[pre-commit.ci] pre-commit autoupdate (#884)

* [pre-commit.ci] pre-commit autoupdate

updates:
- [github.com/rbubley/mirrors-prettier: v3.5.1 → v3.5.3](rbubley/mirrors-prettier@v3.5.1...v3.5.3)
- [github.com/astral-sh/ruff-pre-commit: v0.9.6 → v0.11.5](astral-sh/ruff-pre-commit@v0.9.6...v0.11.5)

* fix precommit

* add lower bound xarray-dataclasses

* fix typo

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Luca Marconato <m.lucalmer@gmail.com>

Author: pre-commit-ci[bot]

.pre-commit-config.yaml

@@ -9,7 +9,7 @@ ci:
     skip: []
 repos:
     - repo: https://github.com/rbubley/mirrors-prettier
-      rev: v3.5.1
+      rev: v3.5.3
       hooks:
           - id: prettier
     - repo: https://github.com/pre-commit/mirrors-mypy
@@ -19,7 +19,7 @@ repos:
             additional_dependencies: [numpy, types-requests]
             exclude: tests/|docs/
     - repo: https://github.com/astral-sh/ruff-pre-commit
-      rev: v0.9.6
+      rev: v0.11.5
       hooks:
           - id: ruff
             args: [--fix, --exit-non-zero-on-fix]

pyproject.toml

@@ -46,6 +46,7 @@ dependencies = [
     "xarray>=2024.10.0",
     "xarray-schema",
     "xarray-spatial>=0.3.5",
+	"xarray-dataclasses>=1.8.0",
     "zarr<3",
 ]
 

src/spatialdata/_core/query/_utils.py

@@ -142,7 +142,7 @@ def _process_data_tree_query_result(query_result: DataTree) -> DataTree | None:
 
     # rechunk the data to avoid irregular chunks
     coords = list(result["scale0"].coords.keys())
-    result = result.chunk({c: "auto" for c in coords})
+    result = result.chunk(dict.fromkeys(coords, "auto"))
 
     from dask.array.core import _check_regular_chunks
 
@@ -156,7 +156,7 @@ def _process_data_tree_query_result(query_result: DataTree) -> DataTree | None:
         # reported here: https://github.com/scverse/spatialdata/issues/821#issuecomment-2632201695
         # seemingly due to this bug: https://github.com/dask/dask/issues/11713
         CHUNK_SIZE = 1024
-        rechunk_strategy = {c: CHUNK_SIZE for c in coords}
+        rechunk_strategy = dict.fromkeys(coords, CHUNK_SIZE)
         if "c" in coords:
             rechunk_strategy["c"] = result["scale0"]["image"].chunks[0][0]
         result = result.chunk(rechunk_strategy)

tests/models/test_models.py

@@ -446,7 +446,7 @@ def test_model_invalid_names(self, full_sdata, element_type: str, name: str):
     def test_model_not_unique_names(self, full_sdata, element_type: str, names: list[str]):
         element = next(iter(getattr(full_sdata, element_type).values()))
         with pytest.raises(ValidationError, match="Key `.*` is not unique"):
-            SpatialData(**{element_type: {name: element for name in names}})
+            SpatialData(**{element_type: dict.fromkeys(names, element)})
 
     @pytest.mark.parametrize("model", [TableModel])
     @pytest.mark.parametrize("region", [["sample_1"] * 5 + ["sample_2"] * 5])