Error caused by scipy version: 'csr_matrix' object has no attribute 'A'

[Biogod2020]

Since the shorthand .Afor convertomg the csr_matrix to numpy.ndarray has been deprecated in the latest version of scipy. Directly running the raw count for annotation would encounter this error message.

I solved this by modify the environment.yml to ` name: TACCO_env channels:

• conda-forge
• bioconda dependencies:
• python>3.7.0,!=3.8.0
• requests
• joblib
• numba>=0.51.2
• numpy
• matplotlib!=3.7.0
• pyqt!=5.9.2
• seaborn
• sparse_dot_mkl>=0.7.3
• scanpy>=1.7.0
• statsmodels
• anndata
• pandas>=1.1.0
• scipy==1.6.0
• mkl
• mkl-service
• scikit-learn
• threadpoolctl
• pyamg
• tacco

`

[JWatter]

Hi @Biogod2020,

Thanks for letting us know about the errors introduced by the upstream release of scipy! We put out a new tacco release, see the release notes, which takes care off the deprecated functions and includes further maintenance. The recommended way of installing is via conda again: conda install -c conda-forge tacco