BUG set varm["replaced"] as a numpy array
#307
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…h is no longer supported in anndata 0.10.9
BorisMuzellec
requested review from
maikia,
arthurPignetOwkin and
umarteauowkin
as code owners
umarteauowkin
approved these changes
Sep 3, 2024
|
Thanks @umarteauowkin! Yes, it seems like it's the only place |
This was referenced Oct 11, 2024
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Reference Issue or PRs
Fixes #306
What does your PR implement? Be specific.
Starting from v0.10.9, anndata no longer supports pandas DataFrames or Series in varm fields.
This caused a bug when
refit_cookswas set toTrue, but no genes were replaced, as avarm["replaced"]was set as pandas Series filled withFalse.This PR fixes this issue by replacing the Series with a numpy array.
It also solves a second deprecation issue arising in
vst_fit, in which a design matrix was uselessly set withMultiIndexcolumns, which are no longer supported by anndata.Note: in the case were genes are replaced,
varm["replaced"]is automatically defined as an array.