Harmonise formatting: ruff 0.7.4, pyright 1.1.411, line length 88

gertils/pathtools.py

@@ -71,7 +71,8 @@ def _invalidate(self) -> None:
 
 @doc(
     summary=(
-        "Directly in given folder, find all filepaths with a field" " of view embedded in filename."
+        "Directly in given folder, find all filepaths with a field"
+        " of view embedded in filename."
     ),
     parameters=dict(
         folder="Path to folder in which to find files",
@@ -83,7 +84,7 @@ def _invalidate(self) -> None:
         get_fov_sort_key="The function used to try to parse FOV from filename",
     ),
 )
-def find_multiple_paths_by_fov(  # noqa: D103
+def find_multiple_paths_by_fov(
     folder: PathLike, *, extensions: Iterable[str]
 ) -> dict[FieldOfViewFrom1, list[Path]]:
     if isinstance(folder, str):
@@ -108,14 +109,18 @@ def find_multiple_paths_by_fov(  # noqa: D103
         folder="Path to folder in which to find files",
         extension="The extension of files to find",
     ),
-    raises=dict(RuntimeError="If the same FOV is found to correspond to more than one path"),
+    raises=dict(
+        RuntimeError="If the same FOV is found to correspond to more than one path"
+    ),
     returns="Mapping from field of view to filepath",
     see_also=dict(
         find_multiple_paths_by_fov="Similar function, for multiple paths by FOV, no particular extension",
         get_fov_sort_key="The function used to try to parse FOV from filename",
     ),
 )
-def find_single_path_by_fov(folder: PathLike, *, extension: str) -> dict[FieldOfViewFrom1, Path]:  # noqa: D103
+def find_single_path_by_fov(
+    folder: PathLike, *, extension: str
+) -> dict[FieldOfViewFrom1, Path]:
     if isinstance(folder, str):
         folder = Path(folder)
     image_paths: dict[FieldOfViewFrom1, Path] = {}
@@ -140,7 +145,7 @@ def find_single_path_by_fov(folder: PathLike, *, extension: str) -> dict[FieldOf
     ),
     returns="Field of view parsed from filename, if parse succeeded; otherwise, None",
 )
-def get_fov_sort_key(path: PathLike, *, extension: str) -> Optional[FieldOfViewFrom1]:  # noqa: D103
+def get_fov_sort_key(path: PathLike, *, extension: str) -> Optional[FieldOfViewFrom1]:
     # Checked at runtime, since callers may pass any type despite the annotation.
     if not isinstance(cast("object", path), str | Path):
         raise TypeError(

gertils/pixel_value_statistics.py

@@ -78,7 +78,9 @@ def from_image(
         # Only the shape is read here, so that a lazy array such as dask's isn't loaded yet.
         shape = np.shape(img)
         if len(shape) != 3:  # noqa: PLR2004
-            raise ValueError(f"To build {cls.__name__}, image must be 3D, not {len(shape)}D")
+            raise ValueError(
+                f"To build {cls.__name__}, image must be 3D, not {len(shape)}D"
+            )
         planes = _z_window(
             central_z,
             shape[0],
@@ -91,7 +93,11 @@ def from_image(
 
 
 def _z_window(
-    central_z: ZCoordinate, num_planes: int, *, plus_minus_planes: int, require_full_padding: bool
+    central_z: ZCoordinate,
+    num_planes: int,
+    *,
+    plus_minus_planes: int,
+    require_full_padding: bool,
 ) -> slice:
     """Get the z-planes to measure: the one nearest the point, plus padding, cut off at the edges."""
     # Round halves up, as for x and y; round() would round them to the nearest even number.
@@ -117,9 +123,7 @@ def _z_window(
     lower_slice_bound = round_z - plus_minus_planes
     upper_slice_bound = round_z + plus_minus_planes + 1
     if lower_slice_bound < 0 or upper_slice_bound > num_planes:
-        oob_slice_msg = (
-            f"[{lower_slice_bound}, {upper_slice_bound}) slice for image of {num_planes} z-slices"
-        )
+        oob_slice_msg = f"[{lower_slice_bound}, {upper_slice_bound}) slice for image of {num_planes} z-slices"
         if require_full_padding:
             raise ValueError(oob_slice_msg)
         logging.debug(oob_slice_msg)
@@ -179,7 +183,12 @@ def _locate_region(  # noqa: PLR0913
             f"Region x [{left}, {right}), y [{top}, {bottom}) around point ({pt.x}, {pt.y}) "
             f"lies outside the image of {num_cols} x {num_rows} pixels"
         )
-    if require_full_region and (y_min, y_max, x_min, x_max) != (top, bottom, left, right):
+    if require_full_region and (y_min, y_max, x_min, x_max) != (
+        top,
+        bottom,
+        left,
+        right,
+    ):
         raise ValueError(
             f"Region x [{left}, {right}), y [{top}, {bottom}) around point ({pt.x}, {pt.y}) "
             f"extends beyond the image of {num_cols} x {num_rows} pixels"
@@ -191,7 +200,12 @@ def _locate_region(  # noqa: PLR0913
         require_full_padding=require_full_padding,
     )
     return _Region(
-        bounds={"y_min_px": y_min, "y_max_px": y_max, "x_min_px": x_min, "x_max_px": x_max},
+        bounds={
+            "y_min_px": y_min,
+            "y_max_px": y_max,
+            "x_min_px": x_min,
+            "x_max_px": x_max,
+        },
         planes=planes,
         rows=slice(y_min, y_max),
         columns=slice(x_min, x_max),
@@ -222,7 +236,7 @@ def _locate_region(  # noqa: PLR0913
         compute_pixel_statistics="The same, for several channels at once",
     ),
 )
-def compute_pixel_statistics_for_channel(  # noqa: D103, PLR0913
+def compute_pixel_statistics_for_channel(  # noqa: PLR0913
     img: PixelArray,
     pt: ImagePoint3D,
     *,
@@ -243,7 +257,9 @@ def compute_pixel_statistics_for_channel(  # noqa: D103, PLR0913
     )
     # Only the region is read, and of it only the planes of the z-window.
     # Indexing a dask array has no type information; the region is the same kind of array.
-    region_img = cast("PixelArray", img[channel.get, region.planes, region.rows, region.columns])
+    region_img = cast(
+        "PixelArray", img[channel.get, region.planes, region.rows, region.columns]
+    )
     return {
         channel_column: channel.get,
         **region.bounds,
@@ -275,7 +291,7 @@ def compute_pixel_statistics_for_channel(  # noqa: D103, PLR0913
         compute_pixel_statistics_for_channel="The same, for a single channel",
     ),
 )
-def compute_pixel_statistics(  # noqa: D103, PLR0913
+def compute_pixel_statistics(  # noqa: PLR0913
     img: PixelArray,
     pt: ImagePoint3D,
     *,
@@ -301,12 +317,15 @@ def compute_pixel_statistics(  # noqa: D103, PLR0913
         # information; the result is the same kind of array.
         all_channels = cast(
             "PixelArray",
-            img[[ch.get for ch in channels], region.planes, region.rows, region.columns],
+            img[
+                [ch.get for ch in channels], region.planes, region.rows, region.columns
+            ],
         )
         region_imgs = list(np.asarray(all_channels))
     else:
         region_imgs = [
-            np.asarray(img[ch.get, region.planes, region.rows, region.columns]) for ch in channels
+            np.asarray(img[ch.get, region.planes, region.rows, region.columns])
+            for ch in channels
         ]
     return [
         {channel_column: ch.get, **region.bounds, **_statistics_of(region_img).to_dict}

gertils/types.py

@@ -37,7 +37,8 @@ class FieldOfViewFrom1:  # noqa: D101
     def __post_init__(self) -> None:
         if not _is_int(self.get):
             raise TypeError(
-                f"Non-integer as 1-based FOV! {self.get} (type" f" {type(self.get).__name__})"
+                f"Non-integer as 1-based FOV! {self.get} (type"
+                f" {type(self.get).__name__})"
             )
         if self.get < 1:
             raise ValueError(f"1-based FOV view must be positive int; got {self.get}")
@@ -50,7 +51,9 @@ class ImagingChannel:  # noqa: D101
 
     def __post_init__(self) -> None:
         if not _is_int(self.get):
-            raise TypeError(f"Imaging channel must be integer, not {type(self.get).__name__}")
+            raise TypeError(
+                f"Imaging channel must be integer, not {type(self.get).__name__}"
+            )
         if self.get < 0:
             raise ValueError(f"Imaging channel must be nonnegative; got {self.get}")
 
@@ -70,7 +73,8 @@ class NucleusNumber:  # noqa: D101
     def __post_init__(self) -> None:
         if not _is_int(self.get):
             raise TypeError(
-                f"Non-integer as nucleus number! {self.get} (type" f" {type(self.get).__name__})"
+                f"Non-integer as nucleus number! {self.get} (type"
+                f" {type(self.get).__name__})"
             )
         if self.get < 1:
             raise ValueError(f"Nucleus number must be positive int; got {self.get}")
@@ -111,6 +115,8 @@ class TraceIdFrom0:  # noqa: D101
 
     def __post_init__(self) -> None:
         if not _is_int(self.get):
-            raise TypeError(f"Non-integer as trace ID! {self.get} (type {type(self.get).__name__})")
+            raise TypeError(
+                f"Non-integer as trace ID! {self.get} (type {type(self.get).__name__})"
+            )
         if self.get < 0:
             raise ValueError(f"Trace ID must be nonnegative int; got {self.get}")

gertils/zarr_tools.py

@@ -15,14 +15,16 @@
     parameters=dict(root="Path at which datastore is rooted"),
     returns="Array of pixel (or similar) data",
 )
-def read_zarr(root: Path) -> PixelArray:  # noqa: D103
+def read_zarr(root: Path) -> PixelArray:
     logging.debug("Reading ZARR: %s", root)
     if (root / ".zarray").is_file():
         data_root = root
     elif (root / "0" / ".zarray").is_file():
         data_root = root / "0"
     else:
-        raise ZarrParseException(path=root, msg="Failed to find .zarray to indicate data folder")
+        raise ZarrParseException(
+            path=root, msg="Failed to find .zarray to indicate data folder"
+        )
     # The check above found an array, so open it as one; reading is all this function does.
     return np.asarray(zarr.open_array(str(data_root), mode="r"))
 

pyproject.toml

@@ -44,10 +44,10 @@ optional = true
 codespell = "^2.2.2"
 hypothesis = "^6.68.2"
 pre-commit = "^4.0"
-pyright = "^1.1.411"
+pyright = "==1.1.411"
 pytest = "^7.1.0"
 pytest-cov = "^5.0.0"
-ruff = ">=0.3"
+ruff = "==0.7.4"
 
 [tool.poetry.group.lint]
 optional = true
@@ -57,9 +57,11 @@ optional = true
 codespell = "^2.2.2"
 hypothesis = "^6.68.2"
 pre-commit = "^4.0"
-pyright = "^1.1.411"
+# The version looptrace pins, so the projects are type-checked by the same pyright.
+pyright = "==1.1.411"
 pytest = "^7.1.0"
-ruff = ">=0.3"
+# The version looptrace pins, so the projects are formatted and linted by the same ruff.
+ruff = "==0.7.4"
 
 [tool.poetry.group.test]
 optional = true
@@ -83,9 +85,7 @@ strict = ["gertils"]
 reportUnnecessaryTypeIgnoreComment = "error"
 
 [tool.ruff]
-# Black uses line-length = 88, but allows exceptions when breaking the line
-# would lead to other rule violations. Use 100 as a maximum hard limit:
-line-length = 100
+# No line-length: ruff's default of 88, as in the other repositories behind looptrace.
 target-version = "py311"
 
 [tool.ruff.lint]
@@ -134,6 +134,12 @@ ignore = [
     "E501",  # line-too-long
 ]
 
+[tool.ruff.lint.pydocstyle]
+# numpydoc_decorator's @doc writes the docstring of the functions it decorates when the
+# module is imported, so ruff, which only reads the source, doesn't see one. The setting
+# applies only to functions and methods, so classes keep their `# noqa: D101`.
+ignore-decorators = ["numpydoc_decorator.doc"]
+
 [tool.ruff.lint.per-file-ignores]
 "typings/*" = [
     # Stubs copy the signatures of third-party code, which we can't change.

tests/test_get_fov_sort_key.py

@@ -5,7 +5,11 @@
 
 import pytest
 
-from gertils.pathtools import find_multiple_paths_by_fov, find_single_path_by_fov, get_fov_sort_key
+from gertils.pathtools import (
+    find_multiple_paths_by_fov,
+    find_single_path_by_fov,
+    get_fov_sort_key,
+)
 from gertils.types import FieldOfViewFrom1
 
 
@@ -45,10 +49,14 @@ def test_only_one_leading_p_is_removed():
 
 def test_double_zarr_extension_is_parsed_with_a_warning():
     with pytest.warns(FutureWarning, match="Stripping second '.zarr' extension"):
-        assert get_fov_sort_key("P0003.zarr.zarr", extension=".zarr") == FieldOfViewFrom1(3)
+        assert get_fov_sort_key(
+            "P0003.zarr.zarr", extension=".zarr"
+        ) == FieldOfViewFrom1(3)
 
 
-def test_find_multiple_paths_by_fov_keeps_fovs_apart_for_extension_with_digits(tmp_path):
+def test_find_multiple_paths_by_fov_keeps_fovs_apart_for_extension_with_digits(
+    tmp_path,
+):
     for name in ["P0001.nd2", "P0012.nd2"]:
         (tmp_path / name).touch()
     assert find_multiple_paths_by_fov(tmp_path, extensions=[".nd2"]) == {
@@ -80,7 +88,8 @@ def test_file_with_number_zero_is_skipped_in_a_folder_scan(tmp_path):
 
 
 @pytest.mark.parametrize(
-    "filename", ["P 12.zarr", "P+12.zarr", "P1_2.zarr", "P\uff11\uff12.zarr", "P12 .zarr"]
+    "filename",
+    ["P 12.zarr", "P+12.zarr", "P1_2.zarr", "P\uff11\uff12.zarr", "P12 .zarr"],
 )
 def test_fov_number_must_be_plain_ascii_digits(filename):
     assert get_fov_sort_key(filename, extension=".zarr") is None