error from scv.pp.moments(adata)

[QiqiGuo1996]

Hi Team,

I plan to run scv.pp.moments(adata) using example data (scv.datasets.pancreas()), but I got the error pasted below, (Python version 3.10, scvelo version: 0.3.2), do you know how to fix it? please feel free to let me know if you need to see any other information from the attempted run. Thank you so much.

scv.pp.moments(adata)
Traceback (most recent call last):
File "", line 1, in
File "/home/guoqq/.local/lib/python3.10/site-packages/scvelo/preprocessing/moments.py", line 63, in moments
neighbors(
File "/home/guoqq/.local/lib/python3.10/site-packages/scvelo/preprocessing/neighbors.py", line 223, in neighbors
n_duplicate_cells = len(get_duplicate_cells(adata))
File "/home/guoqq/.local/lib/python3.10/site-packages/scvelo/preprocessing/neighbors.py", line 555, in get_duplicate_cells
X_new = np.array(X[idx_dup].A if issparse(X) else X[idx_dup])
AttributeError: 'csr_matrix' object has no attribute 'A'

[WeilerP]

You can either install scvelo from source or downgrade scipy.

[matthieuheitz]

Which version of scipy should it work with?

[pdemko]

Making a fresh conda environment and installing scvelo from source fixed the issue.

[TTTPOB]

tried scipy 1.13.1, works.

[stela2502]

Has that been fixed by now?!
I still get the same error.

scanpy==1.10.3
scvi==1.2.0
torch==2.5.1+cu124
scvelo==0.3.2
loompy==3.0.7
scanpy==1.10.3
igraph==0.11.6
pandas==2.2.3
re==2.2.1
numpy==1.26.4
h5py==3.12.1

[WeilerP]

@stela2502, it's fixed on main but I have not yet released a new version.

[stela2502]

Thank you.
Installing from git worked for me.

[stela2502]

Just a stupid question - is there no way to get a bugfix out in the open more quickly than in 4 month (assuming the fix is out next month). Or would that fix create an error for other people still using the other matrix elements?