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TypeError: metaclass conflict
: matplotlib v3.7.0 is incompatible with scanpy
#2411
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thetorpedodog
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Feb 14, 2023
matplotlib just released v3.7, and unfortunately it introduced an incompatibility with scanpy: scverse/scanpy#2411 Excluding v3.7 works around this issue. This workaround can be removed once scanpy itself excludes v3.7, or if scanpy fixes the root cause.
TypeError: metaclass conflict
: matplotlib v3.7.0 is incompatible with scanpy
thetorpedodog
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Feb 14, 2023
matplotlib just released v3.7, and unfortunately it introduced an incompatibility with scanpy: scverse/scanpy#2411 Excluding v3.7 works around this issue. This workaround can be removed once scanpy itself excludes v3.7, or if scanpy fixes the root cause.
RemyLau
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RemyLau
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* restrict matplotlib below 3.7 to scanpy plotting module error scverse/scanpy#2411 * minor edit
carsten-jahn
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To users: you can work around this in your environments by installing the previous version of matplotlib, for example with:
and/or adding a similar version specification to your |
KenjiKamimoto-wustl122
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Change matplotlib version specification due to the issuehttps://github.com/scverse/scanpy/issues/2411
KenjiKamimoto-wustl122
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Change matplotlib version specification due to the issuehttps://github.com/scverse/scanpy/issues/2411
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This was referenced Feb 18, 2023
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Version >= 3.7 is incompatiable with scanpy, see scverse/scanpy/issues/2411
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abearab
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abearab
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scanpy dependencies set with >=, so have to explicitly select dependencies that we want below a certain value (e.g. numba). matplotlib>3.7 has import issues (scverse/scanpy#2411), so we also specify that.
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Minimal code sample
Start from a fresh venv. (Tested on Python 3.9.2 on Debian Bullseye.)
Then from within that venv:
Versions
You can't get to
scanpy.logging.print_versions()
on account of the crash.The text was updated successfully, but these errors were encountered: