from .preprocessing.utils import show_proportions, cleanup, set_initial_size, get_initial_size
from .preprocessing.neighbors import get_connectivities
from .preprocessing.moments import get_moments

from .tools.utils import *
from .tools.rank_velocity_genes import get_mean_var
from .tools.run import convert_to_adata, convert_to_loom
from .tools.optimization import leastsq, get_weight
from .tools.velocity_graph import vals_to_csr
from .tools.score_genes_cell_cycle import get_phase_marker_genes
from .tools.transition_matrix import transition_matrix as get_transition_matrix
from .tools.transition_matrix import get_cell_transitions

from .plotting.utils import is_categorical, clip, interpret_colorkey, rgb_custom_colormap
from .plotting.velocity_embedding_grid import compute_velocity_on_grid
from .plotting.simulation import compute_dynamics

from .read_load import clean_obs_names, merge
