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,  )

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

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.