Revert convenience sc.tl.densmap

docs/api/tools.md

@@ -20,7 +20,6 @@ Any transformation of the data matrix that is not *preprocessing*. In contrast t
    pp.pca
    tl.tsne
    tl.umap
-   tl.densmap
    tl.draw_graph
    tl.diffmap
 ```

docs/release-notes/2946.feature.md

@@ -1 +1 @@
-Add DensMAP support with {func}`~scanpy.tl.densmap` {smaller}`M Keller`
+Add DensMAP support via `method="densmap"` in {func}`~scanpy.tl.umap` {smaller}`M Keller`

src/scanpy/tools/__init__.py

@@ -24,7 +24,7 @@
 from ._score_genes import score_genes, score_genes_cell_cycle
 from ._sim import sim
 from ._tsne import tsne
-from ._umap import densmap, umap
+from ._umap import umap
 
 if TYPE_CHECKING:
     from typing import Any
@@ -58,5 +58,4 @@ def __getattr__(name: str) -> Any:
     "sim",
     "tsne",
     "umap",
-    "densmap",
 ]

src/scanpy/tools/_umap.py

@@ -1,7 +1,6 @@
 from __future__ import annotations
 
 import warnings
-from functools import partial
 from typing import TYPE_CHECKING, Literal
 
 import numpy as np
@@ -346,7 +345,3 @@ def umap(
         ),
     )
     return adata if copy else None
-
-
-# Convenience function for densMAP
-densmap = partial(umap, method="densmap")

tests/test_embedding.py

@@ -93,23 +93,18 @@ def test_diffmap():
 def test_densmap():
     pbmc = pbmc68k_reduced()
 
-    sc.tl.densmap(pbmc)
+    sc.tl.umap(pbmc, method="densmap")
     d1 = pbmc.obsm["X_densmap"].copy()
-    sc.tl.densmap(pbmc)
+    sc.tl.umap(pbmc, method="densmap")
     d2 = pbmc.obsm["X_densmap"].copy()
     assert_array_equal(d1, d2)
 
-    # Should have same result via sc.tl.umap with "densmap" as method
-    sc.tl.umap(pbmc, method="densmap")
-    d3 = pbmc.obsm["X_densmap"].copy()
-    assert_array_equal(d1, d3)
-
     # Checking if specifying random_state  works, arrays shouldn't be equal
-    sc.tl.densmap(pbmc, random_state=1234)
+    sc.tl.umap(pbmc, method="densmap", random_state=1234)
     d4 = pbmc.obsm["X_densmap"].copy()
     assert_raises(AssertionError, assert_array_equal, d1, d4)
 
     # Checking if specifying dens_lambda  works, arrays shouldn't be equal
-    sc.tl.densmap(pbmc, method_kwds=dict(dens_lambda=2.3456))
+    sc.tl.umap(pbmc, method="densmap", method_kwds=dict(dens_lambda=2.3456))
     d5 = pbmc.obsm["X_densmap"].copy()
     assert_raises(AssertionError, assert_array_equal, d1, d5)