Random test failure of `test_plotting.py::test_paga`

Description

Running the scanpy tests locally (see system information and package versions below), I noticed the test scanpy/tests/test_plotting.py::test_paga sometimes failing due to AssertionError: Error: Image files did not match but passing on a consecutive run.

Did anyone encounter similar problems or does anyone know why this is happening?

Failure message

>>> pytest scanpy/tests/test_plotting.py
scanpy/tests/test_plotting.py .............................................x............F....                                                                                                                             [100%]

=========================================================================================================== FAILURES ============================================================================================================
___________________________________________________________________________________________________________ test_paga ___________________________________________________________________________________________________________

image_comparer = <function make_comparer at 0x7fbce4ade8c0>

    def test_paga(image_comparer):
        # Sometimes things shift a pixel or so, resulting in diffs up to ~27
        # The 1px-edges aren’t that good actually as they’re ignored at this tol …
        save_and_compare_images = image_comparer(ROOT, FIGS, tol=30)
    
        pbmc = sc.datasets.pbmc68k_reduced()
        sc.tl.paga(pbmc, groups='bulk_labels')
    
        common = dict(threshold=0.5, max_edge_width=1.0, random_state=0, show=False)
    
        # delete bulk_labels_colors to test the creation of color list by paga
        del pbmc.uns['bulk_labels_colors']
        sc.pl.paga(pbmc, **common)
        save_and_compare_images('master_paga')
    
        sc.pl.paga(pbmc, color='CST3', **common)
        save_and_compare_images('master_paga_continuous')
    
        pbmc.obs['cool_feature'] = pbmc[:, 'CST3'].X.squeeze()
        sc.pl.paga(pbmc, color='cool_feature', **common)
        save_and_compare_images('master_paga_continuous_obs')
    
        sc.pl.paga(pbmc, color=['CST3', 'GATA2'], **common)
        save_and_compare_images('master_paga_continuous_multiple')
    
        sc.pl.paga_compare(pbmc, legend_fontoutline=2, **common)
        save_and_compare_images('master_paga_compare')
    
        sc.pl.paga_compare(pbmc, color='CST3', legend_fontsize=5, **common)
        save_and_compare_images('master_paga_compare_continuous')
    
        sc.pl.paga_compare(pbmc, basis='X_pca', legend_fontweight='normal', **common)
        save_and_compare_images('master_paga_compare_pca')
    
        colors = {
            c: {cm.Set1(_): 0.33 for _ in range(3)}
            for c in pbmc.obs["bulk_labels"].cat.categories
        }
        colors["Dendritic"] = {cm.Set2(_): 0.25 for _ in range(4)}
    
        sc.pl.paga(pbmc, color=colors, colorbar=False)
>       save_and_compare_images('master_paga_pie')

scanpy/tests/test_plotting.py:917: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

basename = 'master_paga_pie', tolerance = 30

    def save_and_compare(basename, tolerance=None):
        path_actual.mkdir(parents=True, exist_ok=True)
        out_path = path_actual / f'{basename}.png'
        pyplot.savefig(out_path, dpi=40)
        pyplot.close()
        if tolerance is None:
            tolerance = tol
        res = compare_images(
            str(path_expected / f'{basename}.png'), str(out_path), tolerance
        )
>       assert res is None, res
E       AssertionError: Error: Image files did not match.
E           RMS Value: 36.26034272194439
E           Expected:  
E             /Users/philipp/Documents/python/scanpy/scanpy/tests/_images/master_paga_pie.png
E           Actual:    
E             /Users/philipp/Documents/python/scanpy/scanpy/tests/figures/master_paga_pie.png
E           Difference:
E             /Users/philipp/Documents/python/scanpy/scanpy/tests/figures/master_paga_pie-failed-diff.png
E           Tolerance: 
E             30
E       assert 'Error: Image files did not match.\n  RMS Value: 36.26034272194439\n  Expected:  \n    /Users/philipp/Documents/python...    /Users/philipp/Documents/python/scanpy/scanpy/tests/figures/master_paga_pie-failed-diff.png\n  Tolerance: \n    30' is None

scanpy/tests/conftest.py:35: AssertionError
----------------------------------------------------------------------------------------------------- Captured stderr call ------------------------------------------------------------------------------------------------------
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
--> added 'pos', the PAGA positions (adata.uns['paga'])
--> added 'pos', the PAGA positions (adata.uns['paga'])
--> added 'pos', the PAGA positions (adata.uns['paga'])
--> added 'pos', the PAGA positions (adata.uns['paga'])
--> added 'pos', the PAGA positions (adata.uns['paga'])
--> added 'pos', the PAGA positions (adata.uns['paga'])
--> added 'pos', the PAGA positions (adata.uns['paga'])

Versions

-----
anndata     0.7.4
scanpy      1.6.1.dev25+g74ac4d37
sinfo       0.3.1
-----
PIL                 7.2.0
anndata             0.7.4
asciitree           NA
cycler              0.10.0
cython_runtime      NA
dask                2.26.0
dateutil            2.8.1
fasteners           NA
get_version         2.1
h5py                2.10.0
igraph              0.8.2
importlib_metadata  1.7.0
joblib              0.16.0
kiwisolver          1.2.0
legacy_api_wrap     1.2
leidenalg           0.8.1
llvmlite            0.34.0
louvain             0.7.0
matplotlib          3.3.2
monotonic           NA
mpl_toolkits        NA
natsort             7.0.1
numba               0.51.2
numcodecs           0.7.2
numexpr             2.7.1
numpy               1.19.2
packaging           20.4
pandas              1.1.2
pkg_resources       NA
pyparsing           2.4.7
pytz                2020.1
scanpy              1.6.1.dev25+g74ac4d37
scipy               1.5.2
sinfo               0.3.1
six                 1.15.0
sklearn             0.23.2
tables              3.6.1
texttable           1.6.3
tlz                 0.10.0
toolz               0.10.0
yaml                5.3.1
zappy               NA
zarr                2.4.0
zipp                NA
-----
Python 3.7.9 (default, Aug 31 2020, 07:22:35) [Clang 10.0.0 ]
Darwin-19.6.0-x86_64-i386-64bit
12 logical CPU cores, i386
-----
Session information updated at 2020-09-16 13:37

Start by reproducing scanpy/tests/test_plotting.py::test_paga repeatedly and inspect the image comparison in scanpy/tests/conftest.py. Compare the generated master_paga_pie image and failure diff across runs, along with the listed Python and matplotlib versions. Done means the cause of the nondeterministic mismatch is identified and the test passes reliably.