Upload scrublet scores on test failure

.azure-pipelines.yml

@@ -103,6 +103,12 @@ jobs:
       testResultsFormat: NUnit
       testRunTitle: 'Publish test results for $(Agent.JobName)'
 
+  - task: PublishBuildArtifacts@1
+    inputs:
+      pathToPublish: '.pytest_cache/d/debug'
+      artifactName: debug-data
+    condition: eq(variables['TEST_TYPE'], 'coverage')
+
   - script: bash <(curl -s https://codecov.io/bash)
     displayName: 'Upload to codecov.io'
     condition: eq(variables['TEST_TYPE'], 'coverage')

src/testing/scanpy/_pytest/__init__.py

@@ -34,6 +34,8 @@ def _global_test_context(
     sc.settings.logfile = sys.stderr
     sc.settings.verbosity = "hint"
     sc.settings.autoshow = True
+    # create directory for debug data
+    cache.mkdir("debug")
     # reuse data files between test runs (unless overwritten in the test)
     sc.settings.datasetdir = cache.mkdir("scanpy-data")
     # create new writedir for each test run

tests/test_scrublet.py

@@ -117,7 +117,7 @@ def _create_sim_from_parents(adata: AnnData, parents: np.ndarray) -> AnnData:
     )
 
 
-def test_scrublet_data():
+def test_scrublet_data(cache: pytest.Cache):
     """
     Test that Scrublet processing is arranged correctly.
 
@@ -156,14 +156,32 @@ def test_scrublet_data():
         random_state=random_state,
     )
 
-    # Require that the doublet scores are the same whether simulation is via
-    # the main function or manually provided
-    assert_allclose(
-        adata_scrublet_manual_sim.obs["doublet_score"],
-        adata_scrublet_auto_sim.obs["doublet_score"],
-        atol=1e-15,
-        rtol=1e-15,
-    )
+    try:
+        # Require that the doublet scores are the same whether simulation is via
+        # the main function or manually provided
+        assert_allclose(
+            adata_scrublet_manual_sim.obs["doublet_score"],
+            adata_scrublet_auto_sim.obs["doublet_score"],
+            atol=1e-15,
+            rtol=1e-15,
+        )
+    except AssertionError:
+        import zarr
+
+        # try debugging https://github.com/scverse/scanpy/issues/3068
+        cache_path = cache.mkdir("debug")
+        store_manual = zarr.ZipStore(cache_path / "scrublet-manual.zip", mode="w")
+        store_auto = zarr.ZipStore(cache_path / "scrublet-auto.zip", mode="w")
+        z_manual = zarr.zeros(
+            adata_scrublet_manual_sim.shape[0], chunks=10, store=store_manual
+        )
+        z_auto = zarr.zeros(
+            adata_scrublet_auto_sim.shape[0], chunks=10, store=store_auto
+        )
+        z_manual[...] = adata_scrublet_manual_sim.obs["doublet_score"].values
+        z_auto[...] = adata_scrublet_auto_sim.obs["doublet_score"].values
+
+        raise
 
 
 @pytest.fixture(scope="module")