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module 'scanpy' has no attribute 'get'

See original GitHub issue

Hello,

I am using scanpy version 1.4 from bioconda.

I am running one of the examples from the code to query datasets -

import scanpy as sc

pbmc = sc.datasets.pbmc3k()
print(pbmc)
plotdf = sc.get.obs_df(
    pbmc,
    keys=["CD8B", "n_genes"],
    obsm_keys=[("X_umap", 0), ("X_umap", 1)]
)
plotdf.plot.scatter("X_umap0", "X_umap1", c="CD8B")

the library can read the dataset but errors out saying scanpy has no attribute get.

I even tried

    from scanpy.get import obs_df
ModuleNotFoundError: No module named 'scanpy.get'

Did the API change for any of this ? Thanks!

Issue Analytics

State:
Created 4 years ago
Comments:6 (3 by maintainers)

Top GitHub Comments

1reaction

grstcommented, Sep 22, 2019

Actually I’ve always been using the conda package and never had any issues. Github releases are watched by the bioconda-bot, so it should never be out of date, either.

0reactions

jkanchecommented, Sep 21, 2019

some of the datasets like pbmc68k-reduced also seem to have an issue loading in conda.

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