fix: add contextmanager preventing settings leakage between tests

fix: pass raster_write_kwargs recursively when writing list of elements

Author: melonora

src/spatialdata/_core/spatialdata.py

@@ -1359,6 +1359,7 @@ def write_element(
                     overwrite=overwrite,
                     sdata_formats=sdata_formats,
                     shapes_geometry_encoding=shapes_geometry_encoding,
+                    raster_write_kwargs=raster_write_kwargs,
                 )
             return
 

tests/conftest.py

@@ -1,6 +1,8 @@
 from __future__ import annotations
 
 from collections.abc import Sequence
+from contextlib import contextmanager
+from dataclasses import replace
 from pathlib import Path
 from typing import Any
 
@@ -19,6 +21,7 @@
 from skimage import data
 from xarray import DataArray, DataTree
 
+from spatialdata import settings
 from spatialdata._core._deepcopy import deepcopy
 from spatialdata._core.spatialdata import SpatialData
 from spatialdata._types import ArrayLike
@@ -653,3 +656,16 @@ def settings_cls(tmp_path, monkeypatch):
 
     monkeypatch.setattr("spatialdata.config._config_path", lambda: tmp_path / "default_settings.json")
     return Settings
+
+
+@contextmanager
+def temporary_settings(**kwargs):
+    old = replace(settings)
+    try:
+        for k, v in kwargs.items():
+            setattr(settings, k, v)
+        settings.save()
+        yield
+    finally:
+        settings.__dict__.update(old.__dict__)
+        settings.save()

tests/io/test_readwrite.py

@@ -49,6 +49,7 @@
     _get_shapes,
     _get_table,
     _get_tables,
+    temporary_settings,
 )
 
 RNG = default_rng(0)
@@ -806,28 +807,17 @@ def test_write_raster_sharding(
 
 
 def test_write_raster_sharding_with_settings(tmp_path: Path) -> None:
-    from dataclasses import replace
+    with temporary_settings(raster_chunks=(1, 100, 100)):
+        data = da.from_array(RNG.random((1, 1000, 1000)), chunks=(1, 200, 200))
+        element = Image2DModel.parse(data, dims=("c", "y", "x"))
+        name = "element"
+        sdata = SpatialData(images={name: element})
+        path = tmp_path / "data.zarr"
 
-    from spatialdata import settings
-
-    old_settings = replace(settings)
-    settings.raster_chunks = (1, 100, 100)
-    settings.save()
-
-    data = da.from_array(RNG.random((1, 1000, 1000)), chunks=(1, 200, 200))
-    element = Image2DModel.parse(data, dims=("c", "y", "x"))
-    name = "element"
-    sdata = SpatialData(images={name: element})
-    path = tmp_path / "data.zarr"
+        sdata.write(path)
 
-    sdata.write(
-        path,
-    )
-    arr = zarr.open_group(path / "images" / name, mode="r")["s0"]
-    assert arr.chunks == (1, 100, 100)
-    old_settings.save()
-    s = settings.load()
-    assert s.raster_chunks == old_settings.raster_chunks
+        arr = zarr.open_group(path / "images" / name, mode="r")["s0"]
+        assert arr.chunks == (1, 100, 100)
 
 
 @pytest.mark.parametrize("raster_case", RASTER_CASES_MULTISCALE)