Anndata 0.11 and scipy 0.15 fail to load backed sparse anndata object

[ori-kron-wis]

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scipy updated to 0.15.0 recently, and as a result, we have a test that fails now:

example:

Code:

from scipy.sparse import csr_matrix #scipy 1.15.0
import anndata  as ad #anndata 1.11.1
import numpy as np
import os

counts = csr_matrix(np.random.poisson(1, size=(100, 2000)), dtype=np.float32)
adata = ad.AnnData(counts)
path = os.path.join(".", "test_data2.h5ad")
adata.write_h5ad(path)
adata = ad.read_h5ad(path, backed="r") #also r+ fails
adata.X[:100] #fail

Traceback:

Traceback (most recent call last):
  File "<input>", line 11, in <module>
  File "/opt/miniconda3/envs/scvi/lib/python3.12/site-packages/anndata/_core/sparse_dataset.py", line 431, in __getitem__
    sub = self.to_memory()[row_sp_matrix_validated, col_sp_matrix_validated]
          ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/miniconda3/envs/scvi/lib/python3.12/site-packages/scipy/sparse/_index.py", line 30, in __getitem__
    index, new_shape = self._validate_indices(key)
                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/miniconda3/envs/scvi/lib/python3.12/site-packages/scipy/sparse/_index.py", line 274, in _validate_indices
    idx = self._asindices(idx, N)
          ^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/miniconda3/envs/scvi/lib/python3.12/site-packages/scipy/sparse/_index.py", line 316, in _asindices
    max_indx = x.max()
               ^^^^^^^
  File "/opt/miniconda3/envs/scvi/lib/python3.12/site-packages/numpy/_core/_methods.py", line 44, in _amax
    return umr_maximum(a, axis, None, out, keepdims, initial, where)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: '>=' not supported between instances of 'int' and 'NoneType'

This is used to work with scipy 0.14.1

Versions

anndata 1.11.1
scipy 1.15.0

[ilan-gold]

I believe this was addressed by #1806

[ori-kron-wis]

installing from main branch solves the issue. thanks.