Enforce more ruff rules

ome_zarr/cli.py

@@ -40,7 +40,7 @@ def view(args: argparse.Namespace) -> None:
 
 def finder(args: argparse.Namespace) -> None:
     """Wrap the :func:`~ome_zarr.utils.finder` method."""
-    config_logging(logging.WARN, args)
+    config_logging(logging.WARNING, args)
     bff_finder(args.path, args.port)
 
 

ome_zarr/format.py

@@ -2,8 +2,8 @@
 
 import logging
 from abc import ABC, abstractmethod
-from collections.abc import Iterator
-from typing import Any, Dict
+from collections.abc import Iterator, Mapping
+from typing import Any
 
 from zarr.storage import FsspecStore, LocalStore
 
@@ -63,7 +63,7 @@ def zarr_format(self) -> int:  # pragma: no cover
 
     @property
     @abstractmethod
-    def chunk_key_encoding(self) -> Dict[str, str]:  # pragma: no cover
+    def chunk_key_encoding(self) -> dict[str, str]:  # pragma: no cover
         raise NotImplementedError()
 
     @abstractmethod
@@ -134,7 +134,7 @@ class FormatV01(Format):
     Initial format. (2020)
     """
 
-    REQUIRED_PLATE_WELL_KEYS: dict[str, type] = {"path": str}
+    REQUIRED_PLATE_WELL_KEYS: Mapping[str, type] = {"path": str}
 
     @property
     def version(self) -> str:
@@ -145,7 +145,7 @@ def zarr_format(self) -> int:
         return 2
 
     @property
-    def chunk_key_encoding(self) -> Dict[str, str]:
+    def chunk_key_encoding(self) -> dict[str, str]:
         return {"name": "v2", "separator": "."}
 
     def matches(self, metadata: dict) -> bool:
@@ -179,7 +179,7 @@ def generate_well_dict(
     def validate_well_dict(
         self, well: dict, rows: list[str], columns: list[str]
     ) -> None:
-        if any(e not in self.REQUIRED_PLATE_WELL_KEYS for e in well.keys()):
+        if any(e not in self.REQUIRED_PLATE_WELL_KEYS for e in well):
             LOGGER.debug("%s contains unspecified keys", well)
         for key, key_type in self.REQUIRED_PLATE_WELL_KEYS.items():
             if key not in well:
@@ -213,7 +213,7 @@ def version(self) -> str:
         return "0.2"
 
     @property
-    def chunk_key_encoding(self) -> Dict[str, str]:
+    def chunk_key_encoding(self) -> dict[str, str]:
         return {"name": "v2", "separator": "/"}
 
 
@@ -234,7 +234,11 @@ class FormatV04(FormatV03):
     introduce coordinate_transformations in multiscales (Nov 2021)
     """
 
-    REQUIRED_PLATE_WELL_KEYS = {"path": str, "rowIndex": int, "columnIndex": int}
+    REQUIRED_PLATE_WELL_KEYS: Mapping[str, type] = {
+        "path": str,
+        "rowIndex": int,
+        "columnIndex": int,
+    }
 
     @property
     def version(self) -> str:
@@ -367,7 +371,7 @@ def zarr_format(self) -> int:
         return 3
 
     @property
-    def chunk_key_encoding(self) -> Dict[str, str]:
+    def chunk_key_encoding(self) -> dict[str, str]:
         # this is default for Zarr v3. Could return None?
         return {"name": "default", "separator": "/"}
 

ome_zarr/reader.py

@@ -112,7 +112,7 @@ def add(
         prepend: bool = False,
         visibility: bool | None = None,
         plate_labels: bool = False,
-    ) -> "Optional[Node]":
+    ) -> "Node | None":
         """Create a child node if this location has not yet been seen.
 
         Newly created nodes may be considered higher or lower priority than
@@ -269,10 +269,7 @@ class Multiscales(Spec):
     @staticmethod
     def matches(zarr: ZarrLocation) -> bool:
         """is multiscales metadata present?"""
-        if zarr.zgroup:
-            if "multiscales" in zarr.root_attrs:
-                return True
-        return False
+        return bool(zarr.zgroup) and "multiscales" in zarr.root_attrs
 
     def __init__(self, node: Node) -> None:
         super().__init__(node)
@@ -345,7 +342,7 @@ def __init__(self, node: Node) -> None:
 
             try:
                 len(channels)
-            except Exception:
+            except TypeError:
                 LOGGER.warning("error counting channels: %s", channels)
                 return  # EARLY EXIT
 

ome_zarr/scale.py

@@ -26,8 +26,8 @@
 
 LOGGER = logging.getLogger("ome_zarr.scale")
 
-ListOfArrayLike = Union[list[da.Array], list[np.ndarray]]
-ArrayLike = Union[da.Array, np.ndarray]
+ListOfArrayLike = Union[list[da.Array], list[np.ndarray]]  # noqa: UP007  # FIXME
+ArrayLike = Union[da.Array, np.ndarray]  # noqa: UP007  # FIXME
 
 
 @dataclass

ome_zarr/types.py

@@ -1,11 +1,11 @@
 """Definition of complex types for use elsewhere."""
 
 from collections.abc import Callable
-from typing import Any, Union
+from typing import Any
 
-LayerData = Union[tuple[Any], tuple[Any, dict], tuple[Any, dict, str]]
+LayerData = tuple[Any] | tuple[Any, dict] | tuple[Any, dict, str]
 
-PathLike = Union[str, list[str]]
+PathLike = str | list[str]
 
 ReaderFunction = Callable[[PathLike], list[LayerData]]
 

ome_zarr/utils.py

@@ -149,7 +149,7 @@ def find_multiscales(path_to_zattrs):
             plate_name = os.path.basename(path_to_zattrs)
             return [[path_to_zarr, plate_name, os.path.dirname(path_to_zattrs)]]
         else:
-            LOGGER.info(f"No wells found in plate{path_to_zattrs}")
+            LOGGER.info("No wells found in plate%s", path_to_zattrs)
             return []
     elif zattrs.get("bioformats2raw.layout") == 3:
         # Open OME/METADATA.ome.xml
@@ -178,7 +178,7 @@ def find_multiscales(path_to_zattrs):
                     )
                     series += 1
             return images
-        except Exception as ex:
+        except Exception as ex:  # noqa: BLE001
             print(ex)
     elif zattrs.get("multiscales"):
         return [

ome_zarr/writer.py

@@ -77,7 +77,7 @@ def _validate_well_images(
         if isinstance(image, str):
             validated_images.append({"path": str(image)})
         elif isinstance(image, dict):
-            if any(e not in VALID_KEYS for e in image.keys()):
+            if any(e not in VALID_KEYS for e in image):
                 LOGGER.debug("%s contains unspecified keys", image)
             if "path" not in image:
                 raise ValueError(f"{image} must contain a path key")
@@ -106,7 +106,7 @@ def _validate_plate_acquisitions(
     for acquisition in acquisitions:
         if not isinstance(acquisition, dict):
             raise ValueError(f"{acquisition} must be a dictionary")
-        if any(e not in VALID_KEYS for e in acquisition.keys()):
+        if any(e not in VALID_KEYS for e in acquisition):
             LOGGER.debug("%s contains unspecified keys", acquisition)
         if "id" not in acquisition:
             raise ValueError(f"{acquisition} must contain an id key")
@@ -298,7 +298,7 @@ def write_multiscale(
                 del options["chunk_key_encoding"]
             # handle any 'chunks' option from storage_options
             if chunks_opt is not None:
-                data = da.array(data).rechunk(chunks=chunks_opt)
+                data = da.array(data).rechunk(chunks=chunks_opt)  # noqa: PLW2901
             da_delayed = da.to_zarr(
                 arr=data,
                 url=group.store,
@@ -402,7 +402,7 @@ def write_multiscales_metadata(
         if omero_metadata is None:
             raise KeyError("If `'omero'` is present, value cannot be `None`.")
         for c in omero_metadata["channels"]:
-            if "color" in c:
+            if "color" in c:  # noqa: SIM102
                 if not isinstance(c["color"], str) or len(c["color"]) != 6:
                     raise TypeError("`'color'` must be a hex code string.")
             if "window" in c:

pyproject.toml

@@ -57,18 +57,53 @@ Changelog = "https://github.com/ome/ome-zarr-py/blob/master/CHANGELOG.md"
 
 [tool.ruff.lint]
 extend-select = [
-    "I",   # isort
-    # "D",    # pydocstyle            # FIXME
-    # "BLE",  # flake8-blind-except   # FIXME
-    "A",   # flake8-builtins
-    # "G",    # flake8-logging-format # FIXME
+    "S",    # flake8-bandit
+    "BLE",  # flake8-blind-except
+    "B",    # flake8-bugbear
+    "A",    # flake8-builtins
+    "C4",   # flake8-comprehensions
+    "ISC",  # flake8-implicit-str-concat
+    "LOG",  # flake8-logging
+    "G",    # flake8-logging-format
+    "PIE",  # flake8-pie
+    "PYI",  # flake8-pyi
+    "SIM",  # flake8-simplify
+    "TID",  # flake8-tidy-imports
+    "FLY",  # flynt
+    "I",    # isort
+    "PERF", # Perflint
+    # "D",  # pydocstyle  # FIXME
+    "PGH",  # pygrep-hooks
+    "PLE",  # Pylint Error
+    "PLW",  # Pylint Warning
+    "UP",   # pyupgrade
+    "FURB", # refurb
+    "RUF",  # Ruff-specific rules
+]
+
+ignore = [
+    "S101",    # assert
+    "S311",    # suspicious-non-cryptographic-random-usage
+    "S314",    # suspicious-xml-element-tree-usage  # FIXME
+    "B007",    # unused-loop-control-variable
+    "B008",    # function-call-in-default-argument  # FIXME
+    "B011",    # assert-false
+    "B024",    # abstract-base-class-without-abstract-method  # FIXME
+    "B028",    # no-explicit-stacklevel
+    "B905",    # zip-without-explicit-strict
+    "C408",    # unnecessary-collection-call
+    "SIM108",  # if-else-block-instead-of-if-exp
+    "PERF203", # try-except-in-loop
+    "PLW1641", # eq-without-hash  # FIXME
+    "UP038",   # non-pep604-isinstance
+    "RUF005",  # collection-literal-concatenation
 ]
 
 [tool.ruff.lint.extend-per-file-ignores]
 "ome_zarr/csv.py" = ["A005"]
 "ome_zarr/io.py" = ["A005"]
 "ome_zarr/types.py" = ["A005"]
-"tests/*.py" = ["D"]
+"tests/*.py" = ["SIM201", "D"]
 
 [tool.setuptools]
 packages = ["ome_zarr"]

tests/test_cli.py

@@ -144,7 +144,7 @@ def _rotate_and_test(self, *hierarchy: Path, reverse: bool = True):
 
             copy = [list(x.parts) for x in firstpass]
             common = strip_common_prefix(copy)
-            assert "d" == common
+            assert common == "d"
             assert {tuple(x) for x in copy} == {tuple(x) for x in results}
 
         if reverse:

tests/test_writer.py

@@ -876,7 +876,7 @@ def test_minimal_plate(self, fmt):
             attrs = attrs["ome"]
             assert attrs["version"] == fmt.version
         else:
-            attrs["plate"]["version"] == fmt.version
+            assert attrs["plate"]["version"] == fmt.version
 
         assert "plate" in attrs
         assert attrs["plate"]["columns"] == [{"name": "1"}]
@@ -1256,7 +1256,7 @@ def test_multiple_images(self, images):
             {"path": "1"},
             {"path": "2"},
         ]
-        self.root_v3.attrs["ome"]["version"] == FormatV05().version
+        assert self.root_v3.attrs["ome"]["version"] == FormatV05().version
 
     @pytest.mark.parametrize("fmt", (FormatV01(), FormatV02(), FormatV03()))
     def test_version(self, fmt):