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Tutorials for Squidpy
https://squidpy.readthedocs.io/en/stable/
MIT License
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creation of docs with py38 fails #16

Closed hspitzer closed 3 years ago

hspitzer commented 3 years ago

on my image_tutorials branch, creation of docs fails with TypeError: object.__new__(ImageFeature) is not safe, use str.__new__()

I am calling tox -e docs (I also tried py37, but this fails with a different error, and clean-docs which results in the same error). It always occurs when trying to build an example that imports squidpy. When calling the example locally (with python compute_example.py) everything works as expected - so I assume its a versioning issue? Or some new changes in squidpy? My version is from a week ago.

My output is:

here docs installed: affine==2.3.0,alabaster==0.7.12,anndata==0.7.5,appnope==0.1.2,argon2-cffi==20.1.0,astropy==4.2,async-generator==1.10,attrs==20.3.0,Babel==2.9.0,backcall==0.2.0,beautifulsoup4==4.9.3,bleach==3.2.1,certifi==2020.12.5,cffi==1.14.4,cftime==1.3.1,chardet==4.0.0,click==7.1.2,click-plugins==1.1.1,cligj==0.7.1,cycler==0.10.0,dask==2021.1.0,data-science-types==0.2.22,decorator==4.4.2,defusedxml==0.6.0,docrep==0.3.1,docutils==0.16,entrypoints==0.3,enum-tools==0.6.3,esda==2.3.5,get-version==2.1,h5py==3.1.0,idna==2.10,imageio==2.9.0,imagesize==1.2.0,inflect==5.0.2,ipykernel==5.4.3,ipython==7.19.0,ipython-genutils==0.2.0,ipywidgets==7.6.3,jedi==0.18.0,Jinja2==2.11.2,joblib==1.0.0,jsonschema==3.2.0,jupyter-client==6.1.11,jupyter-core==4.7.0,jupyterlab-pygments==0.1.2,jupyterlab-widgets==1.0.0,kiwisolver==1.3.1,legacy-api-wrap==1.2,leidenalg==0.8.3,libpysal==4.3.5,llvmlite==0.35.0,MarkupSafe==1.1.1,matplotlib==3.3.3,memory-profiler==0.58.0,mistune==0.8.4,natsort==7.1.0,nbclient==0.5.1,nbconvert==6.0.7,nbformat==5.1.2,nest-asyncio==1.4.3,netCDF4==1.5.5.1,networkx==2.5,notebook==6.2.0,numba==0.52.0,numexpr==2.7.2,numpy==1.19.5,omnipath==1.0.4,packaging==20.8,pandas==1.2.0,pandocfilters==1.4.3,parso==0.8.1,patsy==0.5.1,pexpect==4.8.0,pickleshare==0.7.5,Pillow==8.1.0,prometheus-client==0.9.0,prompt-toolkit==3.0.10,psutil==5.8.0,ptyprocess==0.7.0,pycparser==2.20,pyerfa==1.7.1.1,Pygments==2.7.4,pypandoc==1.5,pyparsing==2.4.7,pyrsistent==0.17.3,python-dateutil==2.8.1,python-igraph==0.8.3,pytz==2020.5,PyWavelets==1.1.1,PyYAML==5.3.1,pyzmq==21.0.1,rasterio==1.1.8,requests==2.25.1,scanpy @ git+https://github.com/theislab/scanpy@e0c11ca03bf7b931baa40d8736d334eea4912edc,scikit-image==0.18.1,scikit-learn==0.24.0,scipy==1.6.0,seaborn==0.11.1,Send2Trash==1.5.0,sinfo==0.3.1,six==1.15.0,snowballstemmer==2.0.0,snuggs==1.4.7,soupsieve==2.1,Sphinx==3.4.3,sphinx-copybutton==0.3.1,sphinx-gallery==0.8.2,sphinx-last-updated-by-git==0.2.3,sphinx-rtd-theme==0.5.1,sphinxcontrib-applehelp==1.0.2,sphinxcontrib-devhelp==1.0.2,sphinxcontrib-htmlhelp==1.0.3,sphinxcontrib-jsmath==1.0.1,sphinxcontrib-qthelp==1.0.3,sphinxcontrib-serializinghtml==1.1.4,squidpy @ git+https://github.com/theislab/squidpy@d9ae3fbeb65479197a75702521477b80c33e5e15,statsmodels==0.12.1,stdlib-list==0.8.0,tables==3.6.1,terminado==0.9.2,testpath==0.4.4,texttable==1.6.3,threadpoolctl==2.1.0,tifffile==2021.1.14,tornado==6.1,tqdm==4.56.0,traitlets==5.0.5,typing-extensions==3.7.4.3,umap-learn==0.4.6,urllib3==1.26.2,wcwidth==0.2.5,webencodings==0.5.1,widgetsnbextension==3.5.1,wrapt==1.12.1,xarray==0.16.2 docs run-test-pre: PYTHONHASHSEED='1681091251' docs run-test: commands[0] | sphinx-build --color -b html /Users/hannah.spitzer/projects/spatial_scanpy/squidpy_notebooks/docs/source /Users/hannah.spitzer/projects/spatial_scanpy/squidpy_notebooks/docs/build/html Running Sphinx v3.4.3 loading intersphinx inventory from https://docs.python.org/3/objects.inv... loading intersphinx inventory from https://anndata.readthedocs.io/en/stable/objects.inv... loading intersphinx inventory from https://scanpy.readthedocs.io/en/stable/objects.inv... loading intersphinx inventory from https://napari.org/docs/dev/objects.inv... generating gallery... WARNING: optipng binaries not found, PNG images and thumbnails will not be optimized Using pandoc version: 2.11.2 to convert rst text blocks to markdown for .ipynb files generating gallery for auto_examples/graph... [100%] compute_dummy.py WARNING: /Users/hannah.spitzer/projects/spatial_scanpy/squidpy_notebooks/examples/image/compute_smooth.py failed to execute correctly: Traceback (most recent call last): File "/Users/hannah.spitzer/projects/spatial_scanpy/squidpy_notebooks/examples/image/compute_smooth.py", line 19, in import squidpy as sq File "/Users/hannah.spitzer/projects/spatial_scanpy/squidpy_notebooks/.tox/docs/lib/python3.8/site-packages/squidpy/__init__.py", line 10, in from squidpy._io import read_visium_data File "/Users/hannah.spitzer/projects/spatial_scanpy/squidpy_notebooks/.tox/docs/lib/python3.8/site-packages/squidpy/_io.py", line 10, in from squidpy.im import ImageContainer # type: ignore[attr-defined] File "/Users/hannah.spitzer/projects/spatial_scanpy/squidpy_notebooks/.tox/docs/lib/python3.8/site-packages/squidpy/im/__init__.py", line 3, in from squidpy.im.segment import ( File "/Users/hannah.spitzer/projects/spatial_scanpy/squidpy_notebooks/.tox/docs/lib/python3.8/site-packages/squidpy/im/segment.py", line 14, in from squidpy.constants._constants import SegmentationBackend File "/Users/hannah.spitzer/projects/spatial_scanpy/squidpy_notebooks/.tox/docs/lib/python3.8/site-packages/squidpy/constants/_constants.py", line 11, in class ImageFeature(ModeEnum): # noqa: D101 File "/Users/hannah.spitzer/projects/spatial_scanpy/squidpy_notebooks/.tox/docs/lib/python3.8/site-packages/squidpy/constants/_utils.py", line 59, in __new__ res: ABCEnumMeta = super().__new__(cls, clsname, bases, namespace) # type: ignore[assignment] File "/Users/hannah.spitzer/opt/miniconda3/envs/squidpy/lib/python3.8/enum.py", line 215, in __new__ enum_member = __new__(enum_class) TypeError: object.__new__(ImageFeature) is not safe, use str.__new__() Extension error: Handler for event 'builder-inited' threw an exception (exception: object.__new__(ImageFeature) is not safe, use str.__new__()) ERROR: InvocationError for command /Users/hannah.spitzer/projects/spatial_scanpy/squidpy_notebooks/.tox/docs/bin/sphinx-build --color -b html docs/source docs/build/html (exited with code 2) ___________________________________
michalk8 commented 3 years ago

Can you please try tox -e docs --recreate? Note that you have to have in your environment variable

SQUIDPY_DOWNLOAD_TOKEN=<your_github_username>@<your_personal_token>

(this makes sure CI works, will not be needed once we're public).

michalk8 commented 3 years ago

I.e. I run it as: SQUIDPY_DOWNLOAD_TOKEN=... tox -e docs

hspitzer commented 3 years ago

I indeed forgot to export SQUIDPY_DOWNLOAD_TOKEN, but its still giving me the same error. I just ran: export SQUIDPY_DOWNLOAD_TOKEN=... tox -e docs --recreate output is:

here

docs create: /Users/hannah.spitzer/projects/spatial_scanpy/squidpy_notebooks/.tox/docs
docs installdeps: -r/Users/hannah.spitzer/projects/spatial_scanpy/squidpy_notebooks/docs/requirements.txt, git+https://github.com/theislab/squidpy
docs installed: affine==2.3.0,alabaster==0.7.12,anndata==0.7.5,appnope==0.1.2,argon2-cffi==20.1.0,astropy==4.2,async-generator==1.10,attrs==20.3.0,Babel==2.9.0,backcall==0.2.0,beautifulsoup4==4.9.3,bleach==3.2.1,certifi==2020.12.5,cffi==1.14.4,cftime==1.3.1,chardet==4.0.0,click==7.1.2,click-plugins==1.1.1,cligj==0.7.1,cycler==0.10.0,dask==2021.1.0,data-science-types==0.2.22,decorator==4.4.2,defusedxml==0.6.0,docrep==0.3.1,docutils==0.16,entrypoints==0.3,enum-tools==0.6.3,esda==2.3.5,get-version==2.1,h5py==3.1.0,idna==2.10,imageio==2.9.0,imagesize==1.2.0,inflect==5.0.2,ipykernel==5.4.3,ipython==7.19.0,ipython-genutils==0.2.0,ipywidgets==7.6.3,jedi==0.18.0,Jinja2==2.11.2,joblib==1.0.0,jsonschema==3.2.0,jupyter-client==6.1.11,jupyter-core==4.7.0,jupyterlab-pygments==0.1.2,jupyterlab-widgets==1.0.0,kiwisolver==1.3.1,legacy-api-wrap==1.2,leidenalg==0.8.3,libpysal==4.3.5,llvmlite==0.35.0,MarkupSafe==1.1.1,matplotlib==3.3.3,memory-profiler==0.58.0,mistune==0.8.4,natsort==7.1.0,nbclient==0.5.1,nbconvert==6.0.7,nbformat==5.1.2,nest-asyncio==1.4.3,netCDF4==1.5.5.1,networkx==2.5,notebook==6.2.0,numba==0.52.0,numexpr==2.7.2,numpy==1.19.5,omnipath==1.0.4,packaging==20.8,pandas==1.2.0,pandocfilters==1.4.3,parso==0.8.1,patsy==0.5.1,pexpect==4.8.0,pickleshare==0.7.5,Pillow==8.1.0,prometheus-client==0.9.0,prompt-toolkit==3.0.10,psutil==5.8.0,ptyprocess==0.7.0,pycparser==2.20,pyerfa==1.7.1.1,Pygments==2.7.4,pypandoc==1.5,pyparsing==2.4.7,pyrsistent==0.17.3,python-dateutil==2.8.1,python-igraph==0.8.3,pytz==2020.5,PyWavelets==1.1.1,PyYAML==5.3.1,pyzmq==21.0.1,rasterio==1.1.8,requests==2.25.1,scanpy @ git+https://github.com/theislab/scanpy@e0c11ca03bf7b931baa40d8736d334eea4912edc,scikit-image==0.18.1,scikit-learn==0.24.0,scipy==1.6.0,seaborn==0.11.1,Send2Trash==1.5.0,sinfo==0.3.1,six==1.15.0,snowballstemmer==2.0.0,snuggs==1.4.7,soupsieve==2.1,Sphinx==3.4.3,sphinx-copybutton==0.3.1,sphinx-gallery==0.8.2,sphinx-last-updated-by-git==0.2.3,sphinx-rtd-theme==0.5.1,sphinxcontrib-applehelp==1.0.2,sphinxcontrib-devhelp==1.0.2,sphinxcontrib-htmlhelp==1.0.3,sphinxcontrib-jsmath==1.0.1,sphinxcontrib-qthelp==1.0.3,sphinxcontrib-serializinghtml==1.1.4,squidpy @ git+https://github.com/theislab/squidpy@d9ae3fbeb65479197a75702521477b80c33e5e15,statsmodels==0.12.1,stdlib-list==0.8.0,tables==3.6.1,terminado==0.9.2,testpath==0.4.4,texttable==1.6.3,threadpoolctl==2.1.0,tifffile==2021.1.14,tornado==6.1,tqdm==4.56.0,traitlets==5.0.5,typing-extensions==3.7.4.3,umap-learn==0.4.6,urllib3==1.26.2,wcwidth==0.2.5,webencodings==0.5.1,widgetsnbextension==3.5.1,wrapt==1.12.1,xarray==0.16.2
docs run-test-pre: PYTHONHASHSEED='3779319135'
docs run-test: commands[0] | sphinx-build --color -b html /Users/hannah.spitzer/projects/spatial_scanpy/squidpy_notebooks/docs/source /Users/hannah.spitzer/projects/spatial_scanpy/squidpy_notebooks/docs/build/html
Running Sphinx v3.4.3
loading intersphinx inventory from https://docs.python.org/3/objects.inv...
loading intersphinx inventory from https://anndata.readthedocs.io/en/stable/objects.inv...
loading intersphinx inventory from https://scanpy.readthedocs.io/en/stable/objects.inv...
loading intersphinx inventory from https://napari.org/docs/dev/objects.inv...
WARNING: failed to reach any of the inventories with the following issues:
intersphinx inventory 'https://anndata.readthedocs.io/en/stable/objects.inv' not fetchable due to <class 'requests.exceptions.ConnectionError'>: ('Connection aborted.', ConnectionResetError(54, 'Connection reset by peer'))
WARNING: failed to reach any of the inventories with the following issues:
intersphinx inventory 'https://scanpy.readthedocs.io/en/stable/objects.inv' not fetchable due to <class 'requests.exceptions.ConnectionError'>: ('Connection aborted.', ConnectionResetError(54, 'Connection reset by peer'))
generating gallery...
WARNING: optipng binaries not found, PNG images and thumbnails will not be optimized
Using pandoc version: 2.11.2 to convert rst text blocks to markdown for .ipynb files
generating gallery for auto_examples/graph... [100%] compute_dummy.py
WARNING: /Users/hannah.spitzer/projects/spatial_scanpy/squidpy_notebooks/examples/image/compute_smooth.py failed to execute correctly: Traceback (most recent call last):
  File "/Users/hannah.spitzer/projects/spatial_scanpy/squidpy_notebooks/examples/image/compute_smooth.py", line 19, in <module>
    import squidpy as sq
  File "/Users/hannah.spitzer/projects/spatial_scanpy/squidpy_notebooks/.tox/docs/lib/python3.8/site-packages/squidpy/__init__.py", line 10, in <module>
    from squidpy._io import read_visium_data
  File "/Users/hannah.spitzer/projects/spatial_scanpy/squidpy_notebooks/.tox/docs/lib/python3.8/site-packages/squidpy/_io.py", line 10, in <module>
    from squidpy.im import ImageContainer  # type: ignore[attr-defined]
  File "/Users/hannah.spitzer/projects/spatial_scanpy/squidpy_notebooks/.tox/docs/lib/python3.8/site-packages/squidpy/im/__init__.py", line 3, in <module>
    from squidpy.im.segment import (
  File "/Users/hannah.spitzer/projects/spatial_scanpy/squidpy_notebooks/.tox/docs/lib/python3.8/site-packages/squidpy/im/segment.py", line 14, in <module>
    from squidpy.constants._constants import SegmentationBackend
  File "/Users/hannah.spitzer/projects/spatial_scanpy/squidpy_notebooks/.tox/docs/lib/python3.8/site-packages/squidpy/constants/_constants.py", line 11, in <module>
    class ImageFeature(ModeEnum):  # noqa: D101
  File "/Users/hannah.spitzer/projects/spatial_scanpy/squidpy_notebooks/.tox/docs/lib/python3.8/site-packages/squidpy/constants/_utils.py", line 59, in __new__
    res: ABCEnumMeta = super().__new__(cls, clsname, bases, namespace)  # type: ignore[assignment]
  File "/Users/hannah.spitzer/opt/miniconda3/envs/squidpy/lib/python3.8/enum.py", line 215, in __new__
    enum_member = __new__(enum_class)
TypeError: object.__new__(ImageFeature) is not safe, use str.__new__()

Extension error:
Handler <function generate_gallery_rst at 0x10a4e2ee0> for event 'builder-inited' threw an exception (exception: object.__new__(ImageFeature) is not safe, use str.__new__())
ERROR: InvocationError for command /Users/hannah.spitzer/projects/spatial_scanpy/squidpy_notebooks/.tox/docs/bin/sphinx-build --color -b html docs/source docs/build/html (exited with code 2)
______________________________________________________________________ summary _______________________________________________________________________
ERROR:   docs: commands failed

it is giving warnings that it cannot read anndata and scanpy. It this related?

michalk8 commented 3 years ago

Hmm, strange. I did recently change the ModeEnum to be a string type, but have never experienced this. Can you try 2 things:

For me, the 1st works (there are only some warning I need to fix), so tox shouldn't have a problem. I've suspected the this is the pip install git+https part, but trying locally, it works fine. If this persists even after the rm -rf .tox, then I will revert the change (not sure if this code works on Python3.7, but I will check it out.)

hspitzer commented 3 years ago

import squidpy does not work for me on python 3.8 . On a fresh Conda with python=3.8 and the following packages (all installed by pip installing squidpy)

packages

> conda list
# packages in environment at /Users/hannah.spitzer/opt/miniconda3/envs/squidpy38:
#
# Name                    Version                   Build  Channel
affine                    2.3.0                    pypi_0    pypi
anndata                   0.7.5                    pypi_0    pypi
appdirs                   1.4.4                    pypi_0    pypi
appnope                   0.1.2                    pypi_0    pypi
argon2-cffi               20.1.0                   pypi_0    pypi
async-generator           1.10                     pypi_0    pypi
attrs                     20.3.0                   pypi_0    pypi
backcall                  0.2.0                    pypi_0    pypi
bleach                    3.2.1                    pypi_0    pypi
ca-certificates           2020.12.5            h033912b_0    conda-forge
certifi                   2020.12.5        py38h50d1736_1    conda-forge
cffi                      1.14.4                   pypi_0    pypi
cfgv                      3.2.0                    pypi_0    pypi
cftime                    1.3.1                    pypi_0    pypi
chardet                   4.0.0                    pypi_0    pypi
click                     7.1.2                    pypi_0    pypi
click-plugins             1.1.1                    pypi_0    pypi
cligj                     0.7.1                    pypi_0    pypi
cycler                    0.10.0                   pypi_0    pypi
dask                      2021.1.0                 pypi_0    pypi
data-science-types        0.2.22                   pypi_0    pypi
decorator                 4.4.2                    pypi_0    pypi
defusedxml                0.6.0                    pypi_0    pypi
distlib                   0.3.1                    pypi_0    pypi
docrep                    0.3.1                    pypi_0    pypi
entrypoints               0.3                      pypi_0    pypi
enum-tools                0.6.3                    pypi_0    pypi
filelock                  3.0.12                   pypi_0    pypi
get-version               2.1                      pypi_0    pypi
h5py                      3.1.0                    pypi_0    pypi
identify                  1.5.13                   pypi_0    pypi
idna                      2.10                     pypi_0    pypi
imageio                   2.9.0                    pypi_0    pypi
inflect                   5.0.2                    pypi_0    pypi
ipykernel                 5.4.3                    pypi_0    pypi
ipython                   7.19.0                   pypi_0    pypi
ipython-genutils          0.2.0                    pypi_0    pypi
ipywidgets                7.6.3                    pypi_0    pypi
jedi                      0.18.0                   pypi_0    pypi
jinja2                    2.11.2                   pypi_0    pypi
joblib                    1.0.0                    pypi_0    pypi
jsonschema                3.2.0                    pypi_0    pypi
jupyter-client            6.1.11                   pypi_0    pypi
jupyter-core              4.7.0                    pypi_0    pypi
jupyterlab-pygments       0.1.2                    pypi_0    pypi
jupyterlab-widgets        1.0.0                    pypi_0    pypi
kiwisolver                1.3.1                    pypi_0    pypi
legacy-api-wrap           1.2                      pypi_0    pypi
leidenalg                 0.8.3                    pypi_0    pypi
libcxx                    11.0.0               h4c3b8ed_1    conda-forge
libffi                    3.3                  h046ec9c_2    conda-forge
llvmlite                  0.35.0                   pypi_0    pypi
markupsafe                1.1.1                    pypi_0    pypi
matplotlib                3.3.3                    pypi_0    pypi
mistune                   0.8.4                    pypi_0    pypi
natsort                   7.1.0                    pypi_0    pypi
nbclient                  0.5.1                    pypi_0    pypi
nbconvert                 6.0.7                    pypi_0    pypi
nbformat                  5.1.2                    pypi_0    pypi
ncurses                   6.2                  h2e338ed_4    conda-forge
nest-asyncio              1.4.3                    pypi_0    pypi
netcdf4                   1.5.5.1                  pypi_0    pypi
networkx                  2.5                      pypi_0    pypi
nodeenv                   1.5.0                    pypi_0    pypi
notebook                  6.2.0                    pypi_0    pypi
numba                     0.52.0                   pypi_0    pypi
numexpr                   2.7.2                    pypi_0    pypi
numpy                     1.19.5                   pypi_0    pypi
omnipath                  1.0.4                    pypi_0    pypi
openssl                   1.1.1i               h35c211d_0    conda-forge
packaging                 20.8                     pypi_0    pypi
pandas                    1.2.0                    pypi_0    pypi
pandocfilters             1.4.3                    pypi_0    pypi
parso                     0.8.1                    pypi_0    pypi
patsy                     0.5.1                    pypi_0    pypi
pexpect                   4.8.0                    pypi_0    pypi
pickleshare               0.7.5                    pypi_0    pypi
pillow                    8.1.0                    pypi_0    pypi
pip                       20.3.3             pyhd8ed1ab_0    conda-forge
pluggy                    0.13.1                   pypi_0    pypi
pre-commit                2.9.3                    pypi_0    pypi
prometheus-client         0.9.0                    pypi_0    pypi
prompt-toolkit            3.0.10                   pypi_0    pypi
ptyprocess                0.7.0                    pypi_0    pypi
py                        1.10.0                   pypi_0    pypi
pycparser                 2.20                     pypi_0    pypi
pygments                  2.7.4                    pypi_0    pypi
pyparsing                 2.4.7                    pypi_0    pypi
pyrsistent                0.17.3                   pypi_0    pypi
python                    3.8.6           h624753d_4_cpython    conda-forge
python-dateutil           2.8.1                    pypi_0    pypi
python-igraph             0.8.3                    pypi_0    pypi
python_abi                3.8                      1_cp38    conda-forge
pytz                      2020.5                   pypi_0    pypi
pywavelets                1.1.1                    pypi_0    pypi
pyyaml                    5.3.1                    pypi_0    pypi
pyzmq                     21.0.1                   pypi_0    pypi
rasterio                  1.1.8                    pypi_0    pypi
readline                  8.0                  h0678c8f_2    conda-forge
requests                  2.25.1                   pypi_0    pypi
scanpy                    1.6.1                    pypi_0    pypi
scikit-image              0.18.1                   pypi_0    pypi
scikit-learn              0.24.0                   pypi_0    pypi
scipy                     1.6.0                    pypi_0    pypi
seaborn                   0.11.1                   pypi_0    pypi
send2trash                1.5.0                    pypi_0    pypi
setuptools                49.6.0           py38h50d1736_3    conda-forge
setuptools-scm            5.0.1                    pypi_0    pypi
sinfo                     0.3.1                    pypi_0    pypi
six                       1.15.0                   pypi_0    pypi
snuggs                    1.4.7                    pypi_0    pypi
sqlite                    3.34.0               h17101e1_0    conda-forge
squidpy                   0.1.dev257+gd9ae3fb           dev_0    <develop>
statsmodels               0.12.1                   pypi_0    pypi
stdlib-list               0.8.0                    pypi_0    pypi
tables                    3.6.1                    pypi_0    pypi
terminado                 0.9.2                    pypi_0    pypi
testpath                  0.4.4                    pypi_0    pypi
texttable                 1.6.3                    pypi_0    pypi
threadpoolctl             2.1.0                    pypi_0    pypi
tifffile                  2021.1.14                pypi_0    pypi
tk                        8.6.10               h0419947_1    conda-forge
toml                      0.10.2                   pypi_0    pypi
tornado                   6.1                      pypi_0    pypi
tox                       3.21.1                   pypi_0    pypi
tqdm                      4.56.0                   pypi_0    pypi
traitlets                 5.0.5                    pypi_0    pypi
typing-extensions         3.7.4.3                  pypi_0    pypi
umap-learn                0.4.6                    pypi_0    pypi
urllib3                   1.26.2                   pypi_0    pypi
virtualenv                20.3.1                   pypi_0    pypi
wcwidth                   0.2.5                    pypi_0    pypi
webencodings              0.5.1                    pypi_0    pypi
wheel                     0.36.2             pyhd3deb0d_0    conda-forge
widgetsnbextension        3.5.1                    pypi_0    pypi
wrapt                     1.12.1                   pypi_0    pypi
xarray                    0.16.2                   pypi_0    pypi
xz                        5.2.5                haf1e3a3_1    conda-forge
zlib                      1.2.11            h7795811_1010    conda-forge

with import squidpy as sq I get the same error as above. Python version is 3.8.6

michalk8 commented 3 years ago

No idea why this happens, but thanks for catching it, should be fixed.