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Consistent typing in adata.obs #190

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grst opened this issue Oct 2, 2020 · 3 comments
Closed

Consistent typing in adata.obs #190

grst opened this issue Oct 2, 2020 · 3 comments
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@grst
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grst commented Oct 2, 2020

  • Most columns added to adata.obs should probably be well-defined categoricals
  • Booleans should be booleans / or categoricals, and not strings
  • nan should be nan and not "nan". Categoricals do support nan, but there was an issue with how this is implemented in anndata, maybe this needs to be fixed upstream.
@grst grst added this to the 1.0 milestone Mar 10, 2021
@grst
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grst commented Apr 13, 2021

Anndata supports now categoricals with nan values.

There are still some issues with anndata saving booleans.
Also anndata can't save object dtypes, so we need to make sure to convert those to categoricals appropriately.

@grst
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grst commented Jan 12, 2022

Anndata now also supports nullable booleans: scverse/anndata#504 (comment)

Nullable strings are still not supported (scverse/anndata#679), but less important since categoricals are better in almost all cases anyway.

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grst commented Jun 28, 2022

superseded by #327

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