scverse/scanpy

`TypeError: metaclass conflict`: matplotlib v3.7.0 is incompatible with scanpy

thetorpedodog opened this issue · 1 comments

thetorpedodog commented
  • I have checked that this issue has not already been reported.
  • I have confirmed this bug exists on the latest version of scanpy.
  • Updated: I have confirmed this bug exists on the master branch of scanpy.

Minimal code sample

Start from a fresh venv. (Tested on Python 3.9.2 on Debian Bullseye.)

(new-venv) $ pip install scanpy==1.9.1

Then from within that venv:

import scanpy
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File ".../site-packages/scanpy/__init__.py", line 16, in <module>
    from . import plotting as pl
  File ".../site-packages/scanpy/plotting/__init__.py", line 1, in <module>
    from ._anndata import (
  File ".../site-packages/scanpy/plotting/_anndata.py", line 28, in <module>
    from . import _utils
  File ".../site-packages/scanpy/plotting/_utils.py", line 35, in <module>
    class _AxesSubplot(Axes, axes.SubplotBase, ABC):
TypeError: metaclass conflict: the metaclass of a derived class must be a (non-strict) subclass of the metaclasses of all its bases

Versions

You can't get to scanpy.logging.print_versions() on account of the crash.

thetorpedodog commented

To users: you can work around this in your environments by installing the previous version of matplotlib, for example with:

$ pip install 'matplotlib<3.7'

and/or adding a similar version specification to your pyproject.toml/setup.py/equivalent file, like single-cell-data/TileDB-SOMA@0bc97e8.

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