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is_categorical is deprecated in Pandas 1.1, use is_categorical_dtype instead #419

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gokceneraslan opened this issue Aug 17, 2020 · 1 comment · Fixed by #425
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@gokceneraslan
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Apparently is_categorical is deprecated in pandas 1.1, as you probably already know:

pandas-dev/pandas#33385

Here are the instances I can find:

https://github.com/theislab/anndata/blob/master/anndata/_core/anndata.py#L1094

https://github.com/theislab/anndata/blob/master/anndata/_core/anndata.py#L1192

https://github.com/theislab/anndata/blob/master/anndata/tests/test_readwrite.py#L8

Here is how highly_variable_genes look like, a bit annoying:

image

@ivirshup ivirshup added the bug label Aug 18, 2020
@ivirshup
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Good to know! I've been on pandas<1.1 since it breaks our tests. It might be a bit difficult to make a PR for fixing this until pandas 1.1.1 is released (tracking issue: pandas-dev/pandas#35489).

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