anndata.settings

anndata.settings = SettingsManager( remove_unused_categories=True, check_uniqueness=True, allow_write_nullable_strings=False, zarr_write_format=2, use_sparse_array_on_read=False, min_rows_for_chunked_h5_copy=1000, disallow_forward_slash_in_h5ad=False, auto_shard_zarr_v3=False,  )

This manager allows users to customize settings for the anndata package. Settings here will generally be for advanced use-cases and should be used with caution.

The following options are available:

settings.remove_unused_categories: bool = True

Whether or not to remove unused categories with Categorical.

settings.check_uniqueness: bool = True

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

settings.allow_write_nullable_strings: bool = False

Whether or not to allow writing of pd.arrays.StringArray.

settings.zarr_write_format: int = 2

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

settings.use_sparse_array_on_read: bool = False

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

settings.min_rows_for_chunked_h5_copy: int = 1000

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

settings.disallow_forward_slash_in_h5ad: bool = False

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

settings.auto_shard_zarr_v3: bool = False

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.

For setting an option please use override() (local) or set the above attributes directly (global) i.e., anndata.settings.my_setting = foo. For assignment by environment variable, use the variable name in all caps with ANNDATA_ as the prefix before import of anndata. For boolean environment variable setting, use 1 for True and 0 for False.