ci: fix coverage

[flying-sheep]

See scverse/anndata#2115

[codecov]

❌ 1 Tests Failed:

Tests completed	Failed	Passed	Skipped
2407	1	2406	134

View the full list of 1 ❄️ flaky tests

tests/test_neighbors.py::test_connectivities_euclidean[umap]

Flake rate in main: 8.82% (Passed 31 times, Failed 3 times)

Stack Traces | 0.028s run time

neigh = <scanpy.neighbors.Neighbors object at 0x7f0578e01cd0>, method = 'umap'
conn = [[0.0, 1.0, 0.0, 1.0], [1.0, 0.0, 0.5849691143165735, 0.8277419907567016], [0.0, 0.5849691143165735, 0.0, 1.0], [1.0, 0.8277419907567016, 1.0, 0.0]]
trans = [[0.0, 0.5395987596963403, 0.0, 0.4604012403036599], [0.430368608684738, 0.0, 0.3176747629691457, 0.2519566283461165],...0, 0.40673754271561435, 0.0, 0.5932624572843856], [0.33921243006981133, 0.23275092618009624, 0.42803664375009237, 0.0]]
trans_sym = [[0.0, 0.4818987107873648, 0.0, 0.3951883393150153], [0.48189871078736474, 0.0, 0.3594582764005241, 0.2421634543129348...0.0, 0.3594582764005241, 0.0, 0.5039226836320637], [0.39518833931501524, 0.24216345431293487, 0.5039226836320637, 0.0]]

    #x1B[0m#x1B[37m@pytest#x1B[39;49;00m.mark.parametrize(#x1B[90m#x1B[39;49;00m
        (#x1B[33m"#x1B[39;49;00m#x1B[33mmethod#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, #x1B[33m"#x1B[39;49;00m#x1B[33mconn#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, #x1B[33m"#x1B[39;49;00m#x1B[33mtrans#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, #x1B[33m"#x1B[39;49;00m#x1B[33mtrans_sym#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m),#x1B[90m#x1B[39;49;00m
        [#x1B[90m#x1B[39;49;00m
            pytest.param(#x1B[90m#x1B[39;49;00m
                #x1B[33m"#x1B[39;49;00m#x1B[33mumap#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m,#x1B[90m#x1B[39;49;00m
                connectivities_umap,#x1B[90m#x1B[39;49;00m
                transitions_umap,#x1B[90m#x1B[39;49;00m
                transitions_sym_umap,#x1B[90m#x1B[39;49;00m
                #x1B[96mid#x1B[39;49;00m=#x1B[33m"#x1B[39;49;00m#x1B[33mumap#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m,#x1B[90m#x1B[39;49;00m
            ),#x1B[90m#x1B[39;49;00m
            pytest.param(#x1B[90m#x1B[39;49;00m
                #x1B[33m"#x1B[39;49;00m#x1B[33mgauss#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m,#x1B[90m#x1B[39;49;00m
                connectivities_gauss_knn,#x1B[90m#x1B[39;49;00m
                transitions_gauss_knn,#x1B[90m#x1B[39;49;00m
                transitions_sym_gauss_knn,#x1B[90m#x1B[39;49;00m
                #x1B[96mid#x1B[39;49;00m=#x1B[33m"#x1B[39;49;00m#x1B[33mgauss#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m,#x1B[90m#x1B[39;49;00m
            ),#x1B[90m#x1B[39;49;00m
        ],#x1B[90m#x1B[39;49;00m
    )#x1B[90m#x1B[39;49;00m
    #x1B[94mdef#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[92mtest_connectivities_euclidean#x1B[39;49;00m(neigh: Neighbors, method, conn, trans, trans_sym):#x1B[90m#x1B[39;49;00m
        neigh.compute_neighbors(n_neighbors, method=method)#x1B[90m#x1B[39;49;00m
>       np.testing.assert_allclose(neigh.connectivities.toarray(), conn)#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31mE       AssertionError: #x1B[0m
#x1B[1m#x1B[31mE       Not equal to tolerance rtol=1e-07, atol=0#x1B[0m
#x1B[1m#x1B[31mE       #x1B[0m
#x1B[1m#x1B[31mE       Mismatched elements: 4 / 16 (25%)#x1B[0m
#x1B[1m#x1B[31mE       Max absolute difference among violations: 0.4150308857#x1B[0m
#x1B[1m#x1B[31mE       Max relative difference among violations: 0.7094919638#x1B[0m
#x1B[1m#x1B[31mE        ACTUAL: array([[0., 1., 0., 1.],#x1B[0m
#x1B[1m#x1B[31mE              [1., 0., 1., 1.],#x1B[0m
#x1B[1m#x1B[31mE              [0., 1., 0., 1.],#x1B[0m
#x1B[1m#x1B[31mE              [1., 1., 1., 0.]], dtype=float32)#x1B[0m
#x1B[1m#x1B[31mE        DESIRED: array([[0.      , 1.      , 0.      , 1.      ],#x1B[0m
#x1B[1m#x1B[31mE              [1.      , 0.      , 0.584969, 0.827742],#x1B[0m
#x1B[1m#x1B[31mE              [0.      , 0.584969, 0.      , 1.      ],#x1B[0m
#x1B[1m#x1B[31mE              [1.      , 0.827742, 1.      , 0.      ]])#x1B[0m

#x1B[1m#x1B[31mtests/test_neighbors.py#x1B[0m:192: AssertionError

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