CI: `test_cellxgene_adata` fails — cellxgene-census AnnData now exposes a `layers` entry (live-data drift)

[Elarwei001]

Summary

The live integration test tests/test_cellxgene.py::TestCellxgene::test_cellxgene_adata currently fails on CI (all of py3.12 / py3.13 / py3.14). This is an upstream live-data / dependency drift, not caused by any code change in gget — it surfaces on unrelated PRs (e.g. #233, whose own changes are entirely in gget ucsc + docs).

Symptom

FAILED tests/test_cellxgene.py::TestCellxgene::test_cellxgene_adata
  AssertionError: {... 'layers': [None]} != {...}
  - {'layers': [None], ...}
tests/test_cellxgene.py:53: AssertionError

The actual result now contains an extra 'layers': [None] entry that the expected fixture does not.

Root cause

test_cellxgene_adata calls cellxgene(...), converts the returned AnnData to a dict via repr_dict(), and compares it to expected_result in tests/fixtures/test_cellxgene.json.

repr_dict() includes an attribute only when list(getattr(adata, attr).keys()) is non-empty. cellxgene_census.get_anndata(...) now returns an AnnData whose .layers contains a single entry keyed None, so list(adata.layers.keys()) is [None] and repr_dict adds "layers": [None]. The stored expected_result predates this, so the exact-dict comparison fails.

Timeline (confirms it is drift, not a regression)

• The last CI run on dev (2026-06-28, "Bump dev version") was green, so this test passed then.
• It fails on runs from 2026-07-08 onward → the change is in the upstream cellxgene-census data/library, independent of any gget commit.

Suggested fix

Prefer aligning the test with the new stable reality rather than loosening the assertion:

• Update expected_result in tests/fixtures/test_cellxgene.json to include the new "layers": [None], or
• If the None-keyed layer is considered noise, have repr_dict() drop a layer whose only key is None (and document why), so the comparison stays on the meaningful structure (obs / var / counts).

Reproduce

# with cellxgene-census installed
pytest tests/test_cellxgene.py::TestCellxgene::test_cellxgene_adata