ci: [pre-commit.ci] autoupdate (#330)

<!--pre-commit.ci start-->
updates:
- [github.com/pre-commit/pre-commit-hooks: v4.4.0 →
v4.6.0](pre-commit/pre-commit-hooks@v4.4.0...v4.6.0)
- [github.com/psf/black: 23.7.0 →
24.8.0](psf/black@23.7.0...24.8.0)
- [github.com/astral-sh/ruff-pre-commit: v0.0.282 →
v0.6.3](astral-sh/ruff-pre-commit@v0.0.282...v0.6.3)
- [github.com/pre-commit/mirrors-mypy: v1.4.1 →
v1.11.2](pre-commit/mirrors-mypy@v1.4.1...v1.11.2)
<!--pre-commit.ci end-->

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Grzegorz Bokota <bokota+github@gmail.com>
Co-authored-by: Lorenzo Gaifas <brisvag@gmail.com>

.pre-commit-config.yaml

@@ -7,24 +7,24 @@ exclude: _docs/example_plugin/some_module.py
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.6.0
     hooks:
       - id: check-docstring-first
       - id: end-of-file-fixer
       - id: trailing-whitespace
 
   - repo: https://github.com/psf/black
-    rev: 23.7.0
+    rev: 24.8.0
     hooks:
       - id: black
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.0.282
+    rev: v0.6.4
     hooks:
       - id: ruff
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.4.1
+    rev: v1.11.2
     hooks:
       - id: mypy
         additional_dependencies:

pyproject.toml

@@ -112,6 +112,7 @@ select = [
 
 [tool.ruff.per-file-ignores]
 "src/npe2/cli.py" = ["B008", "A00"]
+"**/test_*.py" = ["RUF018"]
 
 [tool.ruff.pyupgrade]
 # Preserve types, even if a file imports `from __future__ import annotations`.

src/npe2/_dynamic_plugin.py

@@ -203,14 +203,12 @@ def __init__(self, plugin: DynamicPlugin, contrib_type: Type[C]) -> None:
         self._contrib_name = CONTRIB_NAMES[self.contrib_type]
 
     @overload
-    def __call__(self, func: T, **kwargs) -> T:
-        ...
+    def __call__(self, func: T, **kwargs) -> T: ...
 
     @overload
     def __call__(
         self, func: Optional[Literal[None]] = None, **kwargs
-    ) -> Callable[[T], T]:
-        ...
+    ) -> Callable[[T], T]: ...
 
     def __call__(
         self, func: Optional[T] = None, **kwargs

src/npe2/_inspection/_fetch.py

@@ -59,7 +59,7 @@ def _manifest_from_npe2_dist(
     module: str = match.groupdict()["module"]
     attr: str = match.groupdict()["attr"]
 
-    mf_file = Path(dist.locate_file(Path(module.replace(".", os.sep)) / attr))
+    mf_file = Path(dist.locate_file(Path(module.replace(".", os.sep)) / attr))  # type: ignore[arg-type]
     if not mf_file.exists():
         raise ValueError(  # pragma: no cover
             f"manifest {mf_file.name!r} does not exist in distribution "

src/npe2/_inspection/_from_npe1.py

@@ -516,7 +516,7 @@ def get_top_module_path(package_name, top_module: Optional[str] = None) -> Path:
             )
         top_module = top_mods[0]
 
-    path = Path(dist.locate_file(top_module))
+    path = Path(dist.locate_file(top_module))  # type: ignore[arg-type]
     if not path.is_dir() and dist.files:
         for f_path in dist.files:
             if "__editable__" in f_path.name:

src/npe2/_plugin_manager.py

@@ -236,9 +236,9 @@ def __init__(
         self._manifests: Dict[PluginName, PluginManifest] = {}
         self.events = PluginManagerEvents(self)
         self._npe1_adapters: List[NPE1Adapter] = []
-        self._command_menu_map: Dict[
-            str, Dict[str, Dict[str, List[MenuCommand]]]
-        ] = defaultdict(dict)
+        self._command_menu_map: Dict[str, Dict[str, Dict[str, List[MenuCommand]]]] = (
+            defaultdict(dict)
+        )
 
         # up to napari 0.4.15, discovery happened in the init here
         # so if we're running on an older version of napari, we need to discover

src/npe2/_setuptools_plugin.py

@@ -6,6 +6,7 @@
 
 [tool.npe2]
 """
+
 from __future__ import annotations
 
 import os

src/npe2/io_utils.py

@@ -126,8 +126,7 @@ def _read(
     plugin_name: Optional[str] = None,
     return_reader: Literal[False] = False,
     _pm=None,
-) -> List[LayerData]:
-    ...
+) -> List[LayerData]: ...
 
 
 @overload
@@ -138,8 +137,7 @@ def _read(
     plugin_name: Optional[str] = None,
     return_reader: Literal[True],
     _pm=None,
-) -> Tuple[List[LayerData], ReaderContribution]:
-    ...
+) -> Tuple[List[LayerData], ReaderContribution]: ...
 
 
 def _read(
@@ -270,8 +268,7 @@ def _write(
     plugin_name: Optional[str] = None,
     return_writer: Literal[False] = False,
     _pm: Optional[PluginManager] = None,
-) -> List[str]:
-    ...
+) -> List[str]: ...
 
 
 @overload
@@ -282,8 +279,7 @@ def _write(
     plugin_name: Optional[str] = None,
     return_writer: Literal[True],
     _pm: Optional[PluginManager] = None,
-) -> Tuple[List[str], WriterContribution]:
-    ...
+) -> Tuple[List[str], WriterContribution]: ...
 
 
 def _write(
@@ -300,9 +296,11 @@ def _write(
         _pm = PluginManager.instance()
 
     _layer_tuples: List[FullLayerData] = [
-        cast("napari.layers.Layer", x).as_layer_data_tuple()
-        if hasattr(x, "as_layer_data_tuple")
-        else x
+        (
+            cast("napari.layers.Layer", x).as_layer_data_tuple()
+            if hasattr(x, "as_layer_data_tuple")
+            else x
+        )
         for x in layer_data
     ]
     layer_types = [x[2] for x in _layer_tuples]

src/npe2/manifest/contributions/_configuration.py

@@ -45,7 +45,7 @@ class ConfigurationProperty(Draft07JsonSchema):
         "plain text, set this value to `plain`.",
     )
 
-    enum: Optional[conlist(Any, min_items=1, unique_items=True)] = Field(  # type: ignore # noqa: E501
+    enum: Optional[conlist(Any, min_items=1, unique_items=True)] = Field(  # type: ignore
         None,
         description="A list of valid options for this field. If you provide this field,"
         "the settings UI will render a dropdown menu.",

src/npe2/manifest/contributions/_json_schema.py

@@ -110,7 +110,7 @@ class Config:
     unique_items: bool = Field(False)
     max_properties: Optional[int] = Field(None, ge=0)
     min_properties: Optional[int] = Field(0, ge=0)
-    enum: Optional[conlist(Any, min_items=1, unique_items=True)] = Field(None)  # type: ignore  # noqa
+    enum: Optional[conlist(Any, min_items=1, unique_items=True)] = Field(None)  # type: ignore
     type: Union[JsonType, JsonTypeArray] = Field(None)  # type: ignore
     format: Optional[str] = Field(None)
 

src/npe2/manifest/contributions/_readers.py

@@ -1,10 +1,13 @@
 from functools import wraps
-from typing import List, Optional
+from typing import TYPE_CHECKING, List, Optional
 
 from npe2._pydantic_compat import Extra, Field
 from npe2.manifest.utils import Executable, v2_to_v1
 from npe2.types import ReaderFunction
 
+if TYPE_CHECKING:
+    from npe2._command_registry import CommandRegistry
+
 
 class ReaderContribution(Executable[Optional[ReaderFunction]]):
     """Contribute a file reader.
@@ -36,19 +39,26 @@ def __hash__(self):
             (self.command, tuple(self.filename_patterns), self.accepts_directories)
         )
 
-    def exec(self, *, kwargs):
+    def exec(
+        self,
+        args: tuple = (),
+        kwargs: Optional[dict] = None,
+        _registry: Optional["CommandRegistry"] = None,
+    ):
         """
         We are trying to simplify internal npe2 logic to always deal with a
         (list[str], bool) pair instead of Union[PathLike, Seq[Pathlike]]. We
         thus wrap the Reader Contributions to still give them the old api. Later
         on we could add a "if manifest.version == 2" or similar to not have this
         backward-compatibility logic for new plugins.
         """
+        if kwargs is None:  # pragma: no cover
+            kwargs = {}
         kwargs = kwargs.copy()
         stack = kwargs.pop("stack", None)
         assert stack is not None
         kwargs["path"] = v2_to_v1(kwargs["path"], stack)
-        callable_ = super().exec(kwargs=kwargs)
+        callable_ = super().exec(args=args, kwargs=kwargs, _registry=_registry)
 
         if callable_ is None:  # pragma: no cover
             return None

src/npe2/manifest/contributions/_sample_data.py

@@ -25,8 +25,7 @@ class _SampleDataContribution(GenericModel, ABC):
     @abstractmethod
     def open(
         self, *args, _registry: Optional["CommandRegistry"] = None, **kwargs
-    ) -> List[LayerData]:
-        ...
+    ) -> List[LayerData]: ...
 
 
 class SampleDataGenerator(_SampleDataContribution, Executable[List[LayerData]]):

src/npe2/manifest/schema.py

@@ -387,7 +387,8 @@ def _from_entrypoint(
         entry_point: metadata.EntryPoint,
         distribution: Optional[metadata.Distribution] = None,
     ) -> PluginManifest:
-        assert (match := entry_point.pattern.match(entry_point.value))
+        match = entry_point.pattern.match(entry_point.value)
+        assert match is not None
         module = match.group("module")
 
         spec = util.find_spec(module or "")
@@ -397,7 +398,8 @@ def _from_entrypoint(
                 f"entrypoint: {entry_point.value!r}"
             )
 
-        assert (match := entry_point.pattern.match(entry_point.value))
+        match = entry_point.pattern.match(entry_point.value)
+        assert match is not None
         fname = match.group("attr")
 
         for loc in spec.submodule_search_locations or []:

src/npe2/types.py

@@ -30,19 +30,15 @@
 
 class ArrayLike(Protocol):
     @property
-    def shape(self) -> Tuple[int, ...]:
-        ...
+    def shape(self) -> Tuple[int, ...]: ...
 
     @property
-    def ndim(self) -> int:
-        ...
+    def ndim(self) -> int: ...
 
     @property
-    def dtype(self) -> "np.dtype":
-        ...
+    def dtype(self) -> "np.dtype": ...
 
-    def __array__(self) -> "np.ndarray":
-        ...  # pragma: no cover
+    def __array__(self) -> "np.ndarray": ...  # pragma: no cover
 
 
 LayerName = Literal[

tests/fixtures/my-compiled-plugin/my_module/_a.py

@@ -11,13 +11,11 @@
 
 
 @implements.on_activate
-def activate(ctx):
-    ...
+def activate(ctx): ...
 
 
 @implements.on_deactivate
-def deactivate(ctx):
-    ...
+def deactivate(ctx): ...
 
 
 @implements.reader(
@@ -26,8 +24,7 @@ def deactivate(ctx):
     filename_patterns=["*.fzy", "*.fzzy"],
     accepts_directories=True,
 )
-def get_reader(path: str):
-    ...
+def get_reader(path: str): ...
 
 
 @implements.writer(
@@ -42,5 +39,6 @@ def get_reader(path: str):
     filename_extensions=["*.pcd", "*.e57"],
     layer_types=["points{1}", "surface+"],
 )
-def writer_function(path: str, layer_data: List[Tuple[Any, Dict, str]]) -> List[str]:
-    ...
+def writer_function(
+    path: str, layer_data: List[Tuple[Any, Dict, str]]
+) -> List[str]: ...

tests/fixtures/my-compiled-plugin/my_module/_b.py

@@ -8,8 +8,7 @@
 
 
 @implements.widget(id="some_widget", title="Create my widget", display_name="My Widget")
-class SomeWidget:
-    ...
+class SomeWidget: ...
 
 
 @implements.sample_data_generator(
@@ -18,8 +17,7 @@ class SomeWidget:
     key="random_data",
     display_name="Some Random Data (512 x 512)",
 )
-def random_data():
-    ...
+def random_data(): ...
 
 
 @implements.widget(
@@ -28,5 +26,4 @@ def random_data():
     display_name="A Widget From a Function",
     autogenerate=True,
 )
-def make_widget_from_function(x: int, threshold: int):
-    ...
+def make_widget_from_function(x: int, threshold: int): ...

tests/npe1-plugin/npe1_module/__init__.py

@@ -5,31 +5,25 @@
 from napari_plugin_engine import napari_hook_implementation
 
 
-class MyWidget:
-    ...
+class MyWidget: ...
 
 
-def some_function(x: int):
-    ...
+def some_function(x: int): ...
 
 
-def gen_data():
-    ...
+def gen_data(): ...
 
 
 @napari_hook_implementation
-def napari_get_reader(path):
-    ...
+def napari_get_reader(path): ...
 
 
 @napari_hook_implementation
-def napari_write_image(path, data, meta):
-    ...
+def napari_write_image(path, data, meta): ...
 
 
 @napari_hook_implementation
-def napari_write_labels(path, data, meta):
-    ...
+def napari_write_labels(path, data, meta): ...
 
 
 @napari_hook_implementation
@@ -79,8 +73,7 @@ def napari_experimental_provide_theme():
 @napari_hook_implementation
 def napari_experimental_provide_dock_widget():
     @magic_factory
-    def local_widget(y: str):
-        ...
+    def local_widget(y: str): ...
 
     return [
         MyWidget,
@@ -91,7 +84,6 @@ def local_widget(y: str):
 
 @napari_hook_implementation
 def napari_experimental_provide_function():
-    def local_function(x: int):
-        ...
+    def local_function(x: int): ...
 
     return [some_function, local_function]