fix: obsm data frame have correct indices for python - #44
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ilan-gold wants to merge 2 commits into
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This was referenced Aug 25, 2026
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There is no specific language around this in our spec (which I just realized) and I did the work already, so I'm going to open this PR but previously,
dataframes from this packages (on-disk) in{obs,var}mlacked the matching index which would violate our python data structure's internal check: https://github.com/scverse/anndata/blob/01350d5fbea14a257edf3570608f2f0fdcd3883a/src/anndata/_core/aligned_mapping.py#L357-L366. Thus they were rendered unreadable. I need to investigate the history of this now, though. This is the source of the bug I mentioned in scverse/rustar-aligner#1 (comment).UPDATE: This behavior is traced back to scverse/anndata@f47db8c#diff-742a387bf5be7fca99f2c79f893d0a62ca524b6579a14bf5d9db8612ed1ca739R31-R46 with no explanation, so now it's just a matter of how bad breaking that behavior is.