fix AttributeError: 'AnnData' object has no attribute '_get_X'

.github/workflows/benchmarks.yml

@@ -66,7 +66,7 @@ jobs:
       - uses: actions/setup-python@v6
         name: Install Python
         with:
-          python-version: "3.11"
+          python-version: "3.12"
           cache-dependency-path: pyproject.toml
 
       - uses: tlambert03/setup-qt-libs@v1
@@ -140,7 +140,7 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           PLATFORM: ${{ matrix.runs-on }}
-          PYTHON: "3.11"
+          PYTHON: "3.12"
           BACKEND: ${{ matrix.benchmark-name }}
           RUN_ID: ${{ github.run_id }}
           TITLE: "[test-bot] Benchmark tests failing"

.github/workflows/test.yml

@@ -24,7 +24,7 @@ jobs:
       fail-fast: false
       matrix:
         platform: [ubuntu-latest, macos-latest] # [ubuntu-latest, windows-latest, macos-latest]
-        python-version: ["3.11", "3.13"]
+        python-version: ["3.12", "3.13", "3.14"]
 
     steps:
       - uses: actions/checkout@v6

.readthedocs.yaml

@@ -3,7 +3,7 @@ version: 2
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.11"
+    python: "3.12"
 sphinx:
   configuration: docs/conf.py
   fail_on_warning: false

asv.conf.json

@@ -35,7 +35,7 @@
   "show_commit_url": "http://github.com/napari/napari/commit/",
 
   // The Pythons you'd like to test against.
-  "pythons": ["3.11"],
+  "pythons": ["3.12"],
 
   // The directory (relative to the current directory) to cache the Python
   // environments in.

setup.cfg

@@ -20,17 +20,17 @@ classifiers =
     Topic :: Software Development :: Testing
     Programming Language :: Python
     Programming Language :: Python :: 3
-    Programming Language :: Python :: 3.11
     Programming Language :: Python :: 3.12
     Programming Language :: Python :: 3.13
+    Programming Language :: Python :: 3.14
     Operating System :: OS Independent
     License :: OSI Approved :: BSD License
 
 
 [options]
 packages = find:
 include_package_data = True
-python_requires = >=3.11
+python_requires = >=3.12
 setup_requires = setuptools_scm
 # add your package requirements here
 install_requires =

src/napari_spatialdata/_model.py

@@ -136,7 +136,8 @@ def get_var(
         except KeyError:
             raise KeyError(f"Key `{name}` not found in `adata.var_names`.") from None
 
-        column = self.adata._get_X(layer=self.adata_layer)[ix]
+        X = self.adata.X if self.adata_layer is None else self.adata.layers[self.adata_layer]
+        column = X[ix]
         index = self.adata.obs[[self.instance_key]].set_index(self.instance_key).index
         return column, self._format_key(name, adata_layer=True), index
 

tests/conftest.py

@@ -219,7 +219,6 @@ def adata_shapes() -> AnnData:
     obsm_shapes = {"spatial": rng.integers(0, blobs.shape[0], size=(n_obs_shapes, 2))}
     return AnnData(
         rng.normal(size=(n_obs_shapes, n_var)),
-        dtype=np.float64,
         obs=obs_shapes,
         obsm=obsm_shapes,
         uns=uns_shapes,
@@ -295,7 +294,6 @@ def generate_adata(n_var: int, obs: pd.DataFrame, obsm: dict[Any, Any], uns: dic
         obs=obs,
         obsm=obsm,
         uns=uns,
-        dtype=np.float64,
     )
 
 

tox.ini

@@ -1,11 +1,12 @@
 [tox]
-envlist = py{310,312}-{linux,macos,windows}
+envlist = py{312,313,314}-{linux,macos,windows}
 isolated_build=true
 
 [gh-actions]
 python =
-    3.10: py310
     3.12: py312
+    3.13: py313
+    3.14: py314
 
 [gh-actions:env]
 PLATFORM =