Add SCVIDataModule, pytorch_scvi.ipynb
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* Updating pytorch_scvi notebook to fix UMAP plots * `pytorch_scvi.ipynb`: rm metadata, some warnings * `pytorch_scvi`: update `nnz` comment --------- Co-authored-by: Konstantinos Tsitsimpikos <kostas.t@tiledb.com> Co-authored-by: Ryan Williams <ryan.williams@tiledb.com>
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| if not inplace: | ||
| obs_df = obs_df.copy() |
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Since pandas is moving towards Copy-Over-Write logic soon (defauly behaviour in Pandas3.0 +). We may want to be proactive and remove this inplace behaviour
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_add_batch_col(inplace=True) is used at both call-sites in this file, to avoid an unnecessary copy. The implementation doesn't use any deprecated Pandas kwargs/APIs, and we'll want to support pandas<3 for some years, so I would leave this as-is.
Or: how would you propose rewriting it (without adding an unnecessary copy())?
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Porting @mlin's
SCVIDataModuleandpytorch_scvi.ipynbfrom chanzuckerberg/cellxgene-census#1368.TODO: