scikit-misc cannot be initiated when sc.pp.highly_variable_genes(adata, n_top_genes=5000, flavor='seurat_v3')

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Hello Scanpy, When I’m running sc.pp.highly_variable_genes(adata, n_top_genes=5000, flavor=‘seurat_v3’), it asks me to install scikit-misc, which is already installed. Please see the picture below. Could you please help me to solve this issue? Thanks! Best, YJ Note: Please read this guide detailing how to provide the necessary information for us to reproduce your bug.

Minimal code sample (that we can copy&paste without having any data)

# Your code here

[Paste the error output produced by the above code here]

Versions

3.8

[Paste the output of scanpy.logging.print_versions() leaving a blank line after the details tag]

scanpy==1.8.2 anndata==0.7.8 umap==0.5.2 numpy==1.20.3 scipy==1.7.2 pandas==1.3.4 scikit-learn==1.0.1 statsmodels==0.13.1 python-igraph==0.9.8 pynndescent==0.5.5 scvelo==0.2.4 scanpy==1.8.2 anndata==0.7.8 loompy==3.0.6 numpy==1.20.3 scipy==1.7.2 matplotlib==3.5.0 sklearn==1.0.1 pandas==1.3.4 cellrank==1.5.0 scanpy==1.8.2 anndata==0.7.8 numpy==1.20.3 numba==0.54.1 scipy==1.7.2 pandas==1.3.4 pygpcca==1.0.2 scikit-learn==1.0.1 statsmodels==0.13.1 python-igraph==0.9.8 scvelo==0.2.4 pygam==0.8.0 matplotlib==3.5.0 seaborn==0.11.2

[maarten-compbio]

I found a workaround that does not require downloading the .whl file for numpy=1.19.5. By default, MKL is included when you install numpy with conda. It’s good to do this in a new environment.

conda create -n scanpy_env
conda activate scanpy_env
conda install numpy=1.19
conda install seaborn scikit-learn statsmodels numba pytables
conda install -c conda-forge python-igraph leidenalg
pip install scanpy==1.8.1

Now I can run sc.pp.highly_variable_genes() with no problem.

[hyjforesight]

Hello @davidhbrann, Thanks for the suggestion. I found that numpy‑1.19.5+mkl‑cp36‑cp36m‑win_amd64.whl only supports python 3.6, but the support of python 3.6 has been dropped by Scanpy. I didn’t find numpy-1.20.3+mkl-cp38-cp38-win_amd64.whl by google yet, but I believe that your solution will work. It seems that numpy‑1.21.5+mkl‑cp38‑cp38‑win_amd64.whl is the only hope, but Scanpy requires numpy<=1.20. I think it’s the compatibility issue. Hope Scanpy can solve this compatibility issue in the future. Thanks! Best, YJ