Apply Sourcery suggestions and fix typos

.pre-commit-config.yaml

@@ -11,6 +11,11 @@ repos:
       - id: ruff
         args: ["--fix", "--show-fixes"]
       - id: ruff-format
+  - repo: https://github.com/sourcery-ai/sourcery
+    rev: v1.37.0
+    hooks:
+      - id: sourcery
+        args: [--diff=git diff HEAD, --no-summary]
   - repo: https://github.com/codespell-project/codespell
     rev: v2.4.1
     hooks:

.sourcery.yaml

@@ -0,0 +1,82 @@
+# 🪄 This is your project's Sourcery configuration file.
+
+# You can use it to get Sourcery working in the way you want, such as
+# ignoring specific refactorings, skipping directories in your project,
+# or writing custom rules.
+
+# 📚 For a complete reference to this file, see the documentation at
+# https://docs.sourcery.ai/Configuration/Project-Settings/
+
+# This file was auto-generated by Sourcery on 2025-06-20 at 14:38.
+
+version: '1'  # The schema version of this config file
+
+ignore: # A list of paths or files which Sourcery will ignore.
+- .git
+- env
+- .env
+- .tox
+- node_modules
+- vendor
+- venv
+- .venv
+- ~/.pyenv
+- ~/.rye
+- ~/.vscode
+- .vscode
+- ~/.cache
+- ~/.config
+- ~/.local
+
+rule_settings:
+  enable:
+  - default
+  disable: []  # A list of rule IDs Sourcery will never suggest.
+  rule_types:
+  - refactoring
+  - suggestion
+  - comment
+  python_version: '3.11' # A string specifying the lowest Python version your project supports. Sourcery will not suggest refactorings requiring a higher Python version.
+
+# rules:  # A list of custom rules Sourcery will include in its analysis.
+# - id: no-print-statements
+#   description: Do not use print statements in the test directory.
+#   pattern: print(...)
+#   language: python
+#   replacement:
+#   condition:
+#   explanation:
+#   paths:
+#     include:
+#     - test
+#     exclude:
+#     - conftest.py
+#   tests: []
+#   tags: []
+
+# rule_tags: {} # Additional rule tags.
+
+# metrics:
+#   quality_threshold: 25.0
+
+# github:
+#   labels: []
+#   ignore_labels:
+#   - sourcery-ignore
+#   request_review: author
+#   sourcery_branch: sourcery/{base_branch}
+
+# clone_detection:
+#   min_lines: 3
+#   min_duplicates: 2
+#   identical_clones_only: false
+
+# proxy:
+#   url:
+#   ssl_certs_file:
+#   no_ssl_verify: false
+
+# coding_assistant:
+#   project_description: ''
+#   enabled: true
+#   recipe_prompts: {}

src/zarr/core/array.py

@@ -660,7 +660,7 @@
                 overwrite=overwrite,
             )
         else:
-            raise ValueError(f"Insupported zarr_format. Got: {zarr_format}")
+            raise ValueError(f"Unsupported zarr_format. Got: {zarr_format}")
 
         if data is not None:
             # insert user-provided data

src/zarr/core/common.py

@@ -152,7 +152,7 @@ def parse_shapelike(data: int | Iterable[int]) -> tuple[int, ...]:
     if not all(isinstance(v, int) for v in data_tuple):
         msg = f"Expected an iterable of integers. Got {data} instead."
         raise TypeError(msg)
-    if not all(v > -1 for v in data_tuple):
+    if any(v < 0 for v in data_tuple):
         msg = f"Expected all values to be non-negative. Got {data} instead."
         raise ValueError(msg)
     return data_tuple

src/zarr/core/metadata/v2.py

@@ -266,11 +266,11 @@ def parse_filters(data: object) -> tuple[numcodecs.abc.Codec, ...] | None:
     """
     Parse a potential tuple of filters
     """
-    out: list[numcodecs.abc.Codec] = []
 
     if data is None:
         return data
     if isinstance(data, Iterable):
+        out: list[numcodecs.abc.Codec] = []
         for idx, val in enumerate(data):
             if isinstance(val, numcodecs.abc.Codec):
                 out.append(val)

src/zarr/core/metadata/v3.py

@@ -94,7 +94,7 @@ def validate_codecs(codecs: tuple[Codec, ...], dtype: ZDType[TBaseDType, TBaseSc
     # TODO: use codec ID instead of class name
     codec_class_name = abc.__class__.__name__
     # TODO: Fix typing here
-    if isinstance(dtype, VariableLengthUTF8) and not codec_class_name == "VLenUTF8Codec":  # type: ignore[unreachable]
+    if isinstance(dtype, VariableLengthUTF8) and codec_class_name != "VLenUTF8Codec":  # type: ignore[unreachable]
         raise ValueError(
             f"For string dtype, ArrayBytesCodec must be `VLenUTF8Codec`, got `{codec_class_name}`."
         )

src/zarr/registry.py

@@ -190,9 +190,9 @@
         if not isinstance(result, BytesBytesCodec):
             msg = f"Expected a dict representation of a BytesBytesCodec; got a dict representation of a {type(result)} instead."
             raise TypeError(msg)
+    elif not isinstance(data, BytesBytesCodec):
+        raise TypeError(f"Expected a BytesBytesCodec. Got {type(data)} instead.")
     else:
-        if not isinstance(data, BytesBytesCodec):
-            raise TypeError(f"Expected a BytesBytesCodec. Got {type(data)} instead.")
         result = data
     return result
 
@@ -210,9 +210,9 @@
         if not isinstance(result, ArrayBytesCodec):
             msg = f"Expected a dict representation of a ArrayBytesCodec; got a dict representation of a {type(result)} instead."
             raise TypeError(msg)
+    elif not isinstance(data, ArrayBytesCodec):
+        raise TypeError(f"Expected a ArrayBytesCodec. Got {type(data)} instead.")
     else:
-        if not isinstance(data, ArrayBytesCodec):
-            raise TypeError(f"Expected a ArrayBytesCodec. Got {type(data)} instead.")
         result = data
     return result
 
@@ -230,9 +230,9 @@
         if not isinstance(result, ArrayArrayCodec):
             msg = f"Expected a dict representation of a ArrayArrayCodec; got a dict representation of a {type(result)} instead."
             raise TypeError(msg)
+    elif not isinstance(data, ArrayArrayCodec):
+        raise TypeError(f"Expected a ArrayArrayCodec. Got {type(data)} instead.")
     else:
-        if not isinstance(data, ArrayArrayCodec):
-            raise TypeError(f"Expected a ArrayArrayCodec. Got {type(data)} instead.")
         result = data
     return result
 

src/zarr/testing/stateful.py

@@ -248,7 +248,7 @@ def delete_dir(self, data: DataObject) -> None:
     #     array_path = data.draw(st.sampled_from(self.all_arrays), label="Array move source")
     #     to_group = data.draw(st.sampled_from(self.all_groups), label="Array move destination")
 
-    #     # fixme renaiming to self?
+    #     # fixme renaming to self?
     #     array_name = os.path.basename(array_path)
     #     assume(self.model.can_add(to_group, array_name))
     #     new_path = f"{to_group}/{array_name}".lstrip("/")
@@ -265,7 +265,7 @@ def delete_dir(self, data: DataObject) -> None:
 
     #     from_group_name = os.path.basename(from_group)
     #     assume(self.model.can_add(to_group, from_group_name))
-    #     # fixme renaiming to self?
+    #     # fixme renaming to self?
     #     new_path = f"{to_group}/{from_group_name}".lstrip("/")
     #     note(f"moving group '{from_group}' -> '{new_path}'")
     #     self.model.rename(from_group, new_path)

tests/conftest.py

@@ -107,7 +107,7 @@ async def store2(request: pytest.FixtureRequest, tmpdir: LEGACY_PATH) -> Store:
 def sync_store(request: pytest.FixtureRequest, tmp_path: LEGACY_PATH) -> Store:
     result = sync(parse_store(request.param, str(tmp_path)))
     if not isinstance(result, Store):
-        raise TypeError("Wrong store class returned by test fixture! got " + result + " instead")
+        raise TypeError(f"Wrong store class returned by test fixture! got {result} instead")
     return result
 
 

tests/test_api.py

@@ -1174,7 +1174,7 @@ async def test_open_falls_back_to_open_group_async(zarr_format: ZarrFormat) -> N
 def test_open_modes_creates_group(tmp_path: pathlib.Path, mode: str) -> None:
     # https://github.com/zarr-developers/zarr-python/issues/2490
     zarr_dir = tmp_path / f"mode-{mode}-test.zarr"
-    if mode in ["r", "r+"]:
+    if mode in {"r", "r+"}:
         # Expect FileNotFoundError to be raised if 'r' or 'r+' mode
         with pytest.raises(FileNotFoundError):
             zarr.open(store=zarr_dir, mode=mode)

tests/test_codec_entrypoints.py

@@ -25,7 +25,7 @@ def set_path() -> Generator[None, None, None]:
 @pytest.mark.usefixtures("set_path")
 @pytest.mark.parametrize("codec_name", ["TestEntrypointCodec", "TestEntrypointGroup.Codec"])
 def test_entrypoint_codec(codec_name: str) -> None:
-    config.set({"codecs.test": "package_with_entrypoint." + codec_name})
+    config.set({"codecs.test": f"package_with_entrypoint.{codec_name}"})
     cls_test = zarr.registry.get_codec_class("test")
     assert cls_test.__qualname__ == codec_name
 
@@ -42,7 +42,7 @@ def test_entrypoint_pipeline() -> None:
 def test_entrypoint_buffer(buffer_name: str) -> None:
     config.set(
         {
-            "buffer": "package_with_entrypoint." + buffer_name,
+            "buffer": f"package_with_entrypoint.{buffer_name}",
             "ndbuffer": "package_with_entrypoint.TestEntrypointNDBuffer",
         }
     )