
__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",])


from . import utils

from ._grid_velocity import GridVelocity
from ._velocity_embedding import VelocityEmbedding
from ._velocity_graph import velocity_graph

# import functions accessed as sdq.tl.<func>: --------------------------------------------
from ._annotate_cells import annotate_cells
from ._time_free_sampling import time_free_sampling

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 ._drift_diffusion_state_characterization import drift, diffusion

from ._dimension_reduction import DimensionReduction


# -----------

# 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 ._final_state_per_simulation import FinalStatePerSimulation

# from ._simulator import Simulator, simulate
from ._simulation import Simulation, 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

from ._annotate_cell_state import annotate_cell_state
from ._annotate_cell_fate import annotate_cell_fate
from ._invert_scaled_gex import invert_scaled_gex
from ._fate_perturbation_experiment import FatePerturbationExperiment
from ._fate_perturbation_screen import FatePerturbationScreen
