diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 6c747ba1..e4bb9835 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -7,13 +7,13 @@ default_stages:
 minimum_pre_commit_version: 3.0.0
 repos:
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.14.1
+    rev: v1.15.0
     hooks:
       - id: mypy
         additional_dependencies: [numpy>=1.25.0]
         files: ^src
   - repo: https://github.com/psf/black
-    rev: 24.10.0
+    rev: 25.1.0
     hooks:
       - id: black
         additional_dependencies: [toml]
@@ -23,7 +23,7 @@ repos:
       - id: prettier
         language_version: system
   - repo: https://github.com/PyCQA/isort
-    rev: 5.13.2
+    rev: 6.0.0
     hooks:
       - id: isort
         additional_dependencies: [toml]
@@ -63,7 +63,7 @@ repos:
       - id: doc8
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.9.3
+    rev: v0.9.6
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]
diff --git a/src/moscot/base/solver.py b/src/moscot/base/solver.py
index b2068007..bd4e736f 100644
--- a/src/moscot/base/solver.py
+++ b/src/moscot/base/solver.py
@@ -41,7 +41,7 @@ def _get_array_data(
         **kwargs: Any,
     ) -> TaggedArrayData:
         def to_tuple(
-            data: Optional[Union[ArrayLike, Tuple[ArrayLike, ArrayLike]]]
+            data: Optional[Union[ArrayLike, Tuple[ArrayLike, ArrayLike]]],
         ) -> Tuple[Optional[ArrayLike], Optional[ArrayLike]]:
             if not isinstance(data, tuple):
                 return data, None
diff --git a/src/moscot/plotting/_utils.py b/src/moscot/plotting/_utils.py
index d21c3e91..32f4617c 100644
--- a/src/moscot/plotting/_utils.py
+++ b/src/moscot/plotting/_utils.py
@@ -358,7 +358,7 @@ def _contrasting_color(r: int, g: int, b: int) -> str:
 
 
 def _input_to_adatas(
-    inp: Union[AnnData, Tuple[AnnData, AnnData], "CompoundProblem"]  # type: ignore[type-arg]
+    inp: Union[AnnData, Tuple[AnnData, AnnData], "CompoundProblem"],  # type: ignore[type-arg]
 ) -> Tuple[AnnData, AnnData]:
     from moscot.base.problems import CompoundProblem