Broken test: TestPreprocessingDistributed::test_normalize_per_cell[dask]

[flying-sheep]

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• 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 master branch of scanpy.

What happened?

In #2235, more gradually enabled some so far disabled tests. Before, all tests in TestPreprocessingDistributed were disabled with the available optional dependencies we run our tests with:

scanpy/scanpy/tests/test_preprocessing_distributed.py

Lines 15 to 22 in 06802b4

	required = ['dask', 'zappy', 'zarr']
	installed = {mod: bool(find_spec(mod)) for mod in required}
	@pytest.mark.skipif(
	not all(installed.values()), reason=f'{required} all required: {installed}'
	)
	class TestPreprocessingDistributed:

now, the dask tests are enabled and only the zappy tests are disabled:

scanpy/scanpy/tests/test_preprocessing_distributed.py

Lines 18 to 31 in 6b9e734

	@needs("zarr")
	class TestPreprocessingDistributed:
	@pytest.fixture()
	def adata(self):
	a = ad.read_zarr(input_file) # regular anndata
	a.X = a.X[:] # convert to numpy array
	return a
	@pytest.fixture(
	params=[
	pytest.param("direct", marks=[needs("zappy")]),
	pytest.param("dask", marks=[needs("dask")]),
	]
	)

Minimal code sample

pytest -v --disable-warnings -k test_normalize_per_cell[dask] --runxfail

Error output

===================================================================================================== test session starts ======================================================================================================
platform linux -- Python 3.8.17, pytest-7.3.1, pluggy-1.0.0 -- /home/phil/Dev/Python/venvs/single-cell/bin/python
cachedir: .pytest_cache
rootdir: /home/phil/Dev/Python/Single Cell/scanpy
configfile: pyproject.toml
testpaths: scanpy
plugins: cov-4.1.0, nunit-1.0.3, memray-1.4.0, xdist-3.3.1
collected 986 items / 985 deselected / 1 selected                                                                                                                                                                              

scanpy/tests/test_preprocessing_distributed.py::TestPreprocessingDistributed::test_normalize_per_cell[dask] FAILED                                                                                                       [100%]

=========================================================================================================== FAILURES ===========================================================================================================
__________________________________________________________________________________ TestPreprocessingDistributed.test_normalize_per_cell[dask] __________________________________________________________________________________

self = <scanpy.tests.test_preprocessing_distributed.TestPreprocessingDistributed object at 0x7fdd21f2e9d0>, adata = AnnData object with n_obs × n_vars = 9999 × 1000
    obs: 'n_counts'
    var: 'gene_ids'
adata_dist = AnnData object with n_obs × n_vars = 9999 × 1000
    obs: 'n_counts'
    var: 'gene_ids'
    uns: 'dist-mode'

    def test_normalize_per_cell(self, adata, adata_dist):
        if adata_dist.uns["dist-mode"] == "dask":
            pytest.xfail("TODO: Test broken for dask")
        normalize_per_cell(adata_dist)
        result = materialize_as_ndarray(adata_dist.X)
        normalize_per_cell(adata)
        assert result.shape == adata.shape
        assert result.shape == (adata.n_obs, adata.n_vars)
>       npt.assert_allclose(result, adata.X)
E       AssertionError: 
E       Not equal to tolerance rtol=1e-07, atol=0
E       
E       Mismatched elements: 688287 / 9999000 (6.88%)
E       Max absolute difference: 573.4154
E       Max relative difference: 11.335767
E        x: array([[0., 0., 0., ..., 0., 0., 0.],
E              [0., 0., 0., ..., 0., 0., 0.],
E              [0., 0., 0., ..., 0., 0., 0.],...
E        y: array([[0., 0., 0., ..., 0., 0., 0.],
E              [0., 0., 0., ..., 0., 0., 0.],
E              [0., 0., 0., ..., 0., 0., 0.],...

scanpy/tests/test_preprocessing_distributed.py:64: AssertionError
----------------------------------------------------------------------------------------------------- Captured stderr call -----------------------------------------------------------------------------------------------------
normalizing by total count per cell
filtered out dask.array<sum-aggregate, shape=(), dtype=int64, chunksize=(), chunktype=numpy.ndarray> cells that have less than 1 counts
    finished (0:00:00): normalized adata.X and added    'n_counts', counts per cell before normalization (adata.obs)
normalizing by total count per cell
filtered out 1 cells that have less than 1 counts
    finished (0:00:00): normalized adata.X and added    'n_counts', counts per cell before normalization (adata.obs)
=================================================================================================== short test summary info ====================================================================================================
FAILED scanpy/tests/test_preprocessing_distributed.py::TestPreprocessingDistributed::test_normalize_per_cell[dask] - AssertionError: 
======================================================================================== 1 failed, 985 deselected, 11 warnings in 3.74s ========================================================================================

Versions

-----
anndata     0.9.0rc2.dev43+g21a76088
scanpy      1.10.0.dev117+g6b9e734f
-----
PIL                 9.1.1
asciitree           NA
awkward             2.2.1
awkward_cpp         NA
beta_ufunc          NA
binom_ufunc         NA
cffi                1.15.0
cloudpickle         2.2.1
cycler              0.10.0
cython_runtime      NA
dask                2023.5.0
dateutil            2.8.2
defusedxml          0.7.1
entrypoints         0.4
fasteners           0.17.3
h5py                3.7.0
hypergeom_ufunc     NA
igraph              0.10.4
importlib_resources NA
jinja2              3.1.2
joblib              1.1.0
kiwisolver          1.4.3
leidenalg           0.9.1
llvmlite            0.38.1
markupsafe          2.1.1
matplotlib          3.7.1
mpl_toolkits        NA
natsort             8.1.0
nbinom_ufunc        NA
numba               0.55.2
numcodecs           0.10.2
numpy               1.22.4
packaging           21.3
pandas              2.0.2
pkg_resources       NA
psutil              5.9.1
pyparsing           3.0.9
pytz                2022.1
scipy               1.8.1
session_info        1.0.0
setuptools          67.8.0
setuptools_scm      NA
six                 1.16.0
sklearn             1.1.1
sphinxcontrib       NA
texttable           1.6.7
threadpoolctl       3.1.0
tlz                 0.12.0
toolz               0.12.0
typing_extensions   NA
wcwidth             0.2.5
yaml                6.0
zarr                2.12.0
zipp                NA
-----
Python 3.8.17 (default, Jun 17 2023, 20:09:37) [GCC 13.1.1 20230429]
Linux-6.3.8-zen1-1-zen-x86_64-with-glibc2.34
-----
Session information updated at 2023-06-23 14:29