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Error in import squidpy: cannot import name 'SparseCSCView' from 'anndata._core.views' #928

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diego-iac opened this issue Dec 11, 2024 · 1 comment

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@diego-iac
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Description

Hi, I'm trying to use squidpy but when I try to import it returns an error. It seems to search for a function in anndata which I couldn't find. I might just have misunderstood the error, and if that's the case, I apologize. Could you please help me understand or resolve this issue?
Thanks in advance
...

Minimal reproducible example

#the package was downloaded from conda with other packages like sainsc. I'm running the code in this environment on Spyder 6. Anndata version=0.11.1
import squidpy as sq
...

Traceback

ImportError                               Traceback (most recent call last)
Cell In[18], line 1
----> 1 import squidpy as sq

File ~/anaconda3/envs/sainsc/lib/python3.12/site-packages/squidpy/__init__.py:5
      1 from __future__ import annotations
      3 from importlib import metadata
----> 5 from squidpy import datasets, gr, im, pl, read, tl
      7 try:
      8     md = metadata.metadata(__name__)

File ~/anaconda3/envs/sainsc/lib/python3.12/site-packages/squidpy/gr/__init__.py:5
      1 """The graph module."""
      3 from __future__ import annotations
----> 5 from squidpy.gr._build import spatial_neighbors
      6 from squidpy.gr._ligrec import ligrec
      7 from squidpy.gr._nhood import centrality_scores, interaction_matrix, nhood_enrichment

File ~/anaconda3/envs/sainsc/lib/python3.12/site-packages/squidpy/gr/_build.py:31
     29 from squidpy._docs import d, inject_docs
     30 from squidpy._utils import NDArrayA
---> 31 from squidpy.gr._utils import (
     32     _assert_categorical_obs,
     33     _assert_positive,
     34     _assert_spatial_basis,
     35     _save_data,
     36 )
     38 __all__ = ["spatial_neighbors"]
     41 @d.dedent
     42 @inject_docs(t=Transform, c=CoordType)
     43 def spatial_neighbors(
   (...)
     56     copy: bool = False,
     57 ) -> tuple[csr_matrix, csr_matrix] | None:

File ~/anaconda3/envs/sainsc/lib/python3.12/site-packages/squidpy/gr/_utils.py:12
     10 import pandas as pd
     11 from anndata import AnnData
---> 12 from anndata._core.views import ArrayView, SparseCSCView, SparseCSRView
     13 from anndata.utils import make_index_unique
     14 from pandas import CategoricalDtype

ImportError: cannot import name 'SparseCSCView' from 'anndata._core.views' (/home/onco-lab/anaconda3/envs/sainsc/lib/python3.12/site-packages/anndata/_core/views.py)
...

Version

Name Version Build Channel

squidpy 1.5.0 pyhd8ed1ab_0 conda-forge

Anndata version=0.11.1
...

@HeesooSong
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#915

I also had the same issue and could fix it by installing version 1.6.2.

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