Anndata.concatenate() fails when .X has a dimension of size 0

>>> from anndata import AnnData
>>> import numpy as np
>>> adata = AnnData(X=np.empty([1,0]))
>>> adata
AnnData object with n_obs × n_vars = 1 × 0
>>> AnnData.concatenate(adata, adata)

Error: IndexError: index 0 is out of bounds for axis 0 with size 0

Running anndata ‘0.7.5’

The reason this is an issue for me is that the scirpy TCR package builds adata like that https://github.com/icbi-lab/scirpy/blob/507c943e50a2d2ba5b0011575030db85dd5b316b/scirpy/io/_convert_anndata.py#L81

A fix or workaround would be great, thanks

[ivirshup]

@gokceneraslan I’ve opened a new issue for that since it seems different. I certainly think it’s a weird thing to do (since you are extending axis=1 with no elements), but I can’t think of a reason why we would want to error for that. It’s also a different bug from this since it’s coming from different code.

[chris-rands]

The argument names appear a bit different e.g. batch_key>label, batch_categories>keys