Cannot import Scanpy #2173
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I used windows 64 and anaconda. Scanpy has been working and I never had this issue before in the last two years. |
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How did you install scanpy? What conda command did you use? |
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Ah, duplicate of #1468 |
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I checked #1468. Tried conda install pytables. But it did not work. |
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Did you look at #454 ? |
And I'd appreciate an answer here. Just want to rule out that you used bioconda. |
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conda install pytables Collecting package metadata (current_repodata.json): ...working... done All requested packages already installed.But there is still ImportError. |
Installed scanpy on jupyter notebook/ anaconda: |
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I have been running the same scripts on the same computer (windows 10) for two years with no problem until recently. |
I tried to downgrade h5py but still did not work. |
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Honestly, I don't use Windows and somebody else needs to chip in here, sorry. |
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@charles-xu-ru you could also try installing numba from conda before installing scanpy. pytables better to install from conda-forge channel along with h5py. |
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I met the same problem. >>> import scanpy.api as sc
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "C:\ProgramData\Miniconda3\lib\site-packages\scanpy\__init__.py", line 14, in <module>
from . import tools as tl
File "C:\ProgramData\Miniconda3\lib\site-packages\scanpy\tools\__init__.py", line 1, in <module>
from ..preprocessing import pca
File "C:\ProgramData\Miniconda3\lib\site-packages\scanpy\preprocessing\__init__.py", line 1, in <module>
from ._recipes import recipe_zheng17, recipe_weinreb17, recipe_seurat
File "C:\ProgramData\Miniconda3\lib\site-packages\scanpy\preprocessing\_recipes.py", line 11, in <module>
from ._normalization import normalize_total
File "C:\ProgramData\Miniconda3\lib\site-packages\scanpy\preprocessing\_normalization.py", line 7, in <module>
from sklearn.utils import sparsefuncs
File "C:\ProgramData\Miniconda3\lib\site-packages\sklearn\__init__.py", line 82, in <module>
from .base import clone
File "C:\ProgramData\Miniconda3\lib\site-packages\sklearn\base.py", line 17, in <module>
from .utils import _IS_32BIT
File "C:\ProgramData\Miniconda3\lib\site-packages\sklearn\utils\__init__.py", line 28, in <module>
from .fixes import np_version, parse_version
File "C:\ProgramData\Miniconda3\lib\site-packages\sklearn\utils\fixes.py", line 20, in <module>
import scipy.stats
File "C:\ProgramData\Miniconda3\lib\site-packages\scipy\stats\__init__.py", line 441, in <module>
from .stats import *
File "C:\ProgramData\Miniconda3\lib\site-packages\scipy\stats\stats.py", line 43, in <module>
from . import distributions
File "C:\ProgramData\Miniconda3\lib\site-packages\scipy\stats\distributions.py", line 8, in <module>
from ._distn_infrastructure import (rv_discrete, rv_continuous, rv_frozen)
File "C:\ProgramData\Miniconda3\lib\site-packages\scipy\stats\_distn_infrastructure.py", line 24, in <module>
from scipy import optimize
File "C:\ProgramData\Miniconda3\lib\site-packages\scipy\optimize\__init__.py", line 400, in <module>
from .optimize import *
File "C:\ProgramData\Miniconda3\lib\site-packages\scipy\optimize\optimize.py", line 36, in <module>
from ._numdiff import approx_derivative
File "C:\ProgramData\Miniconda3\lib\site-packages\scipy\optimize\_numdiff.py", line 6, in <module>
from scipy.sparse.linalg import LinearOperator
File "C:\ProgramData\Miniconda3\lib\site-packages\scipy\sparse\linalg\__init__.py", line 114, in <module>
from .eigen import *
File "C:\ProgramData\Miniconda3\lib\site-packages\scipy\sparse\linalg\eigen\__init__.py", line 9, in <module>
from .arpack import *
File "C:\ProgramData\Miniconda3\lib\site-packages\scipy\sparse\linalg\eigen\arpack\__init__.py", line 20, in <module>
from .arpack import *
File "C:\ProgramData\Miniconda3\lib\site-packages\scipy\sparse\linalg\eigen\arpack\arpack.py", line 42, in <module>
from . import _arpack
ImportError: DLL load failed while importing _arpack: The specified procedure could not be found. |
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Are you two running Windows 10 or 11? @Yiquan-Jiang could you please also provide the full information? OS, environment etc |
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Closing due to lack of information. Feel free to reopen. |
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Hello, I get the same error when importing scanpy on 7bridges. ---------------------------------------------------------------------------
ImportError Traceback (most recent call last)
/tmp/ipykernel_109/912249142.py in <module>
----> 1 import scanpy as sc
/opt/conda/lib/python3.9/site-packages/scanpy/__init__.py in <module>
14 from . import tools as tl
15 from . import preprocessing as pp
---> 16 from . import plotting as pl
17 from . import datasets, logging, queries, external, get, metrics, experimental
18
/opt/conda/lib/python3.9/site-packages/scanpy/plotting/__init__.py in <module>
14 from ._preprocessing import filter_genes_dispersion, highly_variable_genes
15
---> 16 from ._tools.scatterplots import (
17 embedding,
18 pca,
/opt/conda/lib/python3.9/site-packages/scanpy/plotting/_tools/__init__.py in <module>
8 from matplotlib.colors import Normalize
9 from matplotlib import pyplot as pl
---> 10 from matplotlib import rcParams, colormaps
11 from anndata import AnnData
12 from typing import Union, Optional, List, Sequence, Iterable, Mapping, Literal
ImportError: cannot import name 'colormaps' from 'matplotlib' (/opt/conda/lib/python3.9/site-packages/matplotlib/__init__.py) |
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Hi @IfSumia, that’s a very different problem, see the last line: ImportError: cannot import name 'colormaps' from 'matplotlib' (/opt/conda/lib/python3.9/site-packages/matplotlib/__init__.py)This probably means that you should update matplotlib and try again |
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--------------------------------------------------------------------------- ImportError Traceback (most recent call last) ~\AppData\Local\Temp/ipykernel_22924/912249142.py in <module> ----> 1 import scanpy as sc ~\Anaconda3\lib\site-packages\scanpy\__init__.py in <module> 13 Verbosity, 14 ) # start with settings as several tools are using it ---> 15 from . import tools as tl 16 from . import preprocessing as pp 17 from . import plotting as pl ~\Anaconda3\lib\site-packages\scanpy\tools\__init__.py in <module> 15 from ._leiden import leiden 16 from ._louvain import louvain ---> 17 from ._sim import sim 18 from ._score_genes import score_genes, score_genes_cell_cycle 19 from ._dendrogram import dendrogram ~\Anaconda3\lib\site-packages\scanpy\tools\_sim.py in <module> 21 from anndata import AnnData 22 ---> 23 from .. import _utils, readwrite, logging as logg 24 from .._settings import settings 25 from .._compat import Literal ~\Anaconda3\lib\site-packages\scanpy\readwrite.py in <module> 8 import pandas as pd 9 from matplotlib.image import imread ---> 10 import tables 11 import anndata 12 from anndata import ( ~\Anaconda3\lib\site-packages\tables\__init__.py in <module> 40 # Import the user classes from the proper modules 41 from .exceptions import * ---> 42 from .file import File, open_file, copy_file 43 from .node import Node 44 from .group import Group ~\Anaconda3\lib\site-packages\tables\file.py in <module> 21 import numpy as np 22 ---> 23 from . import hdf5extension 24 from . import utilsextension 25 from . import parameters ImportError: DLL load failed: The specified procedure could not be found.The text was updated successfully, but these errors were encountered: