4.2.4. Observation/variable-level matrices - np.random.default_generator() was deprecated

[alexyschuhku]

Hi,

I ran the following Python code block:

adata.obsm["X_umap"] = np.random.default_generator().normal(0, 1, size=(adata.n_obs, 2))
adata.varm["gene_stuff"] = np.random.default_generator().normal(
    0, 1, size=(adata.n_vars, 5)
)
adata.obsm

And I got the error message:

Traceback (most recent call last):
File "", line 1, in
AttributeError: module 'numpy.random' has no attribute 'default_generator'
Traceback (most recent call last):
File "", line 1, in
AttributeError: module 'numpy.random' has no attribute 'default_generator'

Diagnostic:

The error occurs because np.random.default_generator() was deprecated in NumPy version 1.20.0 and later. Instead, you should use np.random.default_rng().

Corrected Code:

import numpy as np

# Generate random UMAP coordinates for observations
adata.obsm["X_umap"] = np.random.default_rng().normal(0, 1, size=(adata.n_obs, 2))

# Generate random data for genes
adata.varm["gene_stuff"] = np.random.default_rng().normal(
    0, 1, size=(adata.n_vars, 5)
)

adata.obsm

Best Regards
Alex Chu