[pre-commit.ci] pre-commit autoupdate

.pre-commit-config.yaml

@@ -7,7 +7,7 @@ default_language_version:
 repos:
   # Formatters
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v4.6.0
     hooks:
       - id: check-ast
       - id: check-builtin-literals
@@ -19,7 +19,7 @@ repos:
         args: [--remove]
 
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.15.1
+    rev: v3.17.0
     hooks:
       - id: pyupgrade
         types: [file]
@@ -36,7 +36,7 @@ repos:
         types_or: [python, pyi]
 
   - repo: https://github.com/psf/black
-    rev: 24.2.0
+    rev: 24.8.0
     hooks:
       - id: black
         types: [file]
@@ -68,7 +68,7 @@ repos:
           - "metadata.vscode metadata.language_info.version"
 
   - repo: https://github.com/nbQA-dev/nbQA
-    rev: 1.8.4
+    rev: 1.8.7
     hooks:
       - id: nbqa-black
         additional_dependencies: [black==22.6.0]
@@ -92,7 +92,7 @@ repos:
         additional_dependencies: [flake8-docstrings, flake8-print>=5.0.0]
 
   - repo: https://github.com/PyCQA/flake8
-    rev: 7.0.0
+    rev: 7.1.1
     hooks:
       - id: flake8
         name: "flake8 lint code"
@@ -104,7 +104,7 @@ repos:
           - "--count"
 
   - repo: https://github.com/PyCQA/flake8
-    rev: 7.0.0
+    rev: 7.1.1
     hooks:
       - id: flake8
         alias: flake8-docs
@@ -116,22 +116,22 @@ repos:
         additional_dependencies: [flake8-docstrings, darglint==1.8.0]
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.9.0
+    rev: v1.11.1
     hooks:
       - id: mypy
         exclude: "docs|benchmark/|.*/tests?/.*"
         additional_dependencies: [types-tabulate, types-attrs]
 
   - repo: https://github.com/econchick/interrogate
-    rev: 1.5.0
+    rev: 1.7.0
     hooks:
       - id: interrogate
         args: [--config=pyproject.toml, glotaran]
         pass_filenames: false
         additional_dependencies: [click<8]
 
   - repo: https://github.com/rstcheck/rstcheck
-    rev: "v6.2.0"
+    rev: "v6.2.4"
     hooks:
       - id: rstcheck
         additional_dependencies: [sphinx]
@@ -150,7 +150,7 @@ repos:
       - id: rst-inline-touching-normal
 
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.2.6
+    rev: v2.3.0
     hooks:
       - id: codespell
         types: [file]

glotaran/model/dataset_model.py

@@ -250,7 +250,7 @@ def get_dataset_model_model_dimension(dataset_model: DatasetModel) -> str:
 
 def iterate_dataset_model_megacomplexes(
     dataset_model: DatasetModel,
-) -> Generator[tuple[Parameter | str | None, Megacomplex | str], None, None]:
+) -> Generator[tuple[Parameter | str | None, Megacomplex | str]]:
     """Iterate the dataset model's megacomplexes.
 
     Parameters
@@ -274,7 +274,7 @@ def iterate_dataset_model_megacomplexes(
 
 def iterate_dataset_model_global_megacomplexes(
     dataset_model: DatasetModel,
-) -> Generator[tuple[Parameter | str | None, Megacomplex | str], None, None]:
+) -> Generator[tuple[Parameter | str | None, Megacomplex | str]]:
     """Iterate the dataset model's global megacomplexes.
 
     Parameters

glotaran/model/model.py

@@ -344,7 +344,7 @@ def get_dataset_groups(self) -> dict[str, DatasetGroup]:
 
     def iterate_items(
         self,
-    ) -> Generator[tuple[str, dict[str, Item] | list[Item]], None, None]:
+    ) -> Generator[tuple[str, dict[str, Item] | list[Item]]]:
         """Iterate items.
 
         Yields
@@ -356,7 +356,7 @@ def iterate_items(
             if META_ITEMS in attr.metadata:
                 yield attr.name, getattr(self, attr.name)
 
-    def iterate_all_items(self) -> Generator[Item, None, None]:
+    def iterate_all_items(self) -> Generator[Item]:
         """Iterate the individual items.
 
         Yields

glotaran/parameter/parameters.py

@@ -259,7 +259,7 @@ def copy(self) -> Parameters:
             {label: parameter.copy() for label, parameter in self._parameters.items()}
         )
 
-    def all(self) -> Generator[Parameter, None, None]:
+    def all(self) -> Generator[Parameter]:
         """Iterate over all parameters.
 
         Yields
@@ -445,7 +445,7 @@ def __eq__(self, other: object) -> bool:
 
 def flatten_parameter_dict(
     parameter_dict: dict,
-) -> Generator[tuple[str, list[Any], dict[str, Any] | None], None, None]:
+) -> Generator[tuple[str, list[Any], dict[str, Any] | None]]:
     """Flatten a parameter dictionary.
 
     Parameters

glotaran/plugin_system/base_registry.py

@@ -419,7 +419,7 @@ def methods_differ_from_baseclass(
     method_names: str | Sequence[str],
     plugin: GenericPluginInstance | type[GenericPluginInstance],
     base_class: type[GenericPluginInstance],
-) -> Generator[bool, None, None]:
+) -> Generator[bool]:
     """Check if a plugins methods implementation differ from its baseclass.
 
     Based on the assumption that ``base_class`` didn't implement the methods
@@ -454,7 +454,7 @@ def methods_differ_from_baseclass_table(
     get_plugin_function: Callable[[str], GenericPluginInstance | type[GenericPluginInstance]],
     base_class: type[GenericPluginInstance],
     plugin_names: bool = False,
-) -> Generator[list[str | bool], None, None]:
+) -> Generator[list[str | bool]]:
     """Create table of which plugins methods differ from their baseclass.
 
     This uses the assumption that all plugins have the same ``base_class``.
@@ -511,7 +511,7 @@ def supported_file_extensions(
     plugin_registry_keys: str | Sequence[str],
     get_plugin_function: Callable[[str], GenericPluginInstance | type[GenericPluginInstance]],
     base_class: type[GenericPluginInstance],
-) -> Generator[str, None, None]:
+) -> Generator[str]:
     """Get file extensions for plugins that support all methods in ``method_names``.
 
     Parameters

glotaran/plugin_system/data_io_registration.py

@@ -343,7 +343,7 @@ def data_io_plugin_table(*, plugin_names: bool = False, full_names: bool = False
 
 def supported_file_extensions_data_io(
     method_names: str | Sequence[str],
-) -> Generator[str, None, None]:
+) -> Generator[str]:
     """Get data io formats that support all methods in ``method_names``.
 
     Parameters

glotaran/plugin_system/project_io_registration.py

@@ -558,7 +558,7 @@ def project_io_plugin_table(
 
 def supported_file_extensions_project_io(
     method_names: str | Sequence[str],
-) -> Generator[str, None, None]:
+) -> Generator[str]:
     """Get project io formats that support all methods in ``method_names``.
 
     Parameters

glotaran/project/dataclass_helpers.py

@@ -186,7 +186,9 @@ def asdict(dataclass: DataclassInstance, folder: Path | None = None) -> dict[str
     for field_item in fields(dataclass):
         if "exclude_from_dict" not in field_item.metadata:
             value = getattr(dataclass, field_item.name)
-            dataclass_dict[field_item.name] = asdict(value) if is_dataclass(value) else value
+            dataclass_dict[field_item.name] = (
+                asdict(value) if is_dataclass(value) else value  # type:ignore[arg-type]
+            )
         if "file_loader" in field_item.metadata:
             value = getattr(dataclass, field_item.name)
             if value.source_path is not None:

glotaran/testing/plugin_system.py

@@ -24,7 +24,7 @@ def _monkeypatch_plugin_registry(
     register_name: str,
     test_registry: MutableMapping[str, _PluginType] | None = None,
     create_new_registry: bool = False,
-) -> Generator[None, None, None]:
+) -> Generator[None]:
     """Contextmanager to monkeypatch any Pluginregistry with name ``register_name``.
 
     Parameters
@@ -64,7 +64,7 @@ def _monkeypatch_plugin_registry(
 def monkeypatch_plugin_registry_megacomplex(
     test_megacomplex: MutableMapping[str, type[Megacomplex]] | None = None,
     create_new_registry: bool = False,
-) -> Generator[None, None, None]:
+) -> Generator[None]:
     """Monkeypatch the :class:`Megacomplex` registry.
 
     Parameters
@@ -89,7 +89,7 @@ def monkeypatch_plugin_registry_megacomplex(
 def monkeypatch_plugin_registry_data_io(
     test_data_io: MutableMapping[str, DataIoInterface] | None = None,
     create_new_registry: bool = False,
-) -> Generator[None, None, None]:
+) -> Generator[None]:
     """Monkeypatch the :class:`DataIoInterface` registry.
 
     Parameters
@@ -114,7 +114,7 @@ def monkeypatch_plugin_registry_data_io(
 def monkeypatch_plugin_registry_project_io(
     test_project_io: MutableMapping[str, ProjectIoInterface] | None = None,
     create_new_registry: bool = False,
-) -> Generator[None, None, None]:
+) -> Generator[None]:
     """Monkeypatch the :class:`ProjectIoInterface` registry.
 
     Parameters
@@ -142,7 +142,7 @@ def monkeypatch_plugin_registry(
     test_data_io: MutableMapping[str, DataIoInterface] | None = None,
     test_project_io: MutableMapping[str, ProjectIoInterface] | None = None,
     create_new_registry: bool = False,
-) -> Generator[None, None, None]:
+) -> Generator[None]:
     """Contextmanager to monkeypatch multiple plugin registries at once.
 
     Parameters

glotaran/utils/io.py

@@ -193,7 +193,7 @@ def load_datasets(dataset_mappable: DatasetMappable) -> DatasetMapping:
 
 
 @contextmanager
-def chdir_context(folder_path: StrOrPath) -> Generator[Path, None, None]:
+def chdir_context(folder_path: StrOrPath) -> Generator[Path]:
     """Context manager to change directory to ``folder_path``.
 
     Parameters

glotaran/utils/tee.py

@@ -27,7 +27,7 @@ def __enter__(self) -> TeeContext:
         TeeContext
             Instance that can be read from.
         """
-        sys.stdout = self  # type:ignore[assignment]
+        sys.stdout = self
         return self
 
     def __exit__(