fix some warnings

Author: flying-sheep

src/scanpy/tools/_tsne.py

@@ -135,10 +135,10 @@ def tsne(  # noqa: PLR0913
     # Backwards compat handling: Remove in scanpy 1.9.0
     if n_jobs != 1 and not use_fast_tsne:
         warnings.warn(
-            "In previous versions of scanpy, calling tsne with n_jobs > 1 would use "
-            "MulticoreTSNE. Now this uses the scikit-learn version of TSNE by default. "
-            "If you'd like the old behaviour (which is deprecated), pass "
-            "'use_fast_tsne=True'. Note, MulticoreTSNE is not actually faster anymore.",
+            "In previous versions of scanpy, calling tsne with `n_jobs` > 1 would use MulticoreTSNE. "
+            "Now this uses the scikit-learn version of TSNE by default. "
+            "If you’d like the old behaviour (which is deprecated), pass `use_fast_tsne=True`. "
+            "Note, MulticoreTSNE is not actually faster anymore.",
             UserWarning,
             stacklevel=2,
         )
@@ -154,18 +154,18 @@ def tsne(  # noqa: PLR0913
     if use_fast_tsne:
         try:
             from MulticoreTSNE import MulticoreTSNE as TSNE
-
-            tsne = TSNE(**params_sklearn)
-            logg.info("    using the 'MulticoreTSNE' package by Ulyanov (2017)")
-            # need to transform to float64 for MulticoreTSNE...
-            X_tsne = tsne.fit_transform(X.astype("float64"))
         except ImportError:
             use_fast_tsne = False
             warnings.warn(
                 "Could not import 'MulticoreTSNE'. Falling back to scikit-learn.",
-                UserWarning,
+                ImportWarning,
                 stacklevel=2,
             )
+        else:
+            tsne = TSNE(**params_sklearn)
+            logg.info("    using the 'MulticoreTSNE' package by Ulyanov (2017)")
+            # need to transform to float64 for MulticoreTSNE...
+            X_tsne = tsne.fit_transform(X.astype("float64"))
     if use_fast_tsne is False:  # In case MultiCore failed to import
         from sklearn.manifold import TSNE
 

tests/test_clustering.py

@@ -189,7 +189,14 @@ def test_clustering_subset(adata_neighbors, clustering, key):
 @pytest.mark.parametrize(
     ("clustering", "default_key", "default_res", "custom_resolutions"),
     [
-        pytest.param(sc.tl.leiden, "leiden", 0.8, [0.9, 1.1], marks=needs.leidenalg),
+        pytest.param(
+            partial(sc.tl.leiden, flavor="leidenalg"),
+            "leiden",
+            0.8,
+            [0.9, 1.1],
+            marks=needs.leidenalg,
+            id="leiden",
+        ),
     ],
 )
 def test_clustering_custom_key(

tests/test_deprecations.py

@@ -6,18 +6,18 @@
 from testing.scanpy._helpers.data import pbmc68k_reduced
 
 
-def test_deprecate_multicore_tsne():
+def test_deprecate_multicore_tsne() -> None:
     pbmc = pbmc68k_reduced()
 
     with pytest.warns(
-        UserWarning, match="calling tsne with n_jobs > 1 would use MulticoreTSNE"
+        UserWarning, match=r"calling tsne with `n_jobs` > 1 would use MulticoreTSNE"
     ):
         sc.tl.tsne(pbmc, n_jobs=2)
 
-    with pytest.warns(FutureWarning, match="Argument `use_fast_tsne` is deprecated"):
-        sc.tl.tsne(pbmc, use_fast_tsne=True)
-
-    with pytest.warns(UserWarning, match="Falling back to scikit-learn"):
+    with (
+        pytest.warns(FutureWarning, match=r"Argument `use_fast_tsne` is deprecated"),
+        pytest.warns(ImportWarning, match=r"MulticoreTSNE"),
+    ):
         sc.tl.tsne(pbmc, use_fast_tsne=True)
 
 

tests/test_preprocessing.py

@@ -280,9 +280,10 @@ def test_scale_zero_center_warns_dask_sparse(array_type):
     adata.X = adata.raw.X
     adata_casted = adata.copy()
     adata_casted.X = array_type(adata_casted.raw.X)
-    with pytest.warns(UserWarning, match="zero-center.*sparse"):
+    with pytest.warns(UserWarning, match=r"zero-center.*sparse"):
         sc.pp.scale(adata_casted)
-    sc.pp.scale(adata)
+    with pytest.warns(UserWarning, match=r"zero-center.*sparse"):
+        sc.pp.scale(adata)
     assert_allclose(adata_casted.X, adata.X, rtol=1e-5, atol=1e-5)
 
 
@@ -292,7 +293,10 @@ def test_scale():
     v = adata[:, 0 : adata.shape[1] // 2]
     # Should turn view to copy https://github.com/scverse/anndata/issues/171#issuecomment-508689965
     assert v.is_view
-    with pytest.warns(Warning, match="view"):
+    with (
+        pytest.warns(UserWarning, match=r"zero-center.*sparse"),
+        pytest.warns(UserWarning, match=r"Received a view"),
+    ):
         sc.pp.scale(v)
     assert not v.is_view
     assert_allclose(v.X.var(axis=0), np.ones(v.shape[1]), atol=0.01)