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feat: multiple outputs - #288

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ilan-gold wants to merge 3 commits into
ig/anndata_13from
ig/multiple_outputs
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ilan-gold wants to merge 3 commits into
ig/anndata_13from
ig/multiple_outputs

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@ilan-gold

@ilan-gold ilan-gold commented Oct 2, 2026 •

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This is a naive implementation of outputting multiple data matrices and represents a breaking change.

As an example, the outputs for an AnnData object with layers["sparse"] and obsm["pca"] would be a dict:

{
    "layers.sparse": ...,
    "obsm.pca": ...,
    "obs": ...,
    ...
}

This is the same string syntax from scanpy (scverse/scanpy#4359) and also nicely leaves the old behavior in tact since X will still map to the string X in the dict (and if using the raw zarr dataset API).

Resolves #252's ask.

@ilan-gold ilan-gold added the skip-gpu-ci Whether gpu ci should be skipped label Oct 2, 2026

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