Summer student from Pinello Lab at Harvard seeking help from Theis Lab

I’m unable to complete the Nestrorowa et al. 2016 paga tutorial. On ln[3]

adata.raw = adata
sc.pp.recipe_weinreb17(adata, log=False)
sc.tl.pca(adata)

I keep getting this output:

---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
<ipython-input-4-bfa4168a87e6> in <module>
      1 adata.raw = adata
----> 2 sc.pp.recipe_weinreb17(adata, log=False)
      3 sc.tl.pca(adata)

/opt/anaconda3/lib/python3.7/site-packages/scanpy/preprocessing/_recipes.py in recipe_weinreb17(adata, log, mean_threshold, cv_threshold, n_pcs, svd_solver, random_state, copy)
     48     )
     49     adata._inplace_subset_var(gene_subset)  # this modifies the object itself
---> 50     X_pca = pp.pca(
     51         pp.zscore_deprecated(adata.X),
     52         n_comps=n_pcs,

AttributeError: module 'scanpy.preprocessing._simple' has no attribute 'pca'

Versions: scanpy==1.5.1 anndata==0.7.4 umap==0.4.6 numpy==1.18.1 scipy==1.4.1 pandas==1.0.1 scikit-learn==0.22.1 statsmodels==0.11.0 python-igraph==0.8.2 louvain==0.7.0 leidenalg==0.7.0

[LuckyMD]

The last minor release of Scanpy was version 1.5.1 in the end of May, so it hasn’t been released yet. You would need to update scanpy to the development version on master. This can be done via pip install git+https://www.github.com/theislab/scanpy@master or by having a local copy of the scanpy repo, updating this and installing from source via pip install . 😃.

[katherineio]

Hello! I’m getting the same AttributeError as well. Is the issue on my end or has the fix not been applied yet?