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


# import functions accessed as sdq.tl.<func>: ---------------------------------

from . import utils


# -- kNN: ---------------------------------------------------------------------
from ._knn import kNN
from ._knn_smoothing import kNNSmoothing


# -- simulation: --------------------------------------------------------------
from ._simulation import Simulation, simulate


# -- post-simulation annotation functions: ------------------------------------
from ._annotate_gene_features import GeneCompatibility, annotate_gene_features
from ._annotate_cell_state import annotate_cell_state
from ._annotate_cell_fate import annotate_cell_fate
from ._invert_scaled_gex import invert_scaled_gex


# -- perturbation: ------------------------------------------------------------
from ._fate_perturbation_experiment import FatePerturbationExperiment
from ._fate_perturbation_screen import FatePerturbationScreen
from ._perturb import perturb
from ._perturb_scan_z_range import perturb_scan_z_range


# -- velocity plotting tools: -------------------------------------------------
from ._grid_velocity import GridVelocity
from ._velocity_embedding import VelocityEmbedding
from ._velocity_graph import velocity_graph



# -- general characterization: ------------------------------------------------
from ._drift_diffusion_state_characterization import drift, diffusion
from ._cell_potential import cell_potential, normalize_cell_potential

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

# from ._grouped_expression import GroupedExpression, grouped_expression
# from ._temporal_expression import temporal_expression


