[pre-commit.ci] pre-commit autoupdate (#323)

* [pre-commit.ci] pre-commit autoupdate

updates:
- [github.com/pre-commit/mirrors-mypy: v1.11.2 → v1.13.0](pre-commit/mirrors-mypy@v1.11.2...v1.13.0)
- [github.com/psf/black: 24.8.0 → 24.10.0](psf/black@24.8.0...24.10.0)
- [github.com/pre-commit/pre-commit-hooks: v4.6.0 → v5.0.0](pre-commit/pre-commit-hooks@v4.6.0...v5.0.0)
- [github.com/asottile/blacken-docs: 1.18.0 → 1.19.1](adamchainz/blacken-docs@1.18.0...1.19.1)
- [github.com/astral-sh/ruff-pre-commit: v0.6.8 → v0.8.3](astral-sh/ruff-pre-commit@v0.6.8...v0.8.3)

* fix precommit

* fix pre-commit

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Luca Marconato <[email protected]>

.pre-commit-config.yaml

@@ -7,13 +7,13 @@ default_stages:
 minimum_pre_commit_version: 2.9.3
 repos:
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.11.2
+    rev: v1.13.0
     hooks:
       - id: mypy
         additional_dependencies: [numpy>=1.23]
         exclude: docs
   - repo: https://github.com/psf/black
-    rev: 24.8.0
+    rev: 24.10.0
     hooks:
       - id: black
         additional_dependencies: [toml]
@@ -22,7 +22,7 @@ repos:
     hooks:
       - id: prettier
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v5.0.0
     hooks:
       - id: detect-private-key
       - id: check-merge-conflict
@@ -45,11 +45,11 @@ repos:
       - id: check-toml
       - id: requirements-txt-fixer
   - repo: https://github.com/asottile/blacken-docs
-    rev: 1.18.0
+    rev: 1.19.1
     hooks:
       - id: blacken-docs
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.6.8
+    rev: v0.8.3
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]

src/napari_spatialdata/_scatterwidgets.py

@@ -489,6 +489,7 @@ def clear_hover_highlight(self) -> None:
     def use_auto_range(self) -> None:
         """Default display of the graph."""
         if self.lut is not None:
+            assert self.color_vec is not None
             color_min = self.color_vec.min()
             color_max = self.color_vec.max()
 
@@ -803,6 +804,7 @@ def create_lut_hist(self) -> pg.HistogramLUTItem:
         st["ticksVisible"] = False
         lut.gradient.restoreState(st)
 
+        assert self.color_vec is not None
         y, x = np.histogram(self.color_vec, bins="auto")
         lut.plot.setData(
             np.concatenate([[np.min(self.color_vec)], (x[:-1] + x[1:]) / 2, [np.max(self.color_vec)]]),
@@ -867,13 +869,15 @@ def get_brushes(self, event: Any = None) -> list[QColor] | None:
         # for discrete data
         if self.discrete_color_widget is not None:
 
+            assert self.color_vec is not None
             return [pg.mkBrush(*x) for x in self.discrete_color_widget.palette.map(self.color_vec + 1) * 255]
 
         # for continuos data
         if self.lut is not None:
 
             level_min, level_max = self.lut.getLevels()
 
+            assert self.color_vec is not None
             data = np.clip(self.color_vec, level_min, level_max)
             data = (data - level_min) / (level_max - level_min)
 

src/napari_spatialdata/_view.py

@@ -416,7 +416,7 @@ def viewer(self) -> napari.Viewer:
     @property
     def model(self) -> DataModel:
         """:mod:`napari` viewer."""
-        return self._model  # type: ignore[no-any-return]
+        return self._model
 
 
 class QtAdataViewWidget(QWidget):
@@ -681,7 +681,7 @@ def viewer(self) -> napari.Viewer:
     @property
     def model(self) -> DataModel:
         """:mod:`napari` viewer."""
-        return self._model  # type: ignore[no-any-return]
+        return self._model
 
     @property
     def layernames(self) -> frozenset[str]:

src/napari_spatialdata/_viewer.py

@@ -419,8 +419,8 @@ def inherit_metadata(self, layers: list[Layer], ref_layer: Layer) -> None:
 
     def _get_table_data(
         self, sdata: SpatialData, element_name: str
-    ) -> tuple[AnnData | None, str | None, list[str | None]]:
-        table_names = list(get_element_annotators(sdata, element_name))
+    ) -> tuple[AnnData | None, str | None, list[str] | None]:
+        table_names: list[str] = list(get_element_annotators(sdata, element_name))
         table_name = table_names[0] if len(table_names) > 0 else None
         adata = _get_init_metadata_adata(sdata, table_name, element_name)
         return adata, table_name, table_names

src/napari_spatialdata/_widgets.py

@@ -202,8 +202,10 @@ def _get_points_properties(self, vec: ArrayLike | pd.Series, **kwargs: Any) -> d
     @_get_points_properties.register(pd.Series)
     def _(self, vec: pd.Series, **kwargs: Any) -> dict[str, Any]:
         layer = kwargs.pop("layer", None)
-        layer_meta = self.model.layer.metadata if self.model.layer is not None else None
-        element_indices = pd.Series(layer_meta["indices"], name="element_indices")
+        layer_metadata = self.model.layer.metadata if self.model.layer is not None else None
+        if layer_metadata is None:
+            raise ValueError("Layer metadata is not available.")
+        element_indices = pd.Series(layer_metadata["indices"], name="element_indices")
         if isinstance(layer, Labels):
             element_indices = element_indices[element_indices != 0]
         # When merging if the row is not present in the other table it will be nan so we can give it a default color
@@ -276,8 +278,10 @@ def _(self, vec: ArrayLike, **kwargs: Any) -> dict[str, Any]:
         else:
             instance_key_col = self.model.adata.obs[self.model.instance_key]
             vec = pd.Series(vec, name="vec", index=instance_key_col)
-            layer_meta = self.model.layer.metadata if self.model.layer is not None else None
-            element_indices = pd.Series(layer_meta["indices"], name="element_indices")
+            layer_metadata = self.model.layer.metadata if self.model.layer is not None else None
+            if layer_metadata is None:
+                raise ValueError("Layer metadata is not available.")
+            element_indices = pd.Series(layer_metadata["indices"], name="element_indices")
             if isinstance(layer, Labels):
                 vec = vec.drop(index=0) if 0 in vec.index else vec
             # element_indices = element_indices[element_indices != 0]

src/napari_spatialdata/utils/_utils.py

@@ -369,7 +369,7 @@ def get_elements_meta_mapping(
     return elements, name_to_add
 
 
-def _get_init_metadata_adata(sdata: SpatialData, table_name: str, element_name: str) -> None | AnnData:
+def _get_init_metadata_adata(sdata: SpatialData, table_name: str | None, element_name: str) -> None | AnnData:
     """
     Retrieve AnnData to be used in layer metadata.