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Can't save anndata after running define_clonotypes #257

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grst opened this issue Mar 26, 2021 · 1 comment
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Can't save anndata after running define_clonotypes #257

grst opened this issue Mar 26, 2021 · 1 comment
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grst commented Mar 26, 2021

reported by @chris-rands in #243:

  • I can't save the object to .h5ad due to TypeError: Can't implicitly convert non-string objects to strings with Above error raised while writing key 'uns/clonotype/cell_indices' of <class 'h5py._hl.files.File'> from /. I encountered this with parts of scanpy also, e.g. theislab/scanpy#1651 (comment)
@grst grst added the bug Something isn't working label Mar 26, 2021
@grst grst mentioned this issue Mar 26, 2021
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@grst grst added this to In progress in scirpy-dev Mar 29, 2021
grst added a commit that referenced this issue Apr 2, 2021
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Fix #257
c23584c
@grst grst mentioned this issue Apr 7, 2021
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grst commented Apr 7, 2021

This issue only appears with h5py >= 3.
See also scverse/anndata#493

grst added a commit that referenced this issue Apr 7, 2021
@grst
Fix #257.
ec11821 
Fix issue saving anndata with h5py >= 3.0
@grst grst closed this as completed in #241 Apr 7, 2021
scirpy-dev automation moved this from In progress to Done Apr 7, 2021
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