[pre-commit.ci] pre-commit autoupdate (scverse#450)

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

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.1.14 → v0.2.1](astral-sh/ruff-pre-commit@v0.1.14...v0.2.1)

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* fixed pre-commit

---------

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

.pre-commit-config.yaml

@@ -27,7 +27,7 @@ repos:
             additional_dependencies: [numpy, types-requests]
             exclude: tests/|docs/
     - repo: https://github.com/astral-sh/ruff-pre-commit
-      rev: v0.1.14
+      rev: v0.2.1
       hooks:
           - id: ruff
             args: [--fix, --exit-non-zero-on-fix]

pyproject.toml

@@ -136,6 +136,10 @@ exclude = [
     "dist",
     "setup.py",
 ]
+line-length = 120
+target-version = "py39"
+
+[tool.ruff.lint]
 ignore = [
     # Do not assign a lambda expression, use a def -> lambda expression assignments are convenient
     "E731",
@@ -154,7 +158,6 @@ ignore = [
     # Missing docstring in magic method
     "D105",
 ]
-line-length = 120
 select = [
     "D", # flake8-docstrings
     "I", # isort
@@ -175,7 +178,10 @@ select = [
     "PGH", # pygrep-hooks
 ]
 unfixable = ["B", "C4", "UP", "BLE", "T20", "RET"]
-target-version = "py39"
+
+[tool.ruff.lint.pydocstyle]
+convention = "numpy"
+
 [tool.ruff.per-file-ignores]
     "tests/*" = ["D", "PT", "B024"]
     "*/__init__.py" = ["F401", "D104", "D107", "E402"]
@@ -188,8 +194,7 @@ target-version = "py39"
     "src/spatialdata/dataloader/datasets.py" = ["D101"]
     "tests/test_models/test_models.py" = ["NPY002"]
     "tests/conftest.py"= ["E402"]
-[tool.ruff.pydocstyle]
-convention = "numpy"
+
 
 # pyupgrade typing rewrite TODO: remove at some point from per-file ignore
 # "UP006", "UP007"

src/spatialdata/_types.py

@@ -11,7 +11,7 @@
 try:
     from numpy.typing import DTypeLike, NDArray
 
-    ArrayLike = NDArray[np.float_]
+    ArrayLike = NDArray[np.float64]
 except (ImportError, TypeError):
     ArrayLike = np.ndarray  # type: ignore[misc]
     DTypeLike = np.dtype  # type: ignore[misc]

src/spatialdata/transformations/_utils.py

@@ -110,9 +110,8 @@ def _(e: MultiscaleSpatialImage, transformations: MappingToCoordinateSystem_t) -
     dims = get_axes_names(e)
     from spatialdata.transformations.transformations import Scale, Sequence
 
-    i = 0
     old_shape: Optional[ArrayLike] = None
-    for scale, node in dict(e).items():
+    for i, (scale, node) in enumerate(dict(e).items()):
         # this is to be sure that the pyramid levels are listed here in the correct order
         assert scale == f"scale{i}"
         assert len(dict(node)) == 1
@@ -135,7 +134,6 @@ def _(e: MultiscaleSpatialImage, transformations: MappingToCoordinateSystem_t) -
         else:
             _set_transformations_xarray(xdata, transformations)
             old_shape = new_shape
-        i += 1
 
 
 @_set_transformations.register(GeoDataFrame)
@@ -195,7 +193,7 @@ def _get_scale(transforms: dict[str, Any]) -> Scale:
 @compute_coordinates.register(SpatialImage)
 def _(data: SpatialImage) -> SpatialImage:
     coords: dict[str, ArrayLike] = {
-        d: np.arange(data.sizes[d], dtype=np.float_) + 0.5 for d in data.sizes if d in ["x", "y", "z"]
+        d: np.arange(data.sizes[d], dtype=np.float64) + 0.5 for d in data.sizes if d in ["x", "y", "z"]
     }
     return data.assign_coords(coords)