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fix: various DPT plot fixes #3864

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codecov bot commented Oct 31, 2025 •
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❌ 6 Tests Failed:

Tests completed Failed Passed Skipped
2411 6 2405 137
View the full list of 6 ❄️ flaky test(s) 
tests/test_clustering.py::test_leiden_random_state[igraph]

Flake rate in main: 100.00% (Passed 0 times, Failed 1 times)

Stack Traces | 0.064s run time 
adata_neighbors = AnnData object with n_obs × n_vars = 700 × 765
    obs: 'bulk_labels', 'n_genes', 'percent_mito', 'n_counts', 'S_score...ghbors', 'pca', 'rank_genes_groups'
    obsm: 'X_pca', 'X_umap'
    varm: 'PCs'
    obsp: 'distances', 'connectivities'
flavor = 'igraph'

    #x1B[0m#x1B[37m@needs#x1B[39;49;00m.leidenalg#x1B[90m#x1B[39;49;00m
    #x1B[37m@needs#x1B[39;49;00m.igraph#x1B[90m#x1B[39;49;00m
    #x1B[37m@pytest#x1B[39;49;00m.mark.parametrize(#x1B[33m"#x1B[39;49;00m#x1B[33mflavor#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, FLAVORS)#x1B[90m#x1B[39;49;00m
    #x1B[94mdef#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[92mtest_leiden_random_state#x1B[39;49;00m(adata_neighbors, flavor):#x1B[90m#x1B[39;49;00m
        is_leiden_alg = flavor == #x1B[33m"#x1B[39;49;00m#x1B[33mleidenalg#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        n_iterations = #x1B[94m2#x1B[39;49;00m #x1B[94mif#x1B[39;49;00m is_leiden_alg #x1B[94melse#x1B[39;49;00m -#x1B[94m1#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        adata_1 = sc.tl.leiden(#x1B[90m#x1B[39;49;00m
            adata_neighbors,#x1B[90m#x1B[39;49;00m
            flavor=flavor,#x1B[90m#x1B[39;49;00m
            random_state=#x1B[94m1#x1B[39;49;00m,#x1B[90m#x1B[39;49;00m
            copy=#x1B[94mTrue#x1B[39;49;00m,#x1B[90m#x1B[39;49;00m
            directed=is_leiden_alg,#x1B[90m#x1B[39;49;00m
            n_iterations=n_iterations,#x1B[90m#x1B[39;49;00m
        )#x1B[90m#x1B[39;49;00m
        adata_1_again = sc.tl.leiden(#x1B[90m#x1B[39;49;00m
            adata_neighbors,#x1B[90m#x1B[39;49;00m
            flavor=flavor,#x1B[90m#x1B[39;49;00m
            random_state=#x1B[94m1#x1B[39;49;00m,#x1B[90m#x1B[39;49;00m
            copy=#x1B[94mTrue#x1B[39;49;00m,#x1B[90m#x1B[39;49;00m
            directed=is_leiden_alg,#x1B[90m#x1B[39;49;00m
            n_iterations=n_iterations,#x1B[90m#x1B[39;49;00m
        )#x1B[90m#x1B[39;49;00m
        adata_2 = sc.tl.leiden(#x1B[90m#x1B[39;49;00m
            adata_neighbors,#x1B[90m#x1B[39;49;00m
            flavor=flavor,#x1B[90m#x1B[39;49;00m
            random_state=#x1B[94m2#x1B[39;49;00m,#x1B[90m#x1B[39;49;00m
            copy=#x1B[94mTrue#x1B[39;49;00m,#x1B[90m#x1B[39;49;00m
            directed=is_leiden_alg,#x1B[90m#x1B[39;49;00m
            n_iterations=n_iterations,#x1B[90m#x1B[39;49;00m
        )#x1B[90m#x1B[39;49;00m
        pd.testing.assert_series_equal(adata_1.obs[#x1B[33m"#x1B[39;49;00m#x1B[33mleiden#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m], adata_1_again.obs[#x1B[33m"#x1B[39;49;00m#x1B[33mleiden#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m])#x1B[90m#x1B[39;49;00m
>       #x1B[94massert#x1B[39;49;00m #x1B[95mnot#x1B[39;49;00m adata_2.obs[#x1B[33m"#x1B[39;49;00m#x1B[33mleiden#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m].equals(adata_1_again.obs[#x1B[33m"#x1B[39;49;00m#x1B[33mleiden#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m])#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31mE       AssertionError: assert not True#x1B[0m
#x1B[1m#x1B[31mE        +  where True = equals(index\nAAAGCCTGGCTAAC-1    0\nAAATTCGATGCACA-1    0\nAACACGTGGTCTTT-1    1\nAAGTGCACGTGCTA-1    2\nACACGAACGGAGTG-1    3\n                   ..\nTGGCACCTCCAACA-8    3\nTGTGAGTGCTTTAC-8    0\nTGTTACTGGCGATT-8    6\nTTCAGTACCGGGAA-8    7\nTTGAGGTGGAGAGC-8    3\nName: leiden, Length: 700, dtype: category\nCategories (12, object): ['0', '1', '2', '3', ..., '8', '9', '10', '11'])#x1B[0m
#x1B[1m#x1B[31mE        +    where equals = index\nAAAGCCTGGCTAAC-1    0\nAAATTCGATGCACA-1    0\nAACACGTGGTCTTT-1    1\nAAGTGCACGTGCTA-1    2\nACACGAACGGAGTG-1    3\n                   ..\nTGGCACCTCCAACA-8    3\nTGTGAGTGCTTTAC-8    0\nTGTTACTGGCGATT-8    6\nTTCAGTACCGGGAA-8    7\nTTGAGGTGGAGAGC-8    3\nName: leiden, Length: 700, dtype: category\nCategories (12, object): ['0', '1', '2', '3', ..., '8', '9', '10', '11'].equals#x1B[0m

#x1B[1m#x1B[31mtests/test_clustering.py#x1B[0m:76: AssertionError
tests/test_paga.py::test_paga_pie

Flake rate in main: 100.00% (Passed 0 times, Failed 1 times)

Stack Traces | 0.1s run time 
image_comparer = <function image_comparer.<locals>.save_and_compare at 0x7fb48745d6c0>
pbmc = AnnData object with n_obs × n_vars = 700 × 765
    obs: 'bulk_labels', 'n_genes', 'percent_mito', 'n_counts', 'S_score...roups', 'paga', 'bulk_labels_sizes'
    obsm: 'X_pca', 'X_umap'
    varm: 'PCs'
    obsp: 'distances', 'connectivities'

    #x1B[0m#x1B[94mdef#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[92mtest_paga_pie#x1B[39;49;00m(image_comparer, pbmc) -> #x1B[94mNone#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
        save_and_compare_images = partial(image_comparer, ROOT, tol=#x1B[94m30#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        colors = {#x1B[90m#x1B[39;49;00m
            c: {cm.Set1(_): #x1B[94m0.33#x1B[39;49;00m #x1B[94mfor#x1B[39;49;00m _ #x1B[95min#x1B[39;49;00m #x1B[96mrange#x1B[39;49;00m(#x1B[94m3#x1B[39;49;00m)}#x1B[90m#x1B[39;49;00m
            #x1B[94mfor#x1B[39;49;00m c #x1B[95min#x1B[39;49;00m pbmc.obs[#x1B[33m"#x1B[39;49;00m#x1B[33mbulk_labels#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m].cat.categories#x1B[90m#x1B[39;49;00m
        }#x1B[90m#x1B[39;49;00m
        colors[#x1B[33m"#x1B[39;49;00m#x1B[33mDendritic#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m] = {cm.Set2(_): #x1B[94m0.25#x1B[39;49;00m #x1B[94mfor#x1B[39;49;00m _ #x1B[95min#x1B[39;49;00m #x1B[96mrange#x1B[39;49;00m(#x1B[94m4#x1B[39;49;00m)}#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        sc.pl.paga(pbmc, color=colors, colorbar=#x1B[94mFalse#x1B[39;49;00m, show=#x1B[94mFalse#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m
>       save_and_compare_images(#x1B[33m"#x1B[39;49;00m#x1B[33mpaga_pie#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31mE       AssertionError: Image files did not match.#x1B[0m
#x1B[1m#x1B[31mE       RMS Value:  71.40438286136829#x1B[0m
#x1B[1m#x1B[31mE       Expected:   file:.../_images/paga_pie/expected.png#x1B[0m
#x1B[1m#x1B[31mE       Actual:     file:.../_images/paga_pie/actual.png#x1B[0m
#x1B[1m#x1B[31mE       Difference: file:.../_images/paga_pie/actual-failed-diff.png#x1B[0m
#x1B[1m#x1B[31mE       Tolerance:  30#x1B[0m

#x1B[1m#x1B[31mtests/test_paga.py#x1B[0m:73: AssertionError
tests/test_paga.py::test_paga_plots[-paga]

Flake rate in main: 100.00% (Passed 0 times, Failed 1 times)

Stack Traces | 0.044s run time 
image_comparer = <function image_comparer.<locals>.save_and_compare at 0x7fb437adc680>
pbmc = AnnData object with n_obs × n_vars = 700 × 765
    obs: 'bulk_labels', 'n_genes', 'percent_mito', 'n_counts', 'S_score...roups', 'paga', 'bulk_labels_sizes'
    obsm: 'X_pca', 'X_umap'
    varm: 'PCs'
    obsp: 'distances', 'connectivities'
test_id = '', func = <function paga at 0x7fb489d42de0>

    #x1B[0m#x1B[37m@pytest#x1B[39;49;00m.mark.parametrize(#x1B[90m#x1B[39;49;00m
        (#x1B[33m"#x1B[39;49;00m#x1B[33mtest_id#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, #x1B[33m"#x1B[39;49;00m#x1B[33mfunc#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m),#x1B[90m#x1B[39;49;00m
        [#x1B[90m#x1B[39;49;00m
            (#x1B[33m"#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, sc.pl.paga),#x1B[90m#x1B[39;49;00m
            (#x1B[33m"#x1B[39;49;00m#x1B[33mcontinuous#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, partial(sc.pl.paga, color=#x1B[33m"#x1B[39;49;00m#x1B[33mCST3#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m)),#x1B[90m#x1B[39;49;00m
            (#x1B[33m"#x1B[39;49;00m#x1B[33mcontinuous_obs#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, partial(sc.pl.paga, color=#x1B[33m"#x1B[39;49;00m#x1B[33mcool_feature#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m)),#x1B[90m#x1B[39;49;00m
            (#x1B[33m"#x1B[39;49;00m#x1B[33mcontinuous_multiple#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, partial(sc.pl.paga, color=[#x1B[33m"#x1B[39;49;00m#x1B[33mCST3#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, #x1B[33m"#x1B[39;49;00m#x1B[33mGATA2#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m])),#x1B[90m#x1B[39;49;00m
            (#x1B[33m"#x1B[39;49;00m#x1B[33mcompare#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, partial(sc.pl.paga_compare, legend_fontoutline=#x1B[94m2#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[33mcompare_continuous#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m,#x1B[90m#x1B[39;49;00m
                partial(sc.pl.paga_compare, color=#x1B[33m"#x1B[39;49;00m#x1B[33mCST3#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, legend_fontsize=#x1B[94m5#x1B[39;49;00m),#x1B[90m#x1B[39;49;00m
                marks=pytest.mark.xfail(reason=#x1B[33m"#x1B[39;49;00m#x1B[33mexpects .uns[#x1B[39;49;00m#x1B[33m'#x1B[39;49;00m#x1B[33mpaga#x1B[39;49;00m#x1B[33m'#x1B[39;49;00m#x1B[33m][#x1B[39;49;00m#x1B[33m'#x1B[39;49;00m#x1B[33mpos#x1B[39;49;00m#x1B[33m'#x1B[39;49;00m#x1B[33m]#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[33m"#x1B[39;49;00m#x1B[33mcompare_pca#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m,#x1B[90m#x1B[39;49;00m
                partial(sc.pl.paga_compare, basis=#x1B[33m"#x1B[39;49;00m#x1B[33mX_pca#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, legend_fontweight=#x1B[33m"#x1B[39;49;00m#x1B[33mnormal#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_paga_plots#x1B[39;49;00m(image_comparer, pbmc, test_id, func):#x1B[90m#x1B[39;49;00m
        save_and_compare_images = partial(image_comparer, ROOT, tol=#x1B[94m30#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        common = #x1B[96mdict#x1B[39;49;00m(threshold=#x1B[94m0.5#x1B[39;49;00m, max_edge_width=#x1B[94m1.0#x1B[39;49;00m, random_state=#x1B[94m0#x1B[39;49;00m, show=#x1B[94mFalse#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        func(pbmc, **common)#x1B[90m#x1B[39;49;00m
>       save_and_compare_images(#x1B[33mf#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[33mpaga_#x1B[39;49;00m#x1B[33m{#x1B[39;49;00mtest_id#x1B[33m}#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m #x1B[94mif#x1B[39;49;00m test_id #x1B[94melse#x1B[39;49;00m #x1B[33m"#x1B[39;49;00m#x1B[33mpaga#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31mE       AssertionError: Image files did not match.#x1B[0m
#x1B[1m#x1B[31mE       RMS Value:  41.64525185902755#x1B[0m
#x1B[1m#x1B[31mE       Expected:   file:.../_images/paga/expected.png#x1B[0m
#x1B[1m#x1B[31mE       Actual:     file:.../_images/paga/actual.png#x1B[0m
#x1B[1m#x1B[31mE       Difference: file:.../_images/paga/actual-failed-diff.png#x1B[0m
#x1B[1m#x1B[31mE       Tolerance:  30#x1B[0m

#x1B[1m#x1B[31mtests/test_paga.py#x1B[0m:60: AssertionError
tests/test_paga.py::test_paga_plots[continuous-func1]

Flake rate in main: 100.00% (Passed 0 times, Failed 1 times)

Stack Traces | 0.085s run time 
image_comparer = <function image_comparer.<locals>.save_and_compare at 0x7fb437b13240>
pbmc = AnnData object with n_obs × n_vars = 700 × 765
    obs: 'bulk_labels', 'n_genes', 'percent_mito', 'n_counts', 'S_score...roups', 'paga', 'bulk_labels_sizes'
    obsm: 'X_pca', 'X_umap'
    varm: 'PCs'
    obsp: 'distances', 'connectivities'
test_id = 'continuous'
func = functools.partial(<function paga at 0x7fb489d42de0>, color='CST3')

    #x1B[0m#x1B[37m@pytest#x1B[39;49;00m.mark.parametrize(#x1B[90m#x1B[39;49;00m
        (#x1B[33m"#x1B[39;49;00m#x1B[33mtest_id#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, #x1B[33m"#x1B[39;49;00m#x1B[33mfunc#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m),#x1B[90m#x1B[39;49;00m
        [#x1B[90m#x1B[39;49;00m
            (#x1B[33m"#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, sc.pl.paga),#x1B[90m#x1B[39;49;00m
            (#x1B[33m"#x1B[39;49;00m#x1B[33mcontinuous#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, partial(sc.pl.paga, color=#x1B[33m"#x1B[39;49;00m#x1B[33mCST3#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m)),#x1B[90m#x1B[39;49;00m
            (#x1B[33m"#x1B[39;49;00m#x1B[33mcontinuous_obs#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, partial(sc.pl.paga, color=#x1B[33m"#x1B[39;49;00m#x1B[33mcool_feature#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m)),#x1B[90m#x1B[39;49;00m
            (#x1B[33m"#x1B[39;49;00m#x1B[33mcontinuous_multiple#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, partial(sc.pl.paga, color=[#x1B[33m"#x1B[39;49;00m#x1B[33mCST3#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, #x1B[33m"#x1B[39;49;00m#x1B[33mGATA2#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m])),#x1B[90m#x1B[39;49;00m
            (#x1B[33m"#x1B[39;49;00m#x1B[33mcompare#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, partial(sc.pl.paga_compare, legend_fontoutline=#x1B[94m2#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[33mcompare_continuous#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m,#x1B[90m#x1B[39;49;00m
                partial(sc.pl.paga_compare, color=#x1B[33m"#x1B[39;49;00m#x1B[33mCST3#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, legend_fontsize=#x1B[94m5#x1B[39;49;00m),#x1B[90m#x1B[39;49;00m
                marks=pytest.mark.xfail(reason=#x1B[33m"#x1B[39;49;00m#x1B[33mexpects .uns[#x1B[39;49;00m#x1B[33m'#x1B[39;49;00m#x1B[33mpaga#x1B[39;49;00m#x1B[33m'#x1B[39;49;00m#x1B[33m][#x1B[39;49;00m#x1B[33m'#x1B[39;49;00m#x1B[33mpos#x1B[39;49;00m#x1B[33m'#x1B[39;49;00m#x1B[33m]#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[33m"#x1B[39;49;00m#x1B[33mcompare_pca#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m,#x1B[90m#x1B[39;49;00m
                partial(sc.pl.paga_compare, basis=#x1B[33m"#x1B[39;49;00m#x1B[33mX_pca#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, legend_fontweight=#x1B[33m"#x1B[39;49;00m#x1B[33mnormal#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_paga_plots#x1B[39;49;00m(image_comparer, pbmc, test_id, func):#x1B[90m#x1B[39;49;00m
        save_and_compare_images = partial(image_comparer, ROOT, tol=#x1B[94m30#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        common = #x1B[96mdict#x1B[39;49;00m(threshold=#x1B[94m0.5#x1B[39;49;00m, max_edge_width=#x1B[94m1.0#x1B[39;49;00m, random_state=#x1B[94m0#x1B[39;49;00m, show=#x1B[94mFalse#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        func(pbmc, **common)#x1B[90m#x1B[39;49;00m
>       save_and_compare_images(#x1B[33mf#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[33mpaga_#x1B[39;49;00m#x1B[33m{#x1B[39;49;00mtest_id#x1B[33m}#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m #x1B[94mif#x1B[39;49;00m test_id #x1B[94melse#x1B[39;49;00m #x1B[33m"#x1B[39;49;00m#x1B[33mpaga#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31mE       AssertionError: Image files did not match.#x1B[0m
#x1B[1m#x1B[31mE       RMS Value:  40.145452243003106#x1B[0m
#x1B[1m#x1B[31mE       Expected:   file:.../_images/paga_continuous/expected.png#x1B[0m
#x1B[1m#x1B[31mE       Actual:     file:.../_images/paga_continuous/actual.png#x1B[0m
#x1B[1m#x1B[31mE       Difference: file:.../_images/paga_continuous/actual-failed-diff.png#x1B[0m
#x1B[1m#x1B[31mE       Tolerance:  30#x1B[0m

#x1B[1m#x1B[31mtests/test_paga.py#x1B[0m:60: AssertionError
tests/test_paga.py::test_paga_plots[continuous_multiple-func3]

Flake rate in main: 100.00% (Passed 0 times, Failed 1 times)

Stack Traces | 0.157s run time 
image_comparer = <function image_comparer.<locals>.save_and_compare at 0x7fb43d5b9f80>
pbmc = AnnData object with n_obs × n_vars = 700 × 765
    obs: 'bulk_labels', 'n_genes', 'percent_mito', 'n_counts', 'S_score...roups', 'paga', 'bulk_labels_sizes'
    obsm: 'X_pca', 'X_umap'
    varm: 'PCs'
    obsp: 'distances', 'connectivities'
test_id = 'continuous_multiple'
func = functools.partial(<function paga at 0x7fb489d42de0>, color=['CST3', 'GATA2'])

    #x1B[0m#x1B[37m@pytest#x1B[39;49;00m.mark.parametrize(#x1B[90m#x1B[39;49;00m
        (#x1B[33m"#x1B[39;49;00m#x1B[33mtest_id#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, #x1B[33m"#x1B[39;49;00m#x1B[33mfunc#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m),#x1B[90m#x1B[39;49;00m
        [#x1B[90m#x1B[39;49;00m
            (#x1B[33m"#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, sc.pl.paga),#x1B[90m#x1B[39;49;00m
            (#x1B[33m"#x1B[39;49;00m#x1B[33mcontinuous#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, partial(sc.pl.paga, color=#x1B[33m"#x1B[39;49;00m#x1B[33mCST3#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m)),#x1B[90m#x1B[39;49;00m
            (#x1B[33m"#x1B[39;49;00m#x1B[33mcontinuous_obs#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, partial(sc.pl.paga, color=#x1B[33m"#x1B[39;49;00m#x1B[33mcool_feature#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m)),#x1B[90m#x1B[39;49;00m
            (#x1B[33m"#x1B[39;49;00m#x1B[33mcontinuous_multiple#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, partial(sc.pl.paga, color=[#x1B[33m"#x1B[39;49;00m#x1B[33mCST3#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, #x1B[33m"#x1B[39;49;00m#x1B[33mGATA2#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m])),#x1B[90m#x1B[39;49;00m
            (#x1B[33m"#x1B[39;49;00m#x1B[33mcompare#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, partial(sc.pl.paga_compare, legend_fontoutline=#x1B[94m2#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[33mcompare_continuous#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m,#x1B[90m#x1B[39;49;00m
                partial(sc.pl.paga_compare, color=#x1B[33m"#x1B[39;49;00m#x1B[33mCST3#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, legend_fontsize=#x1B[94m5#x1B[39;49;00m),#x1B[90m#x1B[39;49;00m
                marks=pytest.mark.xfail(reason=#x1B[33m"#x1B[39;49;00m#x1B[33mexpects .uns[#x1B[39;49;00m#x1B[33m'#x1B[39;49;00m#x1B[33mpaga#x1B[39;49;00m#x1B[33m'#x1B[39;49;00m#x1B[33m][#x1B[39;49;00m#x1B[33m'#x1B[39;49;00m#x1B[33mpos#x1B[39;49;00m#x1B[33m'#x1B[39;49;00m#x1B[33m]#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[33m"#x1B[39;49;00m#x1B[33mcompare_pca#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m,#x1B[90m#x1B[39;49;00m
                partial(sc.pl.paga_compare, basis=#x1B[33m"#x1B[39;49;00m#x1B[33mX_pca#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, legend_fontweight=#x1B[33m"#x1B[39;49;00m#x1B[33mnormal#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_paga_plots#x1B[39;49;00m(image_comparer, pbmc, test_id, func):#x1B[90m#x1B[39;49;00m
        save_and_compare_images = partial(image_comparer, ROOT, tol=#x1B[94m30#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        common = #x1B[96mdict#x1B[39;49;00m(threshold=#x1B[94m0.5#x1B[39;49;00m, max_edge_width=#x1B[94m1.0#x1B[39;49;00m, random_state=#x1B[94m0#x1B[39;49;00m, show=#x1B[94mFalse#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        func(pbmc, **common)#x1B[90m#x1B[39;49;00m
>       save_and_compare_images(#x1B[33mf#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[33mpaga_#x1B[39;49;00m#x1B[33m{#x1B[39;49;00mtest_id#x1B[33m}#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m #x1B[94mif#x1B[39;49;00m test_id #x1B[94melse#x1B[39;49;00m #x1B[33m"#x1B[39;49;00m#x1B[33mpaga#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31mE       AssertionError: Image files did not match.#x1B[0m
#x1B[1m#x1B[31mE       RMS Value:  40.872406680222774#x1B[0m
#x1B[1m#x1B[31mE       Expected:   file:.../_images/paga_continuous_multiple/expected.png#x1B[0m
#x1B[1m#x1B[31mE       Actual:     file:.../_images/paga_continuous_multiple/actual.png#x1B[0m
#x1B[1m#x1B[31mE       Difference: file:.../_images/paga_continuous_multiple/actual-failed-diff.png#x1B[0m
#x1B[1m#x1B[31mE       Tolerance:  30#x1B[0m

#x1B[1m#x1B[31mtests/test_paga.py#x1B[0m:60: AssertionError
tests/test_paga.py::test_paga_plots[continuous_obs-func2]

Flake rate in main: 100.00% (Passed 0 times, Failed 1 times)

Stack Traces | 0.074s run time 
image_comparer = <function image_comparer.<locals>.save_and_compare at 0x7fb43e940fe0>
pbmc = AnnData object with n_obs × n_vars = 700 × 765
    obs: 'bulk_labels', 'n_genes', 'percent_mito', 'n_counts', 'S_score...roups', 'paga', 'bulk_labels_sizes'
    obsm: 'X_pca', 'X_umap'
    varm: 'PCs'
    obsp: 'distances', 'connectivities'
test_id = 'continuous_obs'
func = functools.partial(<function paga at 0x7fb489d42de0>, color='cool_feature')

    #x1B[0m#x1B[37m@pytest#x1B[39;49;00m.mark.parametrize(#x1B[90m#x1B[39;49;00m
        (#x1B[33m"#x1B[39;49;00m#x1B[33mtest_id#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, #x1B[33m"#x1B[39;49;00m#x1B[33mfunc#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m),#x1B[90m#x1B[39;49;00m
        [#x1B[90m#x1B[39;49;00m
            (#x1B[33m"#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, sc.pl.paga),#x1B[90m#x1B[39;49;00m
            (#x1B[33m"#x1B[39;49;00m#x1B[33mcontinuous#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, partial(sc.pl.paga, color=#x1B[33m"#x1B[39;49;00m#x1B[33mCST3#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m)),#x1B[90m#x1B[39;49;00m
            (#x1B[33m"#x1B[39;49;00m#x1B[33mcontinuous_obs#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, partial(sc.pl.paga, color=#x1B[33m"#x1B[39;49;00m#x1B[33mcool_feature#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m)),#x1B[90m#x1B[39;49;00m
            (#x1B[33m"#x1B[39;49;00m#x1B[33mcontinuous_multiple#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, partial(sc.pl.paga, color=[#x1B[33m"#x1B[39;49;00m#x1B[33mCST3#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, #x1B[33m"#x1B[39;49;00m#x1B[33mGATA2#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m])),#x1B[90m#x1B[39;49;00m
            (#x1B[33m"#x1B[39;49;00m#x1B[33mcompare#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, partial(sc.pl.paga_compare, legend_fontoutline=#x1B[94m2#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[33mcompare_continuous#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m,#x1B[90m#x1B[39;49;00m
                partial(sc.pl.paga_compare, color=#x1B[33m"#x1B[39;49;00m#x1B[33mCST3#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, legend_fontsize=#x1B[94m5#x1B[39;49;00m),#x1B[90m#x1B[39;49;00m
                marks=pytest.mark.xfail(reason=#x1B[33m"#x1B[39;49;00m#x1B[33mexpects .uns[#x1B[39;49;00m#x1B[33m'#x1B[39;49;00m#x1B[33mpaga#x1B[39;49;00m#x1B[33m'#x1B[39;49;00m#x1B[33m][#x1B[39;49;00m#x1B[33m'#x1B[39;49;00m#x1B[33mpos#x1B[39;49;00m#x1B[33m'#x1B[39;49;00m#x1B[33m]#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[33m"#x1B[39;49;00m#x1B[33mcompare_pca#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m,#x1B[90m#x1B[39;49;00m
                partial(sc.pl.paga_compare, basis=#x1B[33m"#x1B[39;49;00m#x1B[33mX_pca#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, legend_fontweight=#x1B[33m"#x1B[39;49;00m#x1B[33mnormal#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_paga_plots#x1B[39;49;00m(image_comparer, pbmc, test_id, func):#x1B[90m#x1B[39;49;00m
        save_and_compare_images = partial(image_comparer, ROOT, tol=#x1B[94m30#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        common = #x1B[96mdict#x1B[39;49;00m(threshold=#x1B[94m0.5#x1B[39;49;00m, max_edge_width=#x1B[94m1.0#x1B[39;49;00m, random_state=#x1B[94m0#x1B[39;49;00m, show=#x1B[94mFalse#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        func(pbmc, **common)#x1B[90m#x1B[39;49;00m
>       save_and_compare_images(#x1B[33mf#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[33mpaga_#x1B[39;49;00m#x1B[33m{#x1B[39;49;00mtest_id#x1B[33m}#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m #x1B[94mif#x1B[39;49;00m test_id #x1B[94melse#x1B[39;49;00m #x1B[33m"#x1B[39;49;00m#x1B[33mpaga#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31mE       AssertionError: Image files did not match.#x1B[0m
#x1B[1m#x1B[31mE       RMS Value:  40.49617290527572#x1B[0m
#x1B[1m#x1B[31mE       Expected:   file:.../_images/paga_continuous_obs/expected.png#x1B[0m
#x1B[1m#x1B[31mE       Actual:     file:.../_images/paga_continuous_obs/actual.png#x1B[0m
#x1B[1m#x1B[31mE       Difference: file:.../_images/paga_continuous_obs/actual-failed-diff.png#x1B[0m
#x1B[1m#x1B[31mE       Tolerance:  30#x1B[0m

#x1B[1m#x1B[31mtests/test_paga.py#x1B[0m:60: AssertionError

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@flying-sheep flying-sheep added this to the 1.11.6 milestone Oct 31, 2025
@flying-sheep flying-sheep changed the title Fix dpt_groups_pseudotime fix: various DPT plot fixes Oct 31, 2025
ilan-gold
ilan-gold reviewed Oct 31, 2025
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Are we testing whatever could have triggered the need for islice(cycle(...? It seems like we could add a test for that, at least that things dont crash. No? I guess it's tied to X.shape but just want to be sure we are checking the overflow case i.e., X.shape forcing the cycle to be used

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Whenever the number of subsets is larger than the palette, the old code would crash with an IndexError. (Using zip without strict=True would cause the iteration to end after the shortest iterable runs out)

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test failures are #3865

ilan-gold
ilan-gold approved these changes Nov 2, 2025
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Makes sense! Just wanted to be sure

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@ilan-gold ilan-gold ilan-gold approved these changes

@eroell eroell Awaiting requested review from eroell

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unexpected error in sc.pl.dpt_timeseries and dpt_groups_pseudotime

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@flying-sheep @ilan-gold