ci: pre-commit update

Author: flying-sheep

.pre-commit-config.yaml

@@ -5,24 +5,24 @@ repos:
   - id: trailing-whitespace
   - id: end-of-file-fixer
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.15.21
+  rev: v0.15.22
   hooks:
   - id: ruff-check
     args: [--fix, --preview]
   - id: ruff-format
 - repo: https://github.com/tox-dev/pyproject-fmt
-  rev: v2.25.2
+  rev: v2.25.3
   hooks:
     - id: pyproject-fmt
 - repo: https://github.com/biomejs/pre-commit
-  rev: v2.5.3
+  rev: v2.5.4
   hooks:
   - id: biome-format
 - repo: https://github.com/kynan/nbstripout
   rev: "0.9.1"
   hooks:
     - id: nbstripout
 - repo: https://github.com/zizmorcore/zizmor-pre-commit
-  rev: v1.26.1
+  rev: v1.27.0
   hooks:
     - id: zizmor

docs/examples/scanpy/Tools.ipynb

@@ -296,7 +296,7 @@
    "source": [
     "try:\n",
     "    sc.pl.dpt_groups_pseudotime(adata)\n",
-    "except Exception:  # noqa: BLE001\n",
+    "except Exception:  # ruff:ignore[blind-except]\n",
     "    import traceback\n",
     "\n",
     "    traceback.print_exc()"
@@ -339,7 +339,7 @@
     "    dendrogram_key = f\"dendrogram_{groupby}\"  # _get_dendrogram_key(...)\n",
     "    mat = adata.uns[dendrogram_key][\"correlation_matrix\"]\n",
     "    index = adata.uns[dendrogram_key][\"categories_idx_ordered\"]\n",
-    "    mat = mat[index[::-1], :][:, index]  # TODO: why do we have to flip?  # noqa: TD003\n",
+    "    mat = mat[index[::-1], :][:, index]  # TODO: why do we have to flip?  # ruff:ignore[missing-todo-link]\n",
     "\n",
     "    labels = list(adata.obs[groupby].cat.categories)\n",
     "    labels = np.array(labels).astype(\"str\")[index]\n",
@@ -395,7 +395,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.13.7"
+   "version": "3.13.12"
   }
  },
  "nbformat": 4,

docs/ext/napoleon_attrdoc_fix.py

@@ -31,5 +31,5 @@ def _consume_inline_attribute(self: GoogleDocstring) -> tuple[str, list[str]]:
 def setup(app: Sphinx) -> ExtensionMetadata:
     """Apply the Napoleon monkeypatch."""
     del app
-    GoogleDocstring._consume_inline_attribute = _consume_inline_attribute  # noqa: SLF001
+    GoogleDocstring._consume_inline_attribute = _consume_inline_attribute  # ruff:ignore[private-member-access]
     return ExtensionMetadata(parallel_read_safe=True)

docs/ext/paramdoc.py

@@ -62,12 +62,12 @@ class _Options:
 }
 
 
-def param_formatter(  # noqa: PLR0917
-    app: Sphinx,  # noqa: ARG001
+def param_formatter(  # ruff:ignore[too-many-positional-arguments]
+    app: Sphinx,  # ruff:ignore[unused-function-argument]
     what: Literal["module", "class", "exception", "function", "method", "attribute"],
-    name: str,  # noqa: ARG001
+    name: str,  # ruff:ignore[unused-function-argument]
     obj: object,
-    options: _Options,  # noqa: ARG001
+    options: _Options,  # ruff:ignore[unused-function-argument]
     lines: list[str],
 ) -> None:
     """Format parameter documentation."""
@@ -140,12 +140,12 @@ def _format_child(
     ]
 
 
-def param_skip(  # noqa: PLR0917
-    app: Sphinx,  # noqa: ARG001
+def param_skip(  # ruff:ignore[too-many-positional-arguments]
+    app: Sphinx,  # ruff:ignore[unused-function-argument]
     what: Literal["module", "class", "exception", "function", "method", "attribute"],
-    name: str,  # noqa: ARG001
+    name: str,  # ruff:ignore[unused-function-argument]
     obj: object,
-    skip: bool,  # noqa: FBT001
+    skip: bool,  # ruff:ignore[boolean-type-hint-positional-argument]
     options: _Options,
 ) -> bool | None:
     """Skip undocumentable parameters."""
@@ -168,7 +168,7 @@ def param_skip(  # noqa: PLR0917
         and isinstance(obj, type)
         and issubclass(obj, param.Parameterized)
     ):
-        # HACK: Sphinx incorrectly labels this as a module level discovery  # noqa: FIX004
+        # HACK: Sphinx incorrectly labels this as a module level discovery  # ruff:ignore[line-contains-hack]
         #       We abuse this skip callback to exclude parameters and
         #       include all methods
         members = [

src/hv_anndata/__init__.py

@@ -13,7 +13,7 @@
     register,
 )
 
-A = A  # noqa: PLW0127, RUF067
+A = A  # ruff:ignore[self-assigning-variable, non-empty-init-module]
 """Accessor for anndata.
 
 >>> from hv_anndata import A
@@ -31,7 +31,7 @@
     "register",
 ]
 
-with suppress(ImportError):  # noqa: RUF067
+with suppress(ImportError):  # ruff:ignore[non-empty-init-module]
     from .components import GeneSelector
     from .plotting import (
         ClusterMap,

src/hv_anndata/components.py

@@ -71,7 +71,7 @@ def __init__(self, **params: object) -> None:
         super().__init__(**params)
 
         self.w_key_input = pmui.AutocompleteInput.from_param(
-            self.param._input_key,  # noqa: SLF001
+            self.param._input_key,  # ruff:ignore[private-member-access]
             name="Active Group",
             placeholder="Enter/select group name",
             restrict=False,
@@ -87,12 +87,12 @@ def w_value_input_disabled(value: dict | list, _input_key: str) -> bool:
             )
 
         self.w_value_input = pmui.TextInput.from_param(
-            self.param._input_value,  # noqa: SLF001
+            self.param._input_value,  # ruff:ignore[private-member-access]
             name="New Marker Gene",
             disabled=param.bind(
                 w_value_input_disabled,
                 self.param.value,
-                self.param._input_key,  # noqa: SLF001
+                self.param._input_key,  # ruff:ignore[private-member-access]
             ),
             description="",
             sizing_mode="stretch_width",
@@ -101,7 +101,7 @@ def w_value_input_disabled(value: dict | list, _input_key: str) -> bool:
         pre = "Selected Group " if isinstance(self.value, dict) else ""
         mc_name = f"{pre}Marker Genes"
         self.w_multi_choice = pmui.MultiChoice.from_param(
-            self.param._current_selection,  # noqa: SLF001
+            self.param._current_selection,  # ruff:ignore[private-member-access]
             options=self.param.options,
             name=mc_name,
             searchable=True,
@@ -127,7 +127,7 @@ def w_value_input_disabled(value: dict | list, _input_key: str) -> bool:
         if self.value:
             if isinstance(self.value, dict):
                 keys = list(self.value)
-                self.param._input_key.objects = keys  # noqa: SLF001
+                self.param._input_key.objects = keys  # ruff:ignore[private-member-access]
                 self._input_key = keys[0]
                 if not self.options:
                     self.options = list(

src/hv_anndata/data.py

@@ -18,7 +18,7 @@ def pbmc68k_processed() -> AnnData:
 
     - ``.layers["counts"]`` instead of ``raw``.
     - UMAP computed.
-    """  # noqa: DOC201
+    """  # ruff:ignore[docstring-missing-returns]
     return _pbmc68k_processed().copy()
 
 

src/hv_anndata/interface.py

@@ -70,7 +70,7 @@ class AnnDataInterface(hv.core.Interface):
     @classmethod
     def init(
         cls,
-        eltype: hv.Element,  # noqa: ARG003
+        eltype: hv.Element,  # ruff:ignore[unused-class-method-argument]
         data: AnnData,
         kdims: list[Dimension] | None,
         vdims: list[Dimension] | None,
@@ -93,7 +93,7 @@ def init(
 
     @classmethod
     def dims(cls, dataset: Dataset) -> tuple[Literal["obs", "var"], ...]:
-        """Detect if the data is gridded or columnar and which anndata dimensions it spans."""  # noqa: E501
+        """Detect if the data is gridded or columnar and which anndata dimensions it spans."""  # ruff:ignore[line-too-long]
         vdim = cls._dim(dataset, dataset.vdims[0]) if dataset.vdims else None
         if len(dataset.kdims) == 0 and vdim:
             # e.g. Violin plot doesn’t have kdims
@@ -147,7 +147,7 @@ def _dim(dataset: Dataset, k: Dimension | str | int) -> AdDim:
         )
 
     @classmethod
-    def validate(cls, dataset: Dataset, vdims: bool = True) -> None:  # noqa: FBT001, FBT002
+    def validate(cls, dataset: Dataset, vdims: bool = True) -> None:  # ruff:ignore[boolean-type-hint-positional-argument, boolean-default-value-positional-argument]
         """Check if all dimensions (or key dimensions if `vdims==False`) are present."""
         dims = "all" if vdims else "key"
         not_found = [
@@ -173,7 +173,7 @@ def validate_selection_dim(
         if len(ref.dims) > 1:
             raise DataError(MSG_1D)
         [dim] = ref.dims
-        # TODO: support ranges and sequences  # noqa: TD003
+        # TODO: support ranges and sequences  # ruff:ignore[missing-todo-link]
         if dim not in {"obs", "var"}:  # pragma: no cover
             msg = f"Cannot {action} along unknown dim: {dim}"
             raise AssertionError(msg)
@@ -255,8 +255,8 @@ def select(
     def reindex(
         cls,
         dataset: Dataset,
-        kdims: list[Dimension] | None = None,  # noqa: ARG003
-        vdims: list[Dimension] | None = None,  # noqa: ARG003
+        kdims: list[Dimension] | None = None,  # ruff:ignore[unused-class-method-argument]
+        vdims: list[Dimension] | None = None,  # ruff:ignore[unused-class-method-argument]
     ) -> AnnData:
         """Reindex the data (a no-op)."""
         return dataset.data
@@ -267,18 +267,18 @@ def values(
         data: Dataset,
         ref: Dimension | str,
         /,
-        expanded: bool = True,  # noqa: FBT001, FBT002, ARG003
-        flat: bool = True,  # noqa: FBT001, FBT002
+        expanded: bool = True,  # ruff:ignore[boolean-type-hint-positional-argument, boolean-default-value-positional-argument, unused-class-method-argument]
+        flat: bool = True,  # ruff:ignore[boolean-type-hint-positional-argument, boolean-default-value-positional-argument]
         *,
-        compute: bool = True,  # noqa: ARG003
-        keep_index: bool = False,  # noqa: ARG003
+        compute: bool = True,  # ruff:ignore[unused-class-method-argument]
+        keep_index: bool = False,  # ruff:ignore[unused-class-method-argument]
     ) -> ValueType:
         """Retrieve values for a dimension."""
         ref = cls._dim(data, ref)
         adata = cast("AnnData", data.data)
         values = adata[ref]
         if flat and values.ndim > 1:
-            assert not isinstance(values, ExtensionArray)  # noqa: S101
+            assert not isinstance(values, ExtensionArray)  # ruff:ignore[assert]
             values = values.flatten()
         return _simplify_numpy(values)
 
@@ -332,7 +332,7 @@ def iloc(
     def _iloc_2d(
         cls,
         dims: tuple[Literal["obs", "var"], ...],
-        rows: slice[int | None],  # noqa: ARG003
+        rows: slice[int | None],  # ruff:ignore[unused-class-method-argument]
         cols: slice[None],
     ) -> tuple[slice[int | None], slice[int | None]] | None:
         """Validate indexing. Overridden in `AnnDataGriddedInterface`."""
@@ -351,7 +351,7 @@ def aggregate(
         dataset: Dataset,
         kdims: list[Dimension | str],
         function: Callable[[ValueType], ValueType],
-        **kwargs: Any,  # noqa: ANN401
+        **kwargs: Any,  # ruff:ignore[any-type]
     ) -> tuple[pd.DataFrame, list[Dimension]]:
         """Aggregate the current view."""
         agg = Dataset(
@@ -364,9 +364,9 @@ def aggregate(
     @classmethod
     def unpack_scalar(
         cls,
-        dataset: Dataset,  # noqa: ARG003
+        dataset: Dataset,  # ruff:ignore[unused-class-method-argument]
         data: AnnData | pd.DataFrame,
-    ) -> Any:  # noqa: ANN401
+    ) -> Any:  # ruff:ignore[any-type]
         """Unpacks scalar data if it is a DataFrame containing a single value."""
         if isinstance(data, AnnData):
             return data
@@ -381,7 +381,7 @@ def groupby(
         dimensions: Sequence[str | AdDim],
         container_type: type[T],
         group_type: type[Dataset | dict] | Literal["raw"],
-        **kwargs: Any,  # noqa: ANN401
+        **kwargs: Any,  # ruff:ignore[any-type]
     ) -> T:
         """Group the dataset along the provided dimensions."""
         values = {}
@@ -464,7 +464,7 @@ def coords(
         dataset: Dataset,
         ref: Dimension | str,
         /,
-        ordered: bool = False,  # noqa: FBT001, FBT002
+        ordered: bool = False,  # ruff:ignore[boolean-type-hint-positional-argument, boolean-default-value-positional-argument]
         *,
         expanded: bool = False,
         edges: bool = False,
@@ -473,14 +473,14 @@ def coords(
 
         Ordered ensures coordinates are in ascending order and expanded creates
         ND-array matching the dimensionality of the dataset.
-        """  # noqa: DOC201
+        """  # ruff:ignore[docstring-missing-returns]
         ref = cls._dim(dataset, ref)
         vdim = dataset.vdims[0]
         if expanded:
             data = expand_grid_coords(dataset, ref)
             if edges and data.shape == vdim(dataset.data).shape:
-                data = GridInterface._infer_interval_breaks(data, axis=1)  # noqa: SLF001
-                data = GridInterface._infer_interval_breaks(data, axis=0)  # noqa: SLF001
+                data = GridInterface._infer_interval_breaks(data, axis=1)  # ruff:ignore[private-member-access]
+                data = GridInterface._infer_interval_breaks(data, axis=0)  # ruff:ignore[private-member-access]
             return data
 
         data = ref(dataset.data)
@@ -489,7 +489,7 @@ def coords(
         shape = cls.shape(dataset, gridded=True)
         if ref in dataset.kdims:
             idx = dataset.get_dimension_index(ref)
-            # TODO: don’t do this, it’s broken if diff(shape) == 1  # noqa: TD003
+            # TODO: don’t do this, it’s broken if diff(shape) == 1  # ruff:ignore[missing-todo-link]
             is_edges = (
                 ref in dataset.kdims
                 and len(shape) == dataset.ndims
@@ -498,7 +498,7 @@ def coords(
         else:
             is_edges = False
         if edges and not is_edges:
-            data = GridInterface._infer_interval_breaks(data)  # noqa: SLF001
+            data = GridInterface._infer_interval_breaks(data)  # ruff:ignore[private-member-access]
         elif not edges and is_edges:
             data = data[:-1] + np.diff(data) / 2.0
         return data
@@ -508,11 +508,11 @@ def values(
         cls,
         data: Dataset,
         ref: Dimension | str,
-        expanded: bool = True,  # noqa: FBT001, FBT002
-        flat: bool = True,  # noqa: FBT001, FBT002
+        expanded: bool = True,  # ruff:ignore[boolean-type-hint-positional-argument, boolean-default-value-positional-argument]
+        flat: bool = True,  # ruff:ignore[boolean-type-hint-positional-argument, boolean-default-value-positional-argument]
         *,
-        compute: bool = True,  # noqa: ARG003
-        keep_index: bool = False,  # noqa: ARG003
+        compute: bool = True,  # ruff:ignore[unused-class-method-argument]
+        keep_index: bool = False,  # ruff:ignore[unused-class-method-argument]
     ) -> ValueType:
         """Retrieve values for a dimension."""
         ref = cls._dim(data, ref)
@@ -544,7 +544,7 @@ def values(
                 if transpose != flat:
                     values = values.T
             case _:
-                assert ref in data.vdims, "test_init_errors[tab-x_2d] prevents 2D kdims"  # noqa: S101
+                assert ref in data.vdims, "test_init_errors[tab-x_2d] prevents 2D kdims"  # ruff:ignore[assert]
                 error = (
                     "When requesting data for a value dimension, "
                     "it is invalid to request expanded=False. "