Update pre-commit hooks

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: avl
       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=_tsinfer ]
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.19.1
+    rev: v3.20.0
     hooks:
       - id: pyupgrade
         args: [ --py3-plus, --py39-plus ]
@@ -29,14 +29,14 @@ repos:
       - id: black
         language_version: python3
   - repo: https://github.com/asottile/blacken-docs
-    rev: 1.19.1
+    rev: 1.20.0
     hooks:
       - id: blacken-docs
         args: [--skip-errors]
         additional_dependencies: [black==22.3.0]
         language_version: python3
   - repo: https://github.com/pycqa/flake8
-    rev: 7.1.2
+    rev: 7.3.0
     hooks:
       - id: flake8
         args: [--config=.flake8]

docs/simulation-example.py

@@ -23,7 +23,7 @@
 ts = msprime.sim_mutations(ts, rate=1e-8, random_seed=7)
 ts.dump(name + "-source.trees")
 print(
-    f"Simulated {ts.num_samples} samples over {seq_len/1e6} Mb:",
+    f"Simulated {ts.num_samples} samples over {seq_len / 1e6} Mb:",
     f"{ts.num_trees} trees and {ts.num_sites} sites",
 )
 

tests/test_inference.py

@@ -1411,8 +1411,10 @@ def test_equivalance_many_at_once(self, tmp_path, tmpdir):
             num_groupings,
             2,
         )
-        assert (tmpdir / "work" / f"ancestors_{(num_groupings//2)-1}.trees").exists()
-        assert (tmpdir / "work" / f"ancestors_{num_groupings-1}.trees").exists()
+        assert (
+            tmpdir / "work" / f"ancestors_{(num_groupings // 2) - 1}.trees"
+        ).exists()
+        assert (tmpdir / "work" / f"ancestors_{num_groupings - 1}.trees").exists()
         ts = tsinfer.match_ancestors_batch_finalise(tmpdir / "work")
         ts2 = tsinfer.match_ancestors(samples, ancestors)
         ts.tables.assert_equals(ts2.tables, ignore_provenance=True)

tests/test_variantdata.py

@@ -875,7 +875,7 @@ def test_ancestral_missing_info(tmp_path, caplog):
     anc_state[15] = "n"
     with caplog.at_level(logging.INFO):
         vdata = tsinfer.VariantData(zarr_path, anc_state)
-    assert f"4 sites ({4/ts.num_sites * 100 :.2f}%) were deliberately " in caplog.text
+    assert f"4 sites ({4 / ts.num_sites * 100 :.2f}%) were deliberately " in caplog.text
     inf_ts = tsinfer.infer(vdata)
     for i, (inf_var, var) in enumerate(zip(inf_ts.variants(), ts.variants())):
         if i in [0, 11, 12, 15]:

tsinfer/inference.py

@@ -848,7 +848,7 @@ def match_ancestors_batch_groups(
             ancestors_ts = None
         else:
             ancestors_ts = tskit.load(
-                os.path.join(work_dir, f"ancestors_{group_index_start-1}.trees")
+                os.path.join(work_dir, f"ancestors_{group_index_start - 1}.trees")
             )
         matcher = initialize_ancestor_matcher(
             metadata, ancestors_ts, num_threads=num_threads
@@ -859,7 +859,7 @@ def match_ancestors_batch_groups(
                 for group_index in range(group_index_start, group_index_end)
             }
         )
-        path = os.path.join(work_dir, f"ancestors_{group_index_end-1}.trees")
+        path = os.path.join(work_dir, f"ancestors_{group_index_end - 1}.trees")
         logger.info(f"Dumping to {path}")
         ts.dump(path)
     with open(path + ".resources", "w") as f:
@@ -898,7 +898,7 @@ def match_ancestors_batch_group_partition(work_dir, group_index, partition_index
 
     with provenance.TimingAndMemory() as timing:
         ancestors_ts = tskit.load(
-            os.path.join(work_dir, f"ancestors_{group_index-1}.trees")
+            os.path.join(work_dir, f"ancestors_{group_index - 1}.trees")
         )
         matcher = initialize_ancestor_matcher(metadata, ancestors_ts)
         ancestors_to_match = group["partitions"][partition_index]
@@ -935,7 +935,7 @@ def match_ancestors_batch_group_finalise(work_dir, group_index):
             metadata = json.load(f)
         group = metadata["ancestor_grouping"][group_index]
         ancestors_ts = tskit.load(
-            os.path.join(work_dir, f"ancestors_{group_index-1}.trees")
+            os.path.join(work_dir, f"ancestors_{group_index - 1}.trees")
         )
         matcher = initialize_ancestor_matcher(metadata, ancestors_ts)
         logger.info(