AttributeError: 'SparseCSRView' object has no attribute 'A'

[speed090]

I download scar through this command ： micromamba create -n scar micromamba activate scar git clone https://github.com/Novartis/scar.git cd scar micromamba env create -f scar-gpu.yml micromamba activate scar

I can import scar, however

2024-07-03 13:48:52|INFO|setup_anndata|Use all 199666 droplets. 2024-07-03 13:48:53|INFO|setup_anndata|Estimating ambient profile for ['Gene Expression']...

AttributeError Traceback (most recent call last) Cell In[35], line 3 1 from scar import setup_anndata ----> 3 setup_anndata( 4 adata = hgmm_20k, 5 raw_adata = hgmm_20k_raw, 6 prob = 0.995, 7 kneeplot = True 8 )

File ~/micromamba/envs/scar/lib/python3.11/site-packages/scar/main/_setup.py:145, in setup_anndata(adata, raw_adata, feature_type, prob, min_raw_counts, iterations, n_batch, sample, kneeplot, verbose, figsize) 143 for b in range(n_batch): 144 try: --> 145 count_batch = raw_adata[batch_idx == b].X.astype(int).A 146 except MemoryError: 147 raise MemoryError("use more batches by setting a higher n_batch")

AttributeError: 'SparseCSRView' object has no attribute 'A'

[yalayoubi]

Hi, I am also getting this error, is there a plan to fix this soon?

[speed090]

you should download the specific version python packages. check the packags version!

[CaibinSh]

Thank both of you @yalayoubi @speed090 for reporting and identifying the issue. We have refactored the code to reflect the new changes in scipy. The main branch should work for both scipy 1.13.x and scipy 1.14.x. We will push new release 0.6.1 so that conda install will also work. Best, Caibin