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import fails due to deprecated is_categorical method it pandas #2564

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Michael-Geuenich opened this issue Jul 20, 2023 · 1 comment
Closed
2 of 3 tasks

import fails due to deprecated is_categorical method it pandas #2564

Michael-Geuenich opened this issue Jul 20, 2023 · 1 comment
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@Michael-Geuenich
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Please make sure these conditions are met

  • I have checked that this issue has not already been reported.
  • I have confirmed this bug exists on the latest version of scanpy.
  • (optional) I have confirmed this bug exists on the master branch of scanpy.

What happened?

I installed scanpy as the first package in a brand new conda environment. This worked fine but when importing scanpy I get the error below. It sounds like this is because as of pandas 2.0 is_categorical is deprecated: https://stackoverflow.com/questions/76234312/importerror-cannot-import-name-is-categorical-from-pandas-api-types

This issue is also fixed when I downgrade pandas to 1.5.3.

Minimal code sample

import scanpy as sc

Error output

---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
Untitled-1.ipynb Cell 20 in <cell line: 1>()
----> 1 import scanpy as sc

File ~/mambaforge/envs/basic_comp_bio/lib/python3.9/site-packages/scanpy/__init__.py:18, in <module>
     16 from . import preprocessing as pp
     17 from . import plotting as pl
---> 18 from . import datasets, logging, queries, external, get
     20 from anndata import AnnData, concat
     21 from anndata import (
     22     read_h5ad,
     23     read_csv,
   (...)
     29     read_umi_tools,
     30 )

File ~/mambaforge/envs/basic_comp_bio/lib/python3.9/site-packages/scanpy/external/__init__.py:4, in <module>
      2 from . import pl
      3 from . import pp
----> 4 from . import exporting
      6 import sys
      7 from .. import _utils

File ~/mambaforge/envs/basic_comp_bio/lib/python3.9/site-packages/scanpy/external/exporting.py:14, in <module>
     12 import matplotlib.pyplot as plt
     13 from anndata import AnnData
---> 14 from pandas.api.types import is_categorical
     16 from ..preprocessing._utils import _get_mean_var
     17 from .._utils import NeighborsView

ImportError: cannot import name 'is_categorical' from 'pandas.api.types' (/Users/michael/mambaforge/envs/basic_comp_bio/lib/python3.9/site-packages/pandas/api/types/__init__.py)

Versions

conda list
# packages in environment at /Users/michael/mambaforge/envs/basic_comp_bio:
#
# Name                    Version                   Build  Channel
anndata                   0.9.1              pyhd8ed1ab_0    conda-forge
appnope                   0.1.2           py39hca03da5_1001    anaconda
asttokens                 2.0.5              pyhd3eb1b0_0    anaconda
backcall                  0.2.0              pyhd3eb1b0_0    anaconda
blosc                     1.21.4               hc338f07_0    conda-forge
brotli                    1.0.9                h1a8c8d9_9    conda-forge
brotli-bin                1.0.9                h1a8c8d9_9    conda-forge
brotli-python             1.0.9            py39h23fbdae_9    conda-forge
bzip2                     1.0.8                h3422bc3_4    conda-forge
c-ares                    1.19.1               hb547adb_0    conda-forge
c-blosc2                  2.10.0               h068da5f_0    conda-forge
ca-certificates           2022.4.26            hca03da5_0    anaconda
cached-property           1.5.2                hd8ed1ab_1    conda-forge
cached_property           1.5.2              pyha770c72_1    conda-forge
certifi                   2022.6.15        py39hca03da5_0    anaconda
charset-normalizer        3.2.0              pyhd8ed1ab_0    conda-forge
colorama                  0.4.6              pyhd8ed1ab_0    conda-forge
curl                      8.1.2                hc52a3a8_1    conda-forge
cycler                    0.11.0             pyhd8ed1ab_0    conda-forge
debugpy                   1.5.1            py39hc377ac9_0    anaconda
decorator                 5.1.1              pyhd3eb1b0_0    anaconda
dunamai                   1.18.0             pyhd8ed1ab_0    conda-forge
entrypoints               0.4              py39hca03da5_0    anaconda
executing                 0.8.3              pyhd3eb1b0_0    anaconda
fonttools                 4.41.0           py39h0f82c59_0    conda-forge
freetype                  2.12.1               hd633e50_1    conda-forge
get_version               3.5.4              pyhd8ed1ab_0    conda-forge
gettext                   0.21.1               h0186832_0    conda-forge
git                       2.41.0          pl5321h46e2b6d_0    conda-forge
h5py                      3.9.0           nompi_py39he9c2634_101    conda-forge
hdf5                      1.14.1          nompi_h3aba7b3_100    conda-forge
idna                      3.4                pyhd8ed1ab_0    conda-forge
importlib-metadata        6.8.0              pyha770c72_0    conda-forge
importlib_metadata        6.8.0                hd8ed1ab_0    conda-forge
ipykernel                 6.9.1            py39hca03da5_0    anaconda
ipython                   8.3.0            py39hca03da5_0    anaconda
jedi                      0.18.1           py39hca03da5_1    anaconda
joblib                    1.3.0              pyhd8ed1ab_1    conda-forge
jupyter_client            7.2.2            py39hca03da5_0    anaconda
jupyter_core              4.10.0           py39hca03da5_0    anaconda
kiwisolver                1.4.4            py39haaf3ac1_1    conda-forge
krb5                      1.21.1               h92f50d5_0    conda-forge
lcms2                     2.15                 hd835a16_1    conda-forge
legacy-api-wrap           1.2                        py_0    conda-forge
lerc                      4.0.0                h9a09cb3_0    conda-forge
libaec                    1.0.6                hb7217d7_1    conda-forge
libblas                   3.9.0           17_osxarm64_openblas    conda-forge
libbrotlicommon           1.0.9                h1a8c8d9_9    conda-forge
libbrotlidec              1.0.9                h1a8c8d9_9    conda-forge
libbrotlienc              1.0.9                h1a8c8d9_9    conda-forge
libcblas                  3.9.0           17_osxarm64_openblas    conda-forge
libcurl                   8.1.2                hc52a3a8_1    conda-forge
libcxx                    16.0.6               h4653b0c_0    conda-forge
libdeflate                1.18                 h1a8c8d9_0    conda-forge
libedit                   3.1.20191231         hc8eb9b7_2    conda-forge
libev                     4.33                 h642e427_1    conda-forge
libexpat                  2.5.0                hb7217d7_1    conda-forge
libffi                    3.4.2                h3422bc3_5    conda-forge
libgfortran               5.0.0           12_2_0_hd922786_31    conda-forge
libgfortran5              12.2.0              h0eea778_31    conda-forge
libiconv                  1.17                 he4db4b2_0    conda-forge
libjpeg-turbo             2.1.5.1              h1a8c8d9_0    conda-forge
liblapack                 3.9.0           17_osxarm64_openblas    conda-forge
libllvm14                 14.0.6               hd1a9a77_3    conda-forge
libnghttp2                1.52.0               hae82a92_0    conda-forge
libopenblas               0.3.23          openmp_hc731615_0    conda-forge
libpng                    1.6.39               h76d750c_0    conda-forge
libsodium                 1.0.18               h1a28f6b_0    anaconda
libsqlite                 3.42.0               hb31c410_0    conda-forge
libssh2                   1.11.0               h7a5bd25_0    conda-forge
libtiff                   4.5.1                h23a1a89_0    conda-forge
libwebp-base              1.3.1                hb547adb_0    conda-forge
libxcb                    1.15                 hf346824_0    conda-forge
libzlib                   1.2.13               h53f4e23_5    conda-forge
llvm-openmp               16.0.6               h1c12783_0    conda-forge
llvmlite                  0.40.1           py39hbad4f83_0    conda-forge
lz4-c                     1.9.4                hb7217d7_0    conda-forge
matplotlib-base           3.5.3            py39ha500c34_2    conda-forge
matplotlib-inline         0.1.2              pyhd3eb1b0_2    anaconda
munkres                   1.0.7                      py_1    bioconda
natsort                   8.4.0              pyhd8ed1ab_0    conda-forge
ncurses                   6.4                  h7ea286d_0    conda-forge
nest-asyncio              1.5.5            py39hca03da5_0    anaconda
networkx                  3.1                pyhd8ed1ab_0    conda-forge
numba                     0.57.1           py39he8ed757_0    conda-forge
numexpr                   2.8.4            py39hd28f0be_0    conda-forge
numpy                     1.24.4           py39h485cf63_0    conda-forge
openjpeg                  2.5.0                hbc2ba62_2    conda-forge
openssl                   3.1.1                h53f4e23_1    conda-forge
packaging                 23.1               pyhd8ed1ab_0    conda-forge
pandas                    2.0.3            py39h6b13a34_1    conda-forge
parso                     0.8.3              pyhd3eb1b0_0    anaconda
patsy                     0.5.3              pyhd8ed1ab_0    conda-forge
pcre2                     10.40                hb34f9b4_0    conda-forge
perl                      5.32.1          4_hf2054a2_perl5    conda-forge
pexpect                   4.8.0              pyhd3eb1b0_3    anaconda
pickleshare               0.7.5           pyhd3eb1b0_1003    anaconda
pillow                    10.0.0           py39h1641143_0    conda-forge
pip                       23.2               pyhd8ed1ab_0    conda-forge
platformdirs              3.9.1              pyhd8ed1ab_0    conda-forge
pooch                     1.7.0              pyha770c72_3    conda-forge
prompt-toolkit            3.0.20             pyhd3eb1b0_0    anaconda
pthread-stubs             0.4               h27ca646_1001    conda-forge
ptyprocess                0.7.0              pyhd3eb1b0_2    anaconda
pure_eval                 0.2.2              pyhd3eb1b0_0    anaconda
py-cpuinfo                9.0.0              pyhd8ed1ab_0    conda-forge
pygments                  2.11.2             pyhd3eb1b0_0    anaconda
pynndescent               0.5.10             pyh1a96a4e_0    conda-forge
pyparsing                 3.1.0              pyhd8ed1ab_0    conda-forge
pysocks                   1.7.1              pyha2e5f31_6    conda-forge
pytables                  3.8.0            py39h0da393b_2    conda-forge
python                    3.9.16          hea58f1e_0_cpython    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python-tzdata             2023.3             pyhd8ed1ab_0    conda-forge
python_abi                3.9                      3_cp39    conda-forge
pytz                      2023.3             pyhd8ed1ab_0    conda-forge
pyzmq                     22.3.0           py39hc377ac9_2    anaconda
readline                  8.2                  h92ec313_1    conda-forge
requests                  2.31.0             pyhd8ed1ab_0    conda-forge
scanpy                    1.7.2              pyhdfd78af_0    bioconda
scikit-learn              1.3.0            py39hd5c4a62_0    conda-forge
scipy                     1.11.1           py39ha6b2cbd_0    conda-forge
seaborn                   0.12.2               hd8ed1ab_0    conda-forge
seaborn-base              0.12.2             pyhd8ed1ab_0    conda-forge
setuptools                68.0.0             pyhd8ed1ab_0    conda-forge
setuptools-scm            7.1.0              pyhd8ed1ab_0    conda-forge
setuptools_scm            7.1.0                hd8ed1ab_0    conda-forge
sinfo                     0.3.1                      py_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
snappy                    1.1.10               h17c5cce_0    conda-forge
stack_data                0.2.0              pyhd3eb1b0_0    anaconda
statsmodels               0.14.0           py39h8a366b7_1    conda-forge
stdlib-list               0.8.0              pyhd8ed1ab_0    conda-forge
tbb                       2021.9.0             hffc8910_0    conda-forge
threadpoolctl             3.2.0              pyha21a80b_0    conda-forge
tk                        8.6.12               he1e0b03_0    conda-forge
tomli                     2.0.1              pyhd8ed1ab_0    conda-forge
tornado                   6.1              py39h1a28f6b_0    anaconda
tqdm                      4.65.0             pyhd8ed1ab_1    conda-forge
traitlets                 5.1.1              pyhd3eb1b0_0    anaconda
typing-extensions         4.7.1                hd8ed1ab_0    conda-forge
typing_extensions         4.7.1              pyha770c72_0    conda-forge
tzdata                    2023c                h71feb2d_0    conda-forge
umap-learn                0.5.3            py39h2804cbe_1    conda-forge
unicodedata2              15.0.0           py39h02fc5c5_0    conda-forge
urllib3                   2.0.3              pyhd8ed1ab_1    conda-forge
wcwidth                   0.2.5              pyhd3eb1b0_0    anaconda
wheel                     0.40.0             pyhd8ed1ab_1    conda-forge
xorg-libxau               1.0.11               hb547adb_0    conda-forge
xorg-libxdmcp             1.1.3                h27ca646_0    conda-forge
xz                        5.2.6                h57fd34a_0    conda-forge
zeromq                    4.3.4                hc377ac9_0    anaconda
zipp                      3.16.2             pyhd8ed1ab_0    conda-forge
zlib-ng                   2.0.7                h1a8c8d9_0    conda-forge
zstd                      1.5.2                h4f39d0f_7    conda-forge
@flying-sheep flying-sheep modified the milestone: 1.9.3 Jul 21, 2023
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flying-sheep commented Jul 21, 2023 •
edited

You have scanpy 1.7.3, not the newest version. This is fixed in #2434.

I’ll release 1.9.3 soon with the fix.

@rbutleriii rbutleriii mentioned this issue May 20, 2024
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@flying-sheep @Michael-Geuenich