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Mirror scanpy's image-comparison tolerances to fix CPU plotting test failures #1083

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Merged
sueoglu merged 7 commits into from
Jul 1, 2026
+26 −34
Merged

Mirror scanpy's image-comparison tolerances to fix CPU plotting test failures #1083

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5cf2462
plotting tests tolerance increased, submodule pointer
sueoglu Jun 25, 2026
e5d9214
tolerance increased in the plots of pca_overview and ncp
sueoglu Jun 25, 2026
daace69
exclude matplotlib 3.11 (temporarily)
sueoglu Jun 25, 2026
7477e61
Merge branch 'main' into fix/issue-1082
sueoglu Jun 30, 2026
be9ac5b
Update tests/conftest.py
sueoglu Jul 1, 2026
24f53fa
Update tests/conftest.py
sueoglu Jul 1, 2026
7ac16fc
permalinked the line in scanpy pyproject.toml as ref
sueoglu Jul 1, 2026
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2 changes: 2 additions & 0 deletions pyproject.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -48,6 +48,8 @@ classifiers = [
dependencies = [
"ehrdata",
"scanpy",
# mirroring scanpy: skip 3.11.0 series for now: https://github.com/matplotlib/matplotlib/issues/31575
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"matplotlib>=3.10,!=3.11.0rc1,!=3.11.0rc2,!=3.11",
"scverse-misc[settings]>=0.0.7",
"requests",
"miceforest",
Expand Down
2 changes: 1 addition & 1 deletion submodules/ehrdata
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Submodule ehrdata updated 9 files
+2 −5 .github/workflows/run_notebooks.yaml
+5 −5 .github/workflows/test.yaml
+3 −3 .pre-commit-config.yaml
+6 −1 CHANGELOG.md
+8 −4 pyproject.toml
+41 −87 src/ehrdata/dt/_dataloader.py
+6 −33 src/ehrdata/dt/datasets.py
+5 −0 tests/dt/test_dt.py
+3 −0 tests/io/test_omop.py
4 changes: 3 additions & 1 deletion tests/conftest.py
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Original file line number Diff line number Diff line change
Expand Up @@ -486,7 +486,9 @@ def check_same_image(
fig: Figure | hv.core.overlay.Overlay | hv.element.chart.Scatter | hv.Element,
base_path: Path | os.PathLike,
*,
tol: float,
# default mirrors scanpy's most common image-comparison tolerance (RMS on a
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# 0-255 scale); individual tests bump this where rendering legitimately differs more.
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tol: float = 15,
) -> None:
expected = Path(base_path).parent / (Path(base_path).name + "_expected.png")
if not Path(expected).is_file():
Expand Down
8 changes: 4 additions & 4 deletions tests/plot/test_missingno_pl_api.py
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Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,7 @@ def test_missing_values_barplot(mimic_2, check_same_image, layer, clean_up_plots
check_same_image(
fig=fig,
base_path=f"{_TEST_IMAGE_PATH}/missing_values_barplot",
tol=5,
tol=25,
)


Expand All @@ -43,7 +43,7 @@ def test_missing_values_matrixplot(mimic_2, check_same_image, layer, clean_up_pl
check_same_image(
fig=fig,
base_path=f"{_TEST_IMAGE_PATH}/missing_values_matrix",
tol=2e-1,
tol=25,
)


Expand All @@ -63,7 +63,7 @@ def test_missing_values_heatmap(mimic_2, check_same_image, layer, clean_up_plots
check_same_image(
fig=fig,
base_path=f"{_TEST_IMAGE_PATH}/missing_values_heatmap",
tol=2e-1,
tol=25,
)


Expand All @@ -83,7 +83,7 @@ def test_missing_values_dendogram(mimic_2, check_same_image, layer):
check_same_image(
fig=fig,
base_path=f"{_TEST_IMAGE_PATH}/missing_values_dendogram",
tol=2e-1,
tol=25,
)


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4 changes: 2 additions & 2 deletions tests/plot/test_ncp.py
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Original file line number Diff line number Diff line change
Expand Up @@ -76,7 +76,7 @@ def test_pl_ncp_image(edata_with_ncp: ed.EHRData, check_same_image, hv_backend)
check_same_image(
fig=fig,
base_path=f"{_TEST_IMAGE_PATH}/ncp",
tol=2e-1,
tol=30,
)


Expand Down Expand Up @@ -152,5 +152,5 @@ def test_pl_ncp_cluster_trajectories_image(edata_with_ncp: ed.EHRData, check_sam
check_same_image(
fig=fig,
base_path=f"{_TEST_IMAGE_PATH}/ncp_cluster_trajectories",
tol=2e-1,
tol=35,
)
2 changes: 0 additions & 2 deletions tests/plot/test_sankey.py
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Original file line number Diff line number Diff line change
Expand Up @@ -21,7 +21,6 @@ def test_sankey_plot(diabetes_130_fairlearn_sample_100, check_same_image, hv_bac
check_same_image(
fig=fig,
base_path=f"{_TEST_IMAGE_PATH}/sankey",
tol=2e-1,
)


Expand All @@ -41,7 +40,6 @@ def test_sankey_time_plot(check_same_image, hv_backend):
check_same_image(
fig=fig,
base_path=f"{_TEST_IMAGE_PATH}/sankey_time",
tol=2e-1,
)


Expand Down
30 changes: 11 additions & 19 deletions tests/plot/test_scanpy_pl_api.py
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Original file line number Diff line number Diff line change
Expand Up @@ -26,7 +26,6 @@ def test_scatter_plot(mimic_2, check_same_image):
check_same_image(
fig=fig,
base_path=f"{_TEST_IMAGE_PATH}/scatter_scanpy_plt",
tol=2e-1,
)
plt.close("all")

Expand All @@ -51,7 +50,7 @@ def test_heatmap_plot(edata_mini, check_same_image):
check_same_image(
fig=fig,
base_path=f"{_TEST_IMAGE_PATH}/heatmap_scanpy_plt",
tol=2e-1,
tol=25,
)
plt.close("all")

Expand Down Expand Up @@ -149,7 +148,7 @@ def test_dotplot_plot_image(mimic_2, check_same_image):
check_same_image(
fig=fig,
base_path=f"{_TEST_IMAGE_PATH}/dotplot_scanpy_plt",
tol=2e-1,
tol=25,
)
plt.close("all")

Expand Down Expand Up @@ -181,7 +180,7 @@ def test_tracks_plot(mimic_2, check_same_image):
check_same_image(
fig=fig,
base_path=f"{_TEST_IMAGE_PATH}/tracksplot_scanpy_plt",
tol=2e-1,
tol=25,
)
plt.close("all")

Expand All @@ -206,7 +205,6 @@ def test_violin_plot(mimic_2, check_same_image):
check_same_image(
fig=fig,
base_path=f"{_TEST_IMAGE_PATH}/violin_scanpy_plt",
tol=2e-1,
)
plt.close("all")

Expand Down Expand Up @@ -255,7 +253,7 @@ def test_matrix_plot(mimic_2, check_same_image):
check_same_image(
fig=fig,
base_path=f"{_TEST_IMAGE_PATH}/matrix_scanpy_plot",
tol=2e-1,
tol=25,
)
plt.close("all")

Expand Down Expand Up @@ -287,7 +285,7 @@ def test_stacked_violin_plot(mimic_2, check_same_image):
check_same_image(
fig=fig,
base_path=f"{_TEST_IMAGE_PATH}/stacked_violin_scanpy_plt",
tol=2e-1,
tol=25,
)
plt.close("all")

Expand All @@ -313,7 +311,6 @@ def test_clustermap(mimic_2_encoded, check_same_image):
check_same_image(
fig=fig,
base_path=f"{_TEST_IMAGE_PATH}/clustermap_scanpy",
tol=2e-1,
)
plt.close("all")

Expand Down Expand Up @@ -424,7 +421,7 @@ def test_rank_features_groups_heatmap(mimic_2_encoded, check_same_image):
check_same_image(
fig=fig,
base_path=f"{_TEST_IMAGE_PATH}/rank_features_groups_heatmap_scanpy",
tol=2e-1,
tol=25,
)
plt.close("all")

Expand Down Expand Up @@ -482,7 +479,7 @@ def test_rank_features_groups_dotplot_image(mimic_2_encoded, check_same_image):
check_same_image(
fig=fig,
base_path=f"{_TEST_IMAGE_PATH}/rank_features_groups_dotplot_scanpy",
tol=2e-1,
tol=25,
)
plt.close("all")

Expand All @@ -505,7 +502,6 @@ def test_pca(mimic_2_sample_serv_unit_day_icu, check_same_image):
check_same_image(
fig=fig,
base_path=f"{_TEST_IMAGE_PATH}/pca",
tol=2e-1,
)
plt.close("all")

Expand All @@ -527,7 +523,7 @@ def test_pca_loadings(mimic_2_sample_serv_unit_day_icu, check_same_image):
check_same_image(
fig=fig,
base_path=f"{_TEST_IMAGE_PATH}/pca_loadings",
tol=2e-1,
tol=40,
)

plt.close("all")
Expand All @@ -550,7 +546,7 @@ def test_pca_variance_ration(mimic_2_sample_serv_unit_day_icu, check_same_image)
check_same_image(
fig=fig,
base_path=f"{_TEST_IMAGE_PATH}/pca_variance_ratio",
tol=2e-1,
tol=25,
)

plt.close("all")
Expand All @@ -575,11 +571,7 @@ def test_pca_overview(mimic_2_sample_serv_unit_day_icu, check_same_image, clean_
fig.set_size_inches(8, 6)
fig.subplots_adjust(left=0.2, right=0.8, bottom=0.2, top=0.8)

check_same_image(
fig=fig,
base_path=f"{_TEST_IMAGE_PATH}/pca_overview_{id}",
tol=2e-1,
)
check_same_image(fig=fig, base_path=f"{_TEST_IMAGE_PATH}/pca_overview_{id}", tol=40)


def test_umap_functionality(mimic_2_sample_serv_unit_day_icu):
Expand Down Expand Up @@ -671,5 +663,5 @@ def test_dpt_timeseries(mimic_2_encoded, check_same_image):
check_same_image(
fig=fig,
base_path=f"{_TEST_IMAGE_PATH}/dpt_timeseries",
tol=2e-1,
tol=35,
)
11 changes: 5 additions & 6 deletions tests/tools/cohort_tracking/test_cohort_tracking.py
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Original file line number Diff line number Diff line change
Expand Up @@ -91,7 +91,7 @@ def test_CohortTracker_plot_cohort_barplot_vanilla(edata_mini, check_same_image)
check_same_image(
fig=fig1,
base_path=f"{_TEST_IMAGE_PATH}/cohorttracker_edata_mini_step1_vanilla",
tol=1e-1,
tol=35,
)

ct(edata_mini, label="Second step", operations_done="Some other operations")
Expand All @@ -100,7 +100,7 @@ def test_CohortTracker_plot_cohort_barplot_vanilla(edata_mini, check_same_image)
check_same_image(
fig=fig2,
base_path=f"{_TEST_IMAGE_PATH}/cohorttracker_edata_mini_step2_vanilla",
tol=1e-1,
tol=35,
)


Expand All @@ -117,7 +117,7 @@ def test_CohortTracker_plot_cohort_barplot_use_settings(edata_mini, check_same_i
check_same_image(
fig=fig,
base_path=f"{_TEST_IMAGE_PATH}/cohorttracker_edata_mini_step1_use_settings",
tol=1e-1,
tol=35,
)


Expand All @@ -136,7 +136,7 @@ def test_CohortTracker_plot_cohort_barplot_use_settings_big(edata_mini, check_sa
check_same_image(
fig=fig,
base_path=f"{_TEST_IMAGE_PATH}/cohorttracker_edata_mini_step1_use_settings_big",
tol=1e-1,
tol=35,
)


Expand All @@ -154,7 +154,7 @@ def test_CohortTracker_plot_cohort_barplot_loosing_category(edata_mini, check_sa
check_same_image(
fig=fig,
base_path=f"{_TEST_IMAGE_PATH}/cohorttracker_edata_mini_step2_loose_category",
tol=1e-1,
tol=35,
)


Expand Down Expand Up @@ -234,7 +234,6 @@ def test_CohortTracker_flowchart_image(edata_mini, check_same_image):
check_same_image(
fig=plot,
base_path=f"{_TEST_IMAGE_PATH}/cohorttracker_edata_mini_flowchart",
tol=1e-1,
)


Expand Down
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