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cellbender: keep uns as CellBender's loader gives it - #52
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Checked against real CellBender 0.3.2 output (two samples, full and filtered) and load_anndata_from_input_and_output. Everything matched but uns: - one-element settings (target_false_positive_rate, estimator, ...) were unwrapped to scalars; the loader keeps them as stored; - a filtered file's barcode_indices_for_latents, which places no rows there, was dropped; the loader keeps it in uns. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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From review on #52. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Follow-up to #51 (#29), from checking against real CellBender 0.3.2 output: two samples from a cellgeni ticket,
cellbender.h5andcellbender_filtered.h5each with--raw, compared with CellBender 0.3.2's ownload_anndata_from_input_and_outputandanndata_from_h5.X, both layers, every latent at its barcode, the embedding, var, and
--min-cell-probability 0.5(same cells as CellBender's filtered file) all matched. Two differences, both inuns:target_false_positive_rate,estimator, ...) were unwrapped to scalars. The loader keeps them as stored, souns[...][0]in a notebook broke. They now stay as CellBender wrote them (0.2 stores true scalars and keeps those).barcode_indices_for_latents, which places no rows there, was dropped. The loader keeps it inuns; so do we now.After this, all four real 0.3.2 files and the earlier 0.2.2 run match on every check.
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