Updating pre-commit hooks

Author: jorenretel

.pre-commit-config.yaml

@@ -29,8 +29,8 @@ repos:
     hooks:
     -   id: mypy
         additional_dependencies:
-        -    pydantic==2.1.1
-        -    pydantic-settings==2.0.3
+        -    pydantic==2.12.4
+        -    pydantic-settings==2.12.0
         exclude: "^(build|docs|tests|benchmark|examples)"
 -   repo: https://github.com/asottile/pyupgrade
     rev: v3.10.1

bigwig_loader/bigwig.py

@@ -424,7 +424,7 @@ def _guess_max_rows_per_chunk(
         data_offsets = self.rtree_leaf_nodes["data_offset"]
         data_sizes = self.rtree_leaf_nodes["data_size"]
         if len(data_offsets) > sample_size:
-            sample_indices = sample(range(len(data_offsets)), sample_size)
+            sample_indices = sample(range(len(data_offsets)), sample_size)  # nosec
             data_offsets = data_offsets[sample_indices]
             data_sizes = data_sizes[sample_indices]
 

bigwig_loader/sampler/track_sampler.py

@@ -9,4 +9,6 @@ def __init__(self, total_number_of_tracks: int, sample_size: int):
 
     def __iter__(self) -> Iterator[list[int]]:
         while True:
-            yield sorted(sample(range(self.total_number_of_tracks), self.sample_size))
+            yield sorted(
+                sample(range(self.total_number_of_tracks), self.sample_size)  # nosec
+            )