chanzuckerberg/cellxgene-census

Python CI process killed with tiledbsoma 1.14.1

Closed this issue · 1 comments

ivirshup commented

I can replicate locally, investigating further

To replicate:

import cellxgene_census

census = cellxgene_census.open_soma(census_version="2023-12-15")
ad = cellxgene_census.get_anndata(
    census,
    organism="Homo sapiens",
    X_name="raw",
    obs_coords=slice(100),
    var_coords=slice(200),
    obsm_layers=["scvi"],
)
[1]    155365 killed     ipython

The segfault seems to occur if the user passed a value for obsm_layers IFF there is actually an entry in obsm to retrieve. However, we have a workaround in that we store embeddings separately from census.

ivirshup commented

This has been fixed with tiledbsoma 1.14.2. I'd say let's pin against 1.14.1 (e.g. !=1.14.1), but no need to rush out a release

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