"""
Utility functions for spatial transcriptomics data analysis.
"""
from .adata_utils import ( # Constants; Field discovery; Data access; Validation; Ensure; Standardization
ALTERNATIVE_BATCH_KEYS,
ALTERNATIVE_CELL_TYPE_KEYS,
ALTERNATIVE_CLUSTER_KEYS,
ALTERNATIVE_SPATIAL_KEYS,
BATCH_KEY,
CELL_TYPE_KEY,
CLUSTER_KEY,
SPATIAL_KEY,
ensure_categorical,
ensure_counts_layer,
find_common_genes,
get_analysis_parameter,
get_batch_key,
get_cell_type_key,
get_cluster_key,
get_gene_expression,
get_genes_expression,
get_spatial_key,
standardize_adata,
to_dense,
validate_adata,
validate_adata_basics,
validate_gene_overlap,
validate_obs_column,
validate_var_column,
)
from .compat import (
cellrank_compat,
check_scipy_derivative_status,
ensure_cellrank_compat,
ensure_spatialde_compat,
get_compatibility_info,
numpy2_compat,
patch_scipy_misc_derivative,
)
from .dependency_manager import (
DependencyInfo,
get,
is_available,
require,
validate_r_environment,
validate_scvi_tools,
)
from .device_utils import (
cuda_available,
get_device,
get_ot_backend,
mps_available,
resolve_device_async,
)
from .exceptions import (
ChatSpatialError,
DataCompatibilityError,
DataError,
DataNotFoundError,
DependencyError,
ParameterError,
ProcessingError,
)
from .mcp_utils import mcp_tool_error_handler, suppress_output
__all__ = [
# Exceptions
"ChatSpatialError",
"DataError",
"DataNotFoundError",
"DataCompatibilityError",
"ParameterError",
"ProcessingError",
"DependencyError",
# MCP utilities
"suppress_output",
"mcp_tool_error_handler",
# Constants
"SPATIAL_KEY",
"CELL_TYPE_KEY",
"CLUSTER_KEY",
"BATCH_KEY",
"ALTERNATIVE_SPATIAL_KEYS",
"ALTERNATIVE_CELL_TYPE_KEYS",
"ALTERNATIVE_CLUSTER_KEYS",
"ALTERNATIVE_BATCH_KEYS",
# Field discovery
"get_analysis_parameter",
"get_batch_key",
"get_cell_type_key",
"get_cluster_key",
"get_spatial_key",
# Expression extraction
"to_dense",
"get_gene_expression",
"get_genes_expression",
# Validation
"validate_adata",
"validate_obs_column",
"validate_var_column",
"validate_adata_basics",
"validate_gene_overlap",
"ensure_categorical",
# Gene overlap
"find_common_genes",
# Ensure
"ensure_counts_layer",
# Standardization
"standardize_adata",
# Dependency management
"DependencyInfo",
"require",
"get",
"is_available",
"validate_r_environment",
"validate_scvi_tools",
# Device utilities
"cuda_available",
"mps_available",
"get_device",
"resolve_device_async",
"get_ot_backend",
# Compatibility utilities
"numpy2_compat",
"ensure_cellrank_compat",
"cellrank_compat",
"ensure_spatialde_compat",
"patch_scipy_misc_derivative",
"check_scipy_derivative_status",
"get_compatibility_info",
]
