test: bump the pre-commit group with 4 updates

.pre-commit-config.yaml

@@ -8,18 +8,18 @@ repos:
     - --drop=abstract
     groups: [format]
 - repo: https://github.com/biomejs/pre-commit
-  rev: v2.5.10
+  rev: v2.5.11
   hooks:
   - id: biome-format
     groups: [format]
     exclude: ^\.cruft\.json$ # inconsistent indentation with cruft - file never to be modified manually.
 - repo: https://github.com/tox-dev/pyproject-fmt
-  rev: v2.28.1
+  rev: v2.29.3
   hooks:
   - id: pyproject-fmt
     groups: [format]
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.16.4
+  rev: v0.16.5
   hooks:
   - id: ruff-check
     args: [--fix, --exit-non-zero-on-fix]
@@ -49,7 +49,7 @@ repos:
   - id: no-commit-to-branch
     args: [--branch=main]
 - repo: https://github.com/zizmorcore/zizmor-pre-commit
-  rev: v1.29.0
+  rev: v1.30.0
   hooks:
   - id: zizmor
     args: [--no-progress, --fix]

docs/usage-principles.md

@@ -56,9 +56,10 @@ to initialize an {class}`~anndata.AnnData` object. Possibly add further annotati
 
 ```python
 import pandas as pd
+
 anno = pd.read_csv(filename_sample_annotation)
-adata.obs['cell_groups'] = anno['cell_groups']  # categorical annotation of type pandas.Categorical
-adata.obs['time'] = anno['time']                # numerical annotation of type float
+# annotations of types pandas.Categorical and float
+adata.obs[["cell_groups", "time"]] = anno[["cell_groups", "time"]]
 # alternatively, you could also set the whole dataframe
 # adata.obs = anno
 ```

pyproject.toml

@@ -226,10 +226,18 @@ lint.pylint.max-positional-args = 5
 "pandas.api.types.is_categorical_dtype".msg = "Use isinstance(s.dtype, CategoricalDtype) instead"
 "pandas.value_counts".msg = "Use pd.Series(a).value_counts() instead"
 "pytest.importorskip".msg = "Use the “@needs” decorator/mark instead"
-"scipy.sparse.csc_array".msg = "Use _compat.CSCBase or _compat.CSBase for typing/type checks and add `# noqa: TID251` when constructing"
-"scipy.sparse.csc_matrix".msg = "Use _compat.CSCBase or _compat.CSBase for typing/type checks and add `# noqa: TID251` when constructing"
-"scipy.sparse.csr_array".msg = "Use _compat.CSRBase or _compat.CSBase for typing/type checks and add `# noqa: TID251` when constructing"
-"scipy.sparse.csr_matrix".msg = "Use _compat.CSRBase or _compat.CSBase for typing/type checks and add `# noqa: TID251` when constructing"
+"scipy.sparse.csc_array".msg = """\
+    Use _compat.CSCBase or _compat.CSBase for typing/type checks and add `# noqa: TID251` when constructing\
+    """
+"scipy.sparse.csc_matrix".msg = """\
+    Use _compat.CSCBase or _compat.CSBase for typing/type checks and add `# noqa: TID251` when constructing\
+    """
+"scipy.sparse.csr_array".msg = """\
+    Use _compat.CSRBase or _compat.CSBase for typing/type checks and add `# noqa: TID251` when constructing\
+    """
+"scipy.sparse.csr_matrix".msg = """\
+    Use _compat.CSRBase or _compat.CSBase for typing/type checks and add `# noqa: TID251` when constructing\
+    """
 "scipy.sparse.issparse".msg = "Use isinstance(_, _compat.CSBase) or isinstance(_, _compat.SpBase) instead"
 "scipy.sparse.sparray".msg = "Use _compat.SpBase instead"
 "scipy.sparse.spmatrix".msg = "Use _compat.SpBase instead"