from scvelo.core import (
    clean_obs_names,
    cleanup,
    get_initial_size,
    merge,
    set_initial_size,
    show_proportions,
)
from scvelo.plotting.simulation import compute_dynamics
from scvelo.plotting.utils import (
    clip,
    interpret_colorkey,
    is_categorical,
    rgb_custom_colormap,
)
from scvelo.plotting.velocity_embedding_grid import compute_velocity_on_grid
from scvelo.preprocessing.moments import get_moments
from scvelo.preprocessing.neighbors import get_connectivities
from scvelo.read_load import (
    convert_to_ensembl,
    convert_to_gene_names,
    gene_info,
    load_biomart,
)
from scvelo.tools.optimization import get_weight, leastsq
from scvelo.tools.rank_velocity_genes import get_mean_var
from scvelo.tools.run import convert_to_adata, convert_to_loom
from scvelo.tools.score_genes_cell_cycle import get_phase_marker_genes
from scvelo.tools.transition_matrix import get_cell_transitions
from scvelo.tools.transition_matrix import transition_matrix as get_transition_matrix
from scvelo.tools.utils import *  # noqa
from scvelo.tools.velocity_graph import vals_to_csr

__all__ = [
    "cleanup",
    "clean_obs_names",
    "clip",
    "compute_dynamics",
    "compute_velocity_on_grid",
    "convert_to_adata",
    "convert_to_ensembl",
    "convert_to_gene_names",
    "convert_to_loom",
    "gene_info",
    "get_cell_transitions",
    "get_connectivities",
    "get_initial_size",
    "get_mean_var",
    "get_moments",
    "get_phase_marker_genes",
    "get_transition_matrix",
    "get_weight",
    "interpret_colorkey",
    "is_categorical",
    "leastsq",
    "load_biomart",
    "merge",
    "rgb_custom_colormap",
    "set_initial_size",
    "show_proportions",
    "vals_to_csr",
]
