[pre-commit.ci] pre-commit autoupdate (#852)

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

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.8.6 → v0.9.1](astral-sh/ruff-pre-commit@v0.8.6...v0.9.1)

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

---------

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

.pre-commit-config.yaml

@@ -11,7 +11,7 @@ repos:
       hooks:
           - id: prettier
     - repo: https://github.com/astral-sh/ruff-pre-commit
-      rev: v0.8.6
+      rev: v0.9.1
       hooks:
           - id: ruff
             args: [--fix, --exit-non-zero-on-fix, --unsafe-fixes]

docs/_ext/typed_returns.py

@@ -10,7 +10,7 @@ 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
 

ehrapy/_settings.py

@@ -144,7 +144,7 @@ def file_format_data(self, file_format: str):
         _type_check(file_format, "file_format_data", str)
         file_format_options = {"csv", "h5ad"}
         if file_format not in file_format_options:
-            raise ValueError(f"Cannot set file_format_data to {file_format}. " f"Must be one of {file_format_options}")
+            raise ValueError(f"Cannot set file_format_data to {file_format}. Must be one of {file_format_options}")
         self._file_format_data = file_format
 
     @property
@@ -237,7 +237,7 @@ def cache_compression(self) -> str | None:
     @cache_compression.setter
     def cache_compression(self, cache_compression: str | None):
         if cache_compression not in {"lzf", "gzip", None}:
-            raise ValueError(f"`cache_compression` ({cache_compression}) " "must be in {'lzf', 'gzip', None}")
+            raise ValueError(f"`cache_compression` ({cache_compression}) must be in {{'lzf', 'gzip', None}}")
         self._cache_compression = cache_compression
 
     @property

ehrapy/anndata/_feature_specifications.py

@@ -113,7 +113,7 @@ def infer_feature_types(
 
     if verbose:
         logger.warning(
-            f"{'Features' if len(uncertain_features) >1 else 'Feature'} {str(uncertain_features)[1:-1]} {'were' if len(uncertain_features) >1 else 'was'} detected as categorical features stored numerically."
+            f"{'Features' if len(uncertain_features) > 1 else 'Feature'} {str(uncertain_features)[1:-1]} {'were' if len(uncertain_features) > 1 else 'was'} detected as categorical features stored numerically."
             f"Please verify and correct using `ep.ad.replace_feature_types` if necessary."
         )
 

ehrapy/core/meta_information.py

@@ -23,7 +23,7 @@ def print_version_and_date(*, file=None):  # pragma: no cover
     if file is None:
         file = sys.stdout
     print(
-        f"Running ehrapy {__version__}, " f"on {datetime.now():%Y-%m-%d %H:%M}.",
+        f"Running ehrapy {__version__}, on {datetime.now():%Y-%m-%d %H:%M}.",
         file=file,
     )
 

ehrapy/plot/_scanpy_pl_api.py

@@ -1188,7 +1188,10 @@ def tsne(adata, **kwargs) -> Axes | list[Axes] | None:  # pragma: no cover
         .. image:: /_static/docstring_previews/tsne_1.png
 
         >>> ep.pl.tsne(
-        ...     adata, color=["day_icu_intime", "service_unit"], wspace=0.5, title=["Day of ICU admission", "Service unit"]
+        ...     adata,
+        ...     color=["day_icu_intime", "service_unit"],
+        ...     wspace=0.5,
+        ...     title=["Day of ICU admission", "Service unit"],
         ... )
 
         .. image:: /_static/docstring_previews/tsne_2.png
@@ -1233,7 +1236,10 @@ def umap(adata: AnnData, **kwargs) -> Axes | list[Axes] | None:  # pragma: no co
         .. image:: /_static/docstring_previews/umap_1.png
 
         >>> ep.pl.umap(
-        ...     adata, color=["day_icu_intime", "service_unit"], wspace=0.5, title=["Day of ICU admission", "Service unit"]
+        ...     adata,
+        ...     color=["day_icu_intime", "service_unit"],
+        ...     wspace=0.5,
+        ...     title=["Day of ICU admission", "Service unit"],
         ... )
 
         .. image:: /_static/docstring_previews/umap_2.png

tests/preprocessing/test_quality_control.py

@@ -200,9 +200,9 @@ def test_qc_lab_measurements_multiple_measurements():
 def test_mcar_test_method_output_types(mar_adata, method, expected_output_type):
     """Tests if mcar_test returns the correct output type for different methods."""
     output = mcar_test(mar_adata, method=method)
-    assert isinstance(
-        output, expected_output_type
-    ), f"Output type for method '{method}' should be {expected_output_type}, got {type(output)} instead."
+    assert isinstance(output, expected_output_type), (
+        f"Output type for method '{method}' should be {expected_output_type}, got {type(output)} instead."
+    )
 
 
 def test_mar_data_identification(mar_adata):