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
@@ -14,12 +14,12 @@ repos:
       exclude: argtable3
       verbose: true
   - repo: https://github.com/asottile/reorder_python_imports
-    rev: v3.14.0
+    rev: v3.15.0
     hooks:
       - id: reorder-python-imports
         args: [--unclassifiable-application-module=_msprime]
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.19.1
+    rev: v3.20.0
     hooks:
       - id: pyupgrade
         args: [--py38-plus]
@@ -29,7 +29,7 @@ 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=.flake8]

lib/util.c

@@ -676,7 +676,7 @@ fast_search_alloc(fast_search_t *self, const double *elements, size_t n_elements
      * of the array. The rest of the lookup element indexes point to (max_element *
      * query_multiplier) non-zero element values.
      */
-    self->num_lookups = 2 + (size_t) (max_element * self->query_multiplier);
+    self->num_lookups = 2 + (size_t)(max_element * self->query_multiplier);
 
     self->query_cutoff = ((double) self->num_lookups - 1) / self->query_multiplier;
 

msprime/core.py

@@ -69,7 +69,7 @@ def clear_seed_rng():
 
 
 def get_random_seed() -> int:
-    global _seed_rng_map
+    global _seed_rng_map  # noqa: F824
     pid = os.getpid()
     if pid not in _seed_rng_map:
         # If we don't provide a seed to Random(), Python will seed either
@@ -87,7 +87,7 @@ def set_seed_rng_seed(seed: int):
 
     DO NOT USE THIS FUNCTION!!!
     """
-    global _seed_rng_map
+    global _seed_rng_map  # noqa: F824
     pid = os.getpid()
     _seed_rng_map[pid] = random.Random(seed)