[lint] Switch from black to ruff and update line-length

.pre-commit-config.yaml

@@ -16,7 +16,8 @@ repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
     rev: v0.11.10
     hooks:
-      - id: ruff
+      - id: ruff-check
+      - id: ruff-format
 
   - repo: https://github.com/pre-commit/mirrors-mypy
     # This mypy step is not perfect; in the interest of not reproducing
@@ -28,11 +29,6 @@ repos:
       - id: mypy
         additional_dependencies: [attrs]
 
-  - repo: https://github.com/psf/black
-    rev: "25.1.0"
-    hooks:
-      - id: black
-
   - repo: https://github.com/hukkin/mdformat
     rev: 0.7.22  # Use the ref you want to point at
     hooks:

pyproject.toml

@@ -45,6 +45,8 @@ tag_regex = '^python-(?P<version>[vV]?\d+(?:\.\d+){0,2}[^\+]*)(?:\+.*)?$'
 lint.extend-select = ["I"]
 target-version = "py39"
 fix = true
+preview = true  # enables "beta" rules: https://docs.astral.sh/ruff/preview/
+line-length = 120
 
 [tool.ruff.lint.isort]
 force-single-line = true

python-spec/requirements-py3.12-lint.txt

@@ -1,7 +1,6 @@
 anndata==0.11.3
 array_api_compat==1.11.1
 attrs==25.1.0
-black==25.1.0
 cfgv==3.4.0
 click==8.1.8
 distlib==0.3.9

python-spec/src/somacore/__init__.py

@@ -67,7 +67,6 @@
     "GeometryDataFrame",
     "PointCloudDataFrame",
     "BatchSize",
-    "IOfN",
     "ResultOrder",
     "AxisColumnNames",
     "AxisQuery",

python-spec/src/somacore/collection.py

@@ -219,9 +219,7 @@ def __setitem__(self, key: str, value: _Elem) -> None:
         """Sets an entry into this collection. See :meth:`set` for details."""
         self.set(key, value)
 
-    def set(
-        self, key: str, value: _Elem, *, use_relative_uri: bool | None = None
-    ) -> Self:
+    def set(self, key: str, value: _Elem, *, use_relative_uri: bool | None = None) -> Self:
         """Sets an entry of this collection.
 
         Important note: Because parent objects may need to share

python-spec/src/somacore/data.py

@@ -290,9 +290,7 @@ def create(
         """
         ...
 
-    def resize(
-        self, newshape: Sequence[int | None], check_only: bool = False
-    ) -> StatusAndReason:
+    def resize(self, newshape: Sequence[int | None], check_only: bool = False) -> StatusAndReason:
         """Increases the shape of the array as specified.
 
         Lifecycle: maturing

python-spec/src/somacore/options.py

@@ -60,9 +60,7 @@ class IOfN(ReadPartitions):
     def _validate(self, _, __):
         del _, __  # Unused.
         if not 0 <= self.i < self.n:
-            raise ValueError(
-                f"Partition index {self.i} must be in the range [0, {self.n})"
-            )
+            raise ValueError(f"Partition index {self.i} must be in the range [0, {self.n})")
 
 
 @attrs.define(frozen=True)
@@ -187,7 +185,5 @@ class ResultOrder(enum.Enum):
 SparseNDCoords = Sequence[SparseNDCoord]
 """A sequence of coordinate ranges for reading sparse ndarrays."""
 
-SpatialRegion = Union[
-    Sequence[int], Sequence[float], shapely.geometry.base.BaseGeometry
-]
+SpatialRegion = Union[Sequence[int], Sequence[float], shapely.geometry.base.BaseGeometry]
 """A spatial region used for reading spatial dataframes and multiscale images."""

python-spec/src/somacore/query/axis.py

@@ -22,12 +22,9 @@ def _canonicalize_coords(
         return tuple(_canonicalize_coord(c) for c in in_coords)
     if isinstance(in_coords, (str, bytes)):
         raise TypeError(
-            "Query coordinates must be a normal sequence, not `str` or `bytes`."
-            f" Did you mean {(in_coords,)}?"
+            f"Query coordinates must be a normal sequence, not `str` or `bytes`. Did you mean {(in_coords,)}?"
         )
-    raise TypeError(
-        f"Query coordinates must be a sequence, not a single {type(in_coords)}"
-    )
+    raise TypeError(f"Query coordinates must be a sequence, not a single {type(in_coords)}")
 
 
 def _canonicalize_coord(coord: options.SparseDFCoord) -> options.SparseDFCoord:

python-spec/src/somacore/spatial.py

@@ -663,18 +663,14 @@ def data_axis_order(self) -> tuple[str, ...]:
         """
         ...
 
-    def get_transform_from_level(
-        self, level: int | str
-    ) -> coordinates.CoordinateTransform:
+    def get_transform_from_level(self, level: int | str) -> coordinates.CoordinateTransform:
         """Returns the transformation from user requested level to image reference level.
 
         Lifecycle: experimental
         """
         ...
 
-    def get_transform_to_level(
-        self, level: int | str
-    ) -> coordinates.CoordinateTransform:
+    def get_transform_to_level(self, level: int | str) -> coordinates.CoordinateTransform:
         """Returns the transformation from the image reference level to the user
         requested level.