fix: scalar setting/reshape on CoW .X

.github/workflows/test-gpu.yml

@@ -53,8 +53,9 @@ jobs:
         run: nvidia-smi
 
       - name: Install yq # https://cirun.slack.com/archives/C09SNDRB3A8/p1766512487317849?thread_ts=1766512112.938459&cid=C09SNDRB3A8
+        # https://github.com/mikefarah/yq/issues/2592 forces version pin
         run: |
-          sudo wget -qO /usr/local/bin/yq https://github.com/mikefarah/yq/releases/latest/download/yq_linux_amd64
+          sudo wget -qO /usr/local/bin/yq http://github.com/mikefarah/yq/releases/download/v4.49.2/yq_linux_amd64
           sudo chmod +x /usr/local/bin/yq
 
       - name: Extract max Python version from classifiers

src/anndata/_core/anndata.py

@@ -600,6 +600,14 @@ def X(self) -> XDataType | None:
     def _handle_view_X_cow(self, value: XDataType | None):
         if self._is_view:
             if settings.copy_on_write_X:
+                if np.isscalar(value) and value is not None:
+                    msg = "The ability to set X with a scalar value will be removed in the future.  Initializing as an `np.array` with the shape of the current view."
+                    warnings.warn(msg, FutureWarning, stacklevel=2)
+                    value = np.full(self.shape, fill_value=value)
+                if hasattr(value, "shape") and value.shape != self.shape:
+                    msg = "Automatic reshaping when setting X will be removed in the future."
+                    warnings.warn(msg, FutureWarning, stacklevel=2)
+                    value = value.reshape(self.shape)
                 msg = "Setting element `.X` of view, initializing view as actual."
                 warnings.warn(msg, ImplicitModificationWarning, stacklevel=2)
                 new = self._mutated_copy(X=value)

tests/test_views.py

@@ -1,6 +1,6 @@
 from __future__ import annotations
 
-from contextlib import nullcontext
+from contextlib import ExitStack, nullcontext
 from copy import deepcopy
 from functools import partial
 from importlib.metadata import version
@@ -24,6 +24,7 @@
     SparseCSRArrayView,
     SparseCSRMatrixView,
 )
+from anndata._warnings import ImplicitModificationWarning
 from anndata.compat import NUMPY_2, CSArray, CupyCSCMatrix, DaskArray
 from anndata.tests.helpers import (
     BASE_MATRIX_PARAMS,
@@ -119,21 +120,43 @@ def mapping_name(request):
     return request.param
 
 
+@pytest.fixture(params=[True, False], ids=["CoW", "update"])
+def copy_on_write_X(request):
+    return request.param
+
+
 # ------------------------------------------------------------------------------
 # The test functions
 # ------------------------------------------------------------------------------
 
 
-def test_views():
+def test_views(*, copy_on_write_X: bool):
+    ad.settings.copy_on_write_X = copy_on_write_X
     X = np.array(X_list, dtype="int32")
     adata = ad.AnnData(X, obs=obs_dict, var=var_dict, uns=uns_dict)
 
     assert adata[:, 0].is_view
     assert adata[:, 0].X.tolist() == np.reshape([1, 4, 7], (3, 1)).tolist()
 
-    adata[:2, 0].X = [0, 0]
-
-    assert adata[:, 0].X.tolist() == np.reshape([0, 0, 7], (3, 1)).tolist()
+    ctx_managers = (
+        (
+            pytest.warns(
+                ImplicitModificationWarning, match=r"initializing view as actual"
+            ),
+            pytest.warns(FutureWarning, match=r"Automatic reshaping"),
+        )
+        if copy_on_write_X
+        else ()
+    )
+    with ExitStack() as stack:
+        for mgr in ctx_managers:
+            stack.enter_context(mgr)
+        adata[:2, 0].X = [0, 0]
+
+    assert (
+        adata[:, 0].X.tolist()
+        == np.reshape([1, 4, 7] if copy_on_write_X else [0, 0, 7], (3, 1)).tolist()
+    )
 
     adata_subset = adata[:2, [0, 1]]
 
@@ -385,18 +408,37 @@ def test_not_set_subset_X_dask(matrix_type_no_gpu, subset_func):
 
 
 @IGNORE_SPARSE_EFFICIENCY_WARNING
-def test_set_scalar_subset_X(matrix_type, subset_func):
+def test_set_scalar_subset_X(matrix_type, subset_func, *, copy_on_write_X: bool):
+    ad.settings.copy_on_write_X = copy_on_write_X
     adata = ad.AnnData(matrix_type(np.zeros((10, 10))))
     orig_X_val = adata.X.copy()
     subset_idx = subset_func(adata.obs_names)
 
     adata_subset = adata[subset_idx, :]
-
-    adata_subset.X = 1
-
-    assert adata_subset.is_view
-    assert np.all(asarray(adata[subset_idx, :].X) == 1)
-    if isinstance(adata.X, CupyCSCMatrix):
+    ctx_managers = (
+        (
+            pytest.warns(
+                ImplicitModificationWarning, match=r"initializing view as actual"
+            ),
+            pytest.warns(
+                FutureWarning, match=r"The ability to set X with a scalar value"
+            ),
+        )
+        if copy_on_write_X
+        else ()
+    )
+    with ExitStack() as stack:
+        for mgr in ctx_managers:
+            stack.enter_context(mgr)
+        adata_subset.X = 1
+
+    assert adata_subset.is_view != copy_on_write_X
+    assert np.all(
+        asarray((adata_subset if copy_on_write_X else adata[subset_idx, :]).X) == 1
+    )
+    if copy_on_write_X:
+        assert (asarray(orig_X_val) == asarray(adata.X)).all()
+    elif isinstance(adata.X, CupyCSCMatrix):
         # Comparison broken for CSC matrices
         # https://github.com/cupy/cupy/issues/7757
         assert asarray(orig_X_val.tocsr() != adata.X.tocsr()).sum() == mul(