
__module_name__ = "__init__.py"
__doc__ = """tools __init__ module. Sub-package of the main scdiffeq API."""
__author__ = ", ".join(["Michael E. Vinyard",])
__email__ = ", ".join(["mvinyard@broadinstitute.org",])


# import functions accessed as sdq.tl.<func>: --------------------------------------------
from ._annotate_cells import annotate_cells
from ._time_free_sampling import time_free_sampling
from ._hyperparams import HyperParams
from ._reconstruct_function import reconstruct_function
from ._versions import Versions, configure_version
from ._func_from_version import func_from_version
from ._umap import UMAP
# from ._fetch import fetch
from ._drift_diffusion_state_characterization import drift, diffusion

from ._dimension_reduction import DimensionReduction


# -----------
# from ._data_formatter import DataFormatter
# from ._x_use import X_use, fetch_formatted_data
from ._knn import kNN
from ._knn_smoothing import kNNSmoothing

from ._negative_cross_entropy import NegativeCrossEntropy

from ._sum_norm_df import sum_norm_df


from ._feature_correlation import (
    FeatureCorrelation,
    drift_correlated_features,
    diffusion_correlated_features,
    potential_correlated_features,
)

from ._cell_potential import cell_potential, normalize_cell_potential
from ._norm import L2Norm

from ._final_state_per_simulation import FinalStatePerSimulation
from ._simulator import Simulator, simulate
from ._perturbation import Perturbation, perturb

from ._grouped_expression import GroupedExpression, grouped_expression
from ._annotate_gene_features import GeneCompatibility, annotate_gene_features
# from ._compared_temporal_gene_expression import TemporalGeneExpression, compared_temporal_gene_expression
# from ._smoothed_expression import SmoothedExpression, smoothed_expression
from ._temporal_expression import temporal_expression

