Backport PR scverse#2734 on branch 1.9.x (Make _validate_palette work…

… with arrays) (scverse#2735)

Co-authored-by: Philipp A <flying-sheep@web.de>

docs/release-notes/1.9.7.md

@@ -2,3 +2,4 @@
 
 ```{rubric} Bug fixes
 ```
+- Fix handling of numpy array palettes (e.g. after write-read cycle) {pr}`2734` {smaller}`P Angerer`

scanpy/plotting/_utils.py

@@ -326,7 +326,7 @@ def default_palette(
         return palette
 
 
-def _validate_palette(adata, key):
+def _validate_palette(adata: anndata.AnnData, key: str) -> None:
     """
     checks if the list of colors in adata.uns[f'{key}_colors'] is valid
     and updates the color list in adata.uns[f'{key}_colors'] if needed.
@@ -354,8 +354,9 @@ def _validate_palette(adata, key):
                 break
         _palette.append(color)
     # Don't modify if nothing changed
-    if _palette is not None and list(_palette) != list(adata.uns[color_key]):
-        adata.uns[color_key] = _palette
+    if _palette is None or np.equal(_palette, adata.uns[color_key]).all():
+        return
+    adata.uns[color_key] = _palette
 
 
 def _set_colors_for_categorical_obs(

scanpy/tests/test_plotting_utils.py

@@ -0,0 +1,28 @@
+from typing import cast
+import numpy as np
+import pytest
+
+from anndata import AnnData
+from matplotlib import colormaps
+from matplotlib.colors import ListedColormap
+
+from scanpy.plotting._utils import _validate_palette
+
+
+viridis = cast(ListedColormap, colormaps["viridis"])
+
+
+@pytest.mark.parametrize(
+    "palette",
+    [
+        pytest.param(viridis.colors, id="viridis"),
+        pytest.param(["b", "#cccccc", "r", "yellow", "lightblue"], id="named"),
+        pytest.param([(1, 0, 0, 1), (0, 0, 1, 1)], id="rgba"),
+    ],
+)
+@pytest.mark.parametrize("typ", [np.asarray, list])
+def test_validate_palette_no_mod(palette, typ):
+    palette = typ(palette)
+    adata = AnnData(uns=dict(test_colors=palette))
+    _validate_palette(adata, "test")
+    assert palette is adata.uns["test_colors"], "Palette should not be modified"