[pre-commit.ci] pre-commit autoupdate

.pre-commit-config.yaml

@@ -5,7 +5,7 @@ default_stages:
 minimum_pre_commit_version: 2.9.3
 repos:
     - repo: https://github.com/astral-sh/ruff-pre-commit
-      rev: v0.8.1
+      rev: v0.9.1
       hooks:
           - id: ruff
             types_or: [python, pyi, jupyter]
@@ -17,7 +17,7 @@ repos:
       hooks:
           - id: blacken-docs
     - repo: https://github.com/pre-commit/mirrors-mypy
-      rev: v1.13.0
+      rev: v1.14.1
       hooks:
           - id: mypy
             additional_dependencies: [numpy, pandas, types-requests]

docs/_ext/typed_returns.py

@@ -12,7 +12,7 @@ def _process_return(lines: Iterable[str]) -> Iterator[str]:
         m = re.fullmatch(r"(?P<param>\w+)\s+:\s+(?P<type>[\w.]+)", line)
         if m:
             # Once this is in scanpydoc, we can use the fancy hover stuff
-            yield f'**{m["param"]}** : :class:`~{m["type"]}`'
+            yield f"**{m['param']}** : :class:`~{m['type']}`"
         else:
             yield line
 

src/squidpy/datasets/_dataset.py

@@ -74,8 +74,7 @@
 )
 _slideseqv2 = AMetadata(
     name="slideseqv2",
-    doc_header="Pre-processed SlideseqV2 dataset from `Stickles et al "
-    "<https://doi.org/10.1038/s41587-020-0739-1>`__.",
+    doc_header="Pre-processed SlideseqV2 dataset from `Stickles et al <https://doi.org/10.1038/s41587-020-0739-1>`__.",
     shape=(41786, 4000),
     url="https://ndownloader.figshare.com/files/28242783",
 )

src/squidpy/gr/_build.py

@@ -145,16 +145,16 @@ def spatial_neighbors(
         - :attr:`anndata.AnnData.uns`  ``['{{key_added}}']`` - :class:`dict` containing parameters.
     """
     if isinstance(adata, SpatialData):
-        assert (
-            elements_to_coordinate_systems is not None
-        ), "Since `adata` is a :class:`spatialdata.SpatialData`, `elements_to_coordinate_systems` must not be `None`."
-        assert (
-            table_key is not None
-        ), "Since `adata` is a :class:`spatialdata.SpatialData`, `table_key` must not be `None`."
+        assert elements_to_coordinate_systems is not None, (
+            "Since `adata` is a :class:`spatialdata.SpatialData`, `elements_to_coordinate_systems` must not be `None`."
+        )
+        assert table_key is not None, (
+            "Since `adata` is a :class:`spatialdata.SpatialData`, `table_key` must not be `None`."
+        )
         elements, table = match_element_to_table(adata, list(elements_to_coordinate_systems), table_key)
-        assert table.obs_names.equals(
-            adata.tables[table_key].obs_names
-        ), "The spatialdata table must annotate all elements keys. Some elements are missing, please check the `elements_to_coordinate_systems` dictionary."
+        assert table.obs_names.equals(adata.tables[table_key].obs_names), (
+            "The spatialdata table must annotate all elements keys. Some elements are missing, please check the `elements_to_coordinate_systems` dictionary."
+        )
         regions, region_key, instance_key = get_table_keys(adata.tables[table_key])
         regions = [regions] if isinstance(regions, str) else regions
         ordered_regions_in_table = adata.tables[table_key].obs[region_key].unique()

src/squidpy/gr/_ligrec.py

@@ -441,8 +441,7 @@ def test(
 
         if corr_method is not None:
             logg.info(
-                f"Performing FDR correction across the `{corr_axis.v}` "
-                f"using method `{corr_method}` at level `{alpha}`"
+                f"Performing FDR correction across the `{corr_axis.v}` using method `{corr_method}` at level `{alpha}`"
             )
             res["pvalues"] = _fdr_correct(res["pvalues"], corr_method, corr_axis, alpha=alpha)
 

src/squidpy/im/_container.py

@@ -802,8 +802,7 @@ def generate_spot_crops(
                 obs_library_ids = list(adata.obs[library_id])
             except KeyError:
                 logg.debug(
-                    f"Unable to find library ids in `adata.obs[{library_id!r}]`. "
-                    f"Trying in `adata.uns[{spatial_key!r}]`"
+                    f"Unable to find library ids in `adata.obs[{library_id!r}]`. Trying in `adata.uns[{spatial_key!r}]`"
                 )
                 library_id = Key.uns.library_id(adata, spatial_key=spatial_key, library_id=library_id)
                 if not isinstance(library_id, str):
@@ -1622,7 +1621,7 @@ def _repr_html_(self) -> str:
             )
             s += "</p>"
             if i == 9 and i < len(self) - 1:  # show only first 10 layers
-                s += f"<p style={style!r}>and {len(self) - i  - 1} more...</p>"
+                s += f"<p style={style!r}>and {len(self) - i - 1} more...</p>"
                 break
 
         return s