anndata.settings.override

settings.override(*, check_uniqueness=<no change>, copy_on_write_X=<no change>, allow_write_nullable_strings=<no change>, zarr_write_format=<no change>, use_sparse_array_on_read=<no change>, min_rows_for_chunked_h5_copy=<no change>, disallow_forward_slash_in_h5ad=<no change>, write_csr_csc_indices_with_min_possible_dtype=<no change>, auto_shard_zarr_v3=<no change>, restrict_index_types=<no change>)

Provides local override via keyword arguments as a context manager.

Parameters:

remove_unused_categories bool (default: <no change>)

Whether or not to remove unused categories with Categorical.

check_uniqueness bool (default: <no change>)

Whether or not to check uniqueness of the obs indices on __init__ of AnnData.

copy_on_write_X bool (default: <no change>)

Whether to copy-on-write X. Currently my_adata_view[subset].X = value will write back to the original AnnData object at the subset location. X is the only element where this behavior is implemented though.

allow_write_nullable_strings bool | None (default: <no change>)

Whether or not to allow writing of pd.arrays.[Arrow]StringArray. When set to None, it will be inferred from pd.options.future.infer_string. When set to False explicitly, we will try writing string arrays in the old, non-nullable format.

zarr_write_format Literal[2, 3] (default: <no change>)

Which version of zarr to write to when anndata must internally open a write-able zarr group.

use_sparse_array_on_read bool (default: <no change>)

Whether or not to use scipy.sparse.sparray as the default class when reading in data

min_rows_for_chunked_h5_copy int (default: <no change>)

Minimum number of rows at a time to copy when writing out an H5 Dataset to a new location

disallow_forward_slash_in_h5ad bool (default: <no change>)

Whether or not to disallow the / character in keys for h5ad files

write_csr_csc_indices_with_min_possible_dtype bool (default: <no change>)

Write a csr or csc matrix with the minimum possible data type for indices, always unsigned integer.

auto_shard_zarr_v3 bool | None (default: <no change>)

Whether or not to use zarr’s auto computation of sharding for v3. For v2 this setting will be ignored. The setting will apply to all calls to anndata’s writing mechanism (write_zarr / write_elem) and will not override any user-defined kwargs for shards.

restrict_index_types bool (default: <no change>)

Whether to force coercion to a string index upon declaration of the AnnData object or setting obs/var. “Setting this to False will e.g. also allow MultiIndex indexes upon declaration/setting. “Only integer indices i.e., those caught by pandas.api.types.is_integer_dtype() will always be converted to strings.

Return type:

AbstractContextManager[None]