diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 26408286..bb551a39 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -10,7 +10,7 @@ default_language_version:
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v5.0.0
+    rev: v6.0.0
     hooks:
       - id: check-added-large-files
         args:
@@ -44,22 +44,22 @@ repos:
         args:
           - --strict
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.11.12
+    rev: v0.13.3
     hooks:
       - id: ruff
       - id: ruff-format
   - repo: https://github.com/adamchainz/blacken-docs
-    rev: 1.19.1
+    rev: 1.20.0
     hooks:
       - id: blacken-docs
         additional_dependencies:
           - black
   - repo: https://github.com/pappasam/toml-sort
-    rev: v0.24.2
+    rev: v0.24.3
     hooks:
       - id: toml-sort-fix
   - repo: https://github.com/rbubley/mirrors-prettier
-    rev: v3.5.3
+    rev: v3.6.2
     hooks:
       - id: prettier
   - repo: https://github.com/igorshubovych/markdownlint-cli
@@ -77,7 +77,7 @@ repos:
     hooks:
       - id: actionlint
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.16.0
+    rev: v1.18.2
     hooks:
       - id: mypy
         files: ^glass/
diff --git a/examples/1-basic/density.ipynb b/examples/1-basic/density.ipynb
index 689c057e..9d5b70d1 100644
--- a/examples/1-basic/density.ipynb
+++ b/examples/1-basic/density.ipynb
@@ -161,7 +161,7 @@
     "            axis=1,\n",
     "            return_counts=True,\n",
     "        )\n",
-    "        cube[*indices] += count"
+    "        cube[tuple(indices)] += count"
    ]
   },
   {
diff --git a/glass/_array_api_utils.py b/glass/_array_api_utils.py
index 66d8a1da..ddacdb4b 100644
--- a/glass/_array_api_utils.py
+++ b/glass/_array_api_utils.py
@@ -58,7 +58,8 @@ class Generator:
     __slots__ = ("rng",)
 
     def __init__(
-        self, seed: int | bool | NDArray[np.int_ | np.bool] | None = None
+        self,
+        seed: int | bool | NDArray[np.int_ | np.bool] | None = None,  # noqa: FBT001
     ) -> None:
         self.rng = numpy.random.default_rng(seed=seed)  # type: ignore[arg-type]
 
diff --git a/glass/fields.py b/glass/fields.py
index 2fbc722c..70e087a5 100644
--- a/glass/fields.py
+++ b/glass/fields.py
@@ -42,8 +42,8 @@
 
     def deprecated(msg: str, /) -> Callable[[Callable[_P, _R]], Callable[_P, _R]]:  # type: ignore[no-redef]
         """Backport of Python's warnings.deprecated()."""
-        from functools import wraps
-        from warnings import warn
+        from functools import wraps  # noqa: PLC0415
+        from warnings import warn  # noqa: PLC0415
 
         def decorator(func: Callable[_P, _R], /) -> Callable[_P, _R]:
             @wraps(func)
@@ -1102,9 +1102,9 @@ def regularized_spectra(
     # regularise the cov matrix using the chosen method
     cov_method: Callable[..., NDArray[Any]]
     if method == "clip":
-        from glass.algorithm import cov_clip as cov_method
+        from glass.algorithm import cov_clip as cov_method  # noqa: PLC0415
     elif method == "nearest":
-        from glass.algorithm import cov_nearest as cov_method
+        from glass.algorithm import cov_nearest as cov_method  # noqa: PLC0415
     else:
         msg = f"unknown method '{method}'"  # type: ignore[unreachable]
         raise ValueError(msg)
diff --git a/glass/grf/_core.py b/glass/grf/_core.py
index e9e8243c..0b97367d 100644
--- a/glass/grf/_core.py
+++ b/glass/grf/_core.py
@@ -59,8 +59,8 @@ def dispatch(
     def add(
         impl: Callable[[TransformationT, TransformationT, NDArray[Any]], NDArray[Any]],
     ) -> Callable[[TransformationT, TransformationT, NDArray[Any]], NDArray[Any]]:
-        from inspect import signature
-        from typing import get_type_hints
+        from inspect import signature  # noqa: PLC0415
+        from typing import get_type_hints  # noqa: PLC0415
 
         sig = signature(impl)
         if len(sig.parameters) != 3:
diff --git a/glass/shells.py b/glass/shells.py
index 89025e22..3f85a998 100644
--- a/glass/shells.py
+++ b/glass/shells.py
@@ -757,7 +757,7 @@ def partition_restrict(
         The partition.
 
     """
-    part = np.empty((len(shells),) + np.shape(fz)[:-1])
+    part = np.empty((len(shells), *np.shape(fz)[:-1]))
     for i, w in enumerate(shells):
         zr, fr = restrict(z, fz, w)
         part[i] = np.trapezoid(fr, zr, axis=-1)
diff --git a/glass/user.py b/glass/user.py
index d6a14751..9fb3fdb2 100644
--- a/glass/user.py
+++ b/glass/user.py
@@ -193,7 +193,7 @@ def write_catalog(
         The writer object.
 
     """
-    import fitsio
+    import fitsio  # noqa: PLC0415
 
     with fitsio.FITS(filename, "rw", clobber=True) as fits:
         fits.write(None)