Update pre-commit hooks and fix linting issues

Author: benjeffery

.github/workflows/tests.yml

@@ -9,7 +9,7 @@ on:
 jobs:
   pre-commit:
     name: Lint
-    uses: tskit-dev/.github/.github/workflows/lint.yml@v1
+    uses: tskit-dev/.github/.github/workflows/lint.yml@v2
 
   test:
     name: Python

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v5.0.0
+    rev: v6.0.0
     hooks:
       - id: check-merge-conflict
       - id: debug-statements
@@ -14,13 +14,13 @@ repos:
       exclude: dev-tools|examples
       verbose: true
   - repo: https://github.com/asottile/reorder_python_imports
-    rev: v3.14.0
+    rev: v3.15.0
     hooks:
       - id: reorder-python-imports
         args: [--application-directories=python,
                --unclassifiable-application-module=_tskit]
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.19.1
+    rev: v3.20.0
     hooks:
       - id: pyupgrade
         args: [--py3-plus, --py38-plus]
@@ -30,13 +30,13 @@ repos:
       - id: black
         language_version: python3
   - repo: https://github.com/pycqa/flake8
-    rev: 7.1.2
+    rev: 7.3.0
     hooks:
       - id: flake8
         args: [--config=python/.flake8]
         additional_dependencies: ["flake8-bugbear==23.9.16", "flake8-builtins==2.1.0"]
   - repo: https://github.com/asottile/blacken-docs
-    rev: 1.19.1
+    rev: 1.20.0
     hooks:
       - id: blacken-docs
         args: [--skip-errors]

python/tests/test_tree_stats.py

@@ -53,7 +53,7 @@ def cached_np(func):
     cache = {}
 
     def f(*args):
-        nonlocal cache
+        nonlocal cache  # noqa: F824
         key = tuple(x.tobytes() for x in args)
         if key not in cache:
             cache[key] = func(*args)