broadinstitute/CellBender

load_anndata_from_input_and_output: retain_input_metadata input to nowhere

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Hi there,

Thanks again for supporting this awesome tool! I've perhaps (again) run into something that no one uses, but would be a great add for my use case.

In the documentation for load_anndata_from_input_and_output there's an option to transfer all metadata from an input .h5ad to the final output, using retain_input_metadata = True, I tried this, which did nothing, and looked at the source code - looks like it's commented out for a future feature. Just bumping that this is in fact something someone (myself) would use!

In the meantime I'll do a manual update of .var, .obs, .uns, since I'm not totally familiar with cellbender helper fn's and output does change .var col names from input - if you had some input on what you intended to have there, happy to also take a crack at it and PR.