Dask tests aren’t robust

[flying-sheep]

Please make sure these conditions are met

• I have checked that this issue has not already been reported.
• I have confirmed this bug exists on the latest version of scanpy.
• (optional) I have confirmed this bug exists on the main branch of scanpy.

What happened?

flaky precision tests:

• tests/test_preprocessing.py::test_scale_zero_center_warns_dask_sparse[dask_array_sparse]
• tests/test_highly_variable_genes.py::test_compare_to_upstream[dask_array_sparse-seurat-fgd]

Minimal code sample

hatch test tests/test_preprocessing.py::test_scale_zero_center_warns_dask_sparse[dask_array_sparse] tests/test_highly_variable_genes.py::test_compare_to_upstream[dask_array_sparse-seurat-fgd]

Error output

• https://github.com/scverse/integration-testing/actions/runs/16558022723/job/46822492476
• https://github.com/scverse/integration-testing/actions/runs/16545969290/job/46793649738

Versions

Using Python 3.11.13 environment at: /opt/hostedtoolcache/Python/3.11.13/x64
anndata @ git+https://github.com/scverse/anndata@c29100d6a46238d4d6a9faaf4c3c3b559676208a
array-api-compat==1.12.0
asciitree==0.3.3
click==8.2.1
cloudpickle==3.1.1
contourpy==1.3.3
coverage==7.10.0
cycler==0.12.1
dask==2025.7.0
dask-glm==0.3.2
dask-ml==2025.1.0
deprecated==1.2.18
distributed==2025.7.0
execnet==2.1.1
fast-array-utils==1.2.1
fasteners==0.19
fonttools==4.59.0
fsspec==2025.7.0
h5py==3.14.0
igraph==0.11.9
imageio==2.37.0
importlib-metadata==8.7.0
iniconfig==2.1.0
jinja2==3.1.6
joblib==1.5.1
kiwisolver==1.4.8
lazy-loader==0.4
legacy-api-wrap==1.4.1
leidenalg==0.10.2
llvmlite==0.44.0
locket==1.0.0
markupsafe==3.0.2
matplotlib==3.10.3
msgpack==1.1.1
multipledispatch==1.0.0
natsort==8.4.0
networkx==3.5
numba==0.61.2
numcodecs==0.15.1
numpy==2.2.6
packaging==25.0
pandas==2.3.1
partd==1.4.2
patsy==1.0.1
pillow==11.3.0
pip==25.1.1
pluggy==1.6.0
psutil==7.0.0
pyarrow==21.0.0
pygments==2.19.2
pynndescent==0.5.13
pyparsing==3.2.3
pytest==8.4.1
pytest-cov==6.2.1
pytest-mock==3.14.1
pytest-randomly==3.16.0
pytest-rerunfailures==15.1
pytest-xdist==3.8.0
python-dateutil==2.9.0.post0
pytz==2025.2
pyyaml==6.0.2
scanpy @ file:///home/runner/work/integration-testing/integration-testing/scanpy
scikit-image==0.25.2
scikit-learn==1.7.1
scikit-misc==0.5.1
scipy==1.15.3
seaborn==0.13.2
session-info2==0.2
setuptools==65.5.0
six==1.17.0
sortedcontainers==2.4.0
sparse==0.17.0
statsmodels==0.14.5
tblib==3.1.0
texttable==1.7.0
threadpoolctl==3.6.0
tifffile==2025.6.11
toolz==1.0.0
tornado==6.5.1
tqdm==4.67.1
tuna==0.5.11
typing-extensions==4.14.1
tzdata==2025.2
umap-learn==0.5.9.post2
urllib3==2.5.0
wrapt==1.17.2
zappy==0.2.0
zarr==2.18.7
zict==3.0.0
zipp==3.23.0