from .feature_selection import (
    variance_threshold,
    mad_filter,
    pca_loadings,
    laplacian_score,
    correlation_filter,
    importance_rf,
    top_anova_f_features,
)

from .preprocess import (
    m_transform,
    impute_simple,
    impute_knn,
    normalize,
    clean_inf_nan,
    clean_internal,
    preprocess_clinical,
    prune_network,
    prune_network_by_quantile,
    network_remove_low_variance,
    network_remove_high_zero_fraction,
)

__all__ = [
    "get_logger",
    "set_seed",

    "variance_summary",
    "zero_summary",
    "expression_summary",
    "correlation_summary",
    "nan_summary",
    "sparse_filter"
    "data_stats",

    "variance_threshold",
    "mad_filter",
    "pca_loadings",
    "laplacian_score",
    "correlation_filter",
    "importance_rf",
    "top_anova_f_features",

    "m_transform",
    "impute_simple",
    "impute_knn",
    "normalize",
    "clean_inf_nan",
    "clean_internal",
    "preprocess_clinical",

    "prune_network",
    "prune_network_by_quantile",
    "network_remove_low_variance",
    "network_remove_high_zero_fraction",
]
