Fix all-NaN extra obs after PseudobulkSpace with groups_col#1006
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Fix all-NaN extra obs after PseudobulkSpace with groups_col#1006Zethson wants to merge 1 commit into
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When `groups_col` is provided, `ps_adata.obs.index` is a joined string like "patient_cluster", so reindexing the per-group lookup against that index returned NaN for every extra column. The all-NaN `obs` then made formulaic drop every row, producing an empty-index design matrix that `DeseqDataSet` rejected (#1003). Reindex by the grouping columns themselves instead. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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Summary
pt.tl.PseudobulkSpace()#1003.PseudobulkSpace.computewas called withgroups_col, every obs column not produced bysc.get.aggregate(e.g.Efficacy,Treatment) came out all-NaN. The per-group lookup is aMultiIndex(target_col, groups_col), but it was being reindexed againstps_adata.obs.index, which is the joined"target_groups"string index — so nothing matched.DeseqDataSetrejects: with all-NaN factors, formulaic drops every row.Indexwhen there is one grouping col,MultiIndex.from_framewhen there are two), then re-attachps_adata.obs.index.groups_colis set.