concat errors with one dimensional arrays in obsm #652
Description
Seen in comment by @Hrovatin in #501 (comment)_
import anndata as ad, numpy as np
foo = ad.AnnData(np.ones((5, 20), obsm={"1d-array": np.ones(5)})
ad.concat([foo, foo])Traceback
---------------------------------------------------------------------------
IndexError Traceback (most recent call last)
/var/folders/bd/43q20k0n6z15tdfzxvd22r7c0000gn/T/ipykernel_14520/2434769132.py in <module>
----> 1 ad.concat([a, a])
~/github/anndata/anndata/_core/merge.py in concat(adatas, axis, join, merge, uns_merge, label, keys, index_unique, fill_value, pairwise)
848 [a.layers for a in adatas], axis=axis, reindexers=reindexers
849 )
--> 850 concat_mapping = inner_concat_aligned_mapping(
851 [getattr(a, f"{dim}m") for a in adatas], index=concat_indices
852 )
~/github/anndata/anndata/_core/merge.py in inner_concat_aligned_mapping(mappings, reindexers, index, axis)
455 els = [m[k] for m in mappings]
456 if reindexers is None:
--> 457 cur_reindexers = gen_inner_reindexers(els, new_index=index, axis=axis)
458 else:
459 cur_reindexers = reindexers
~/github/anndata/anndata/_core/merge.py in gen_inner_reindexers(els, new_index, axis)
476 reindexers = [Reindexer(df_indices(el), common_ind) for el in els]
477 else:
--> 478 min_ind = min(el.shape[alt_axis] for el in els)
479 reindexers = [
480 gen_reindexer(pd.RangeIndex(min_ind), pd.RangeIndex(el.shape[alt_axis]))
~/github/anndata/anndata/_core/merge.py in <genexpr>(.0)
476 reindexers = [Reindexer(df_indices(el), common_ind) for el in els]
477 else:
--> 478 min_ind = min(el.shape[alt_axis] for el in els)
479 reindexers = [
480 gen_reindexer(pd.RangeIndex(min_ind), pd.RangeIndex(el.shape[alt_axis]))
IndexError: tuple index out of rangeOff the top of my head, I can't think of a reason this working would be inconsistent with the anndata model. Generally I would expect people to put 1d arrays in obs though.
Might have implications for the concatenation of awkward arrays (#647)