Format code in docstrings with Ruff

.pre-commit-config.yaml

@@ -3,11 +3,14 @@ repos:
     rev: v0.1.8
     hooks:
     -   id: ruff
+        types_or: [python, pyi, jupyter]
         args: ["--fix"]
     -   id: ruff-format
+        types_or: [python, pyi, jupyter]
     # The following can be removed once PLR0917 is out of preview
     -   name: ruff preview rules
         id: ruff
+        types_or: [python, pyi, jupyter]
         args: ["--preview", "--select=PLR0917"]
 -   repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.5.0

pyproject.toml

@@ -194,7 +194,10 @@ exclude_also = [
     "if TYPE_CHECKING:",
 ]
 
-[tool.ruff]
+[tool.ruff.format]
+docstring-code-format = true
+
+[tool.ruff.lint]
 select = [
     "E",       # Error detected by Pycodestyle
     "F",       # Errors detected by Pyflakes
@@ -217,13 +220,13 @@ ignore = [
     # allow I, O, l as variable names -> I is the identity matrix, i, j, k, l is reasonable indexing notation
     "E741",
 ]
-[tool.ruff.per-file-ignores]
+[tool.ruff.lint.per-file-ignores]
 # Do not assign a lambda expression, use a def
 "scanpy/tools/_rank_genes_groups.py" = ["E731"]
-[tool.ruff.isort]
+[tool.ruff.lint.isort]
 known-first-party = ["scanpy"]
 required-imports = ["from __future__ import annotations"]
-[tool.ruff.flake8-tidy-imports.banned-api]
+[tool.ruff.lint.flake8-tidy-imports.banned-api]
 "pytest.importorskip".msg = "Use the “@needs” decorator/mark instead"
 "pandas.api.types.is_categorical_dtype".msg = "Use isinstance(s.dtype, CategoricalDtype) instead"
 "pandas.value_counts".msg = "Use pd.Series(a).value_counts() instead"

scanpy/external/pp/_hashsolo.py

@@ -332,7 +332,7 @@ def hashsolo(
     >>> import anndata
     >>> import scanpy.external as sce
     >>> adata = anndata.read_h5ad("data.h5ad")
-    >>> sce.pp.hashsolo(adata, ['Hash1', 'Hash2', 'Hash3'])
+    >>> sce.pp.hashsolo(adata, ["Hash1", "Hash2", "Hash3"])
     >>> adata.obs.head()
     """
     print(

scanpy/neighbors/__init__.py

@@ -440,7 +440,7 @@ def transitions(self) -> np.ndarray | csr_matrix:
 
         Is conjugate to the symmetrized transition matrix via::
 
-            self.transitions = self.Z *  self.transitions_sym / self.Z
+            self.transitions = self.Z * self.transitions_sym / self.Z
 
         where ``self.Z`` is the diagonal matrix storing the normalization of the
         underlying kernel matrix.
@@ -461,7 +461,7 @@ def transitions_sym(self) -> np.ndarray | csr_matrix | None:
 
         Is conjugate to the transition matrix via::
 
-            self.transitions_sym = self.Z /  self.transitions * self.Z
+            self.transitions_sym = self.Z / self.transitions * self.Z
 
         where ``self.Z`` is the diagonal matrix storing the normalization of the
         underlying kernel matrix.

scanpy/plotting/_baseplot_class.py

@@ -814,8 +814,8 @@ def show(self, return_axes: bool | None = None):
         -------
         >>> import scanpy as sc
         >>> adata = sc.datasets.pbmc68k_reduced()
-        >>> markers = ['C1QA', 'PSAP', 'CD79A', 'CD79B', 'CST3', 'LYZ']
-        >>> sc.pl._baseplot_class.BasePlot(adata, markers, groupby='bulk_labels').show()
+        >>> markers = ["C1QA", "PSAP", "CD79A", "CD79B", "CST3", "LYZ"]
+        >>> sc.pl._baseplot_class.BasePlot(adata, markers, groupby="bulk_labels").show()
         """
 
         self.make_figure()
@@ -848,8 +848,10 @@ def savefig(self, filename: str, bbox_inches: str | None = "tight", **kwargs):
         -------
         >>> import scanpy as sc
         >>> adata = sc.datasets.pbmc68k_reduced()
-        >>> markers = ['C1QA', 'PSAP', 'CD79A', 'CD79B', 'CST3', 'LYZ']
-        >>> sc.pl._baseplot_class.BasePlot(adata, markers, groupby='bulk_labels').savefig('plot.pdf')
+        >>> markers = ["C1QA", "PSAP", "CD79A", "CD79B", "CST3", "LYZ"]
+        >>> sc.pl._baseplot_class.BasePlot(adata, markers, groupby="bulk_labels").savefig(
+        ...     "plot.pdf"
+        ... )
         """
         self.make_figure()
         plt.savefig(filename, bbox_inches=bbox_inches, **kwargs)