Fix and update pre-commit

Author: benjeffery

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.1.0
+    rev: v4.3.0
     hooks:
       - id: check-merge-conflict
       - id: debug-statements
@@ -12,33 +12,33 @@ repos:
     hooks:
     -   id: copyright-year
   - repo: https://github.com/benjeffery/pre-commit-clang-format
-    rev: c21a74d089aaeb86c2c19df371c7e7bf40c07207
+    rev: '1.0'
     hooks:
     - id: clang-format
       exclude: dev-tools|examples
       verbose: true
   - repo: https://github.com/asottile/reorder_python_imports
-    rev: v3.0.1
+    rev: v3.9.0
     hooks:
       - id: reorder-python-imports
         args: [--application-directories=python,
                --unclassifiable-application-module=_tskit]
   - repo: https://github.com/asottile/pyupgrade
-    rev: v2.31.1
+    rev: v3.2.2
     hooks:
       - id: pyupgrade
         args: [--py3-plus, --py37-plus]
   - repo: https://github.com/psf/black
-    rev: 22.3.0
+    rev: 22.10.0
     hooks:
       - id: black
         language_version: python3
-  - repo: https://gitlab.com/pycqa/flake8
-    rev: 3.9.2
+  - repo: https://github.com/pycqa/flake8
+    rev: 5.0.4
     hooks:
       - id: flake8
         args: [--config=python/.flake8]
-        additional_dependencies: ["flake8-bugbear==22.3.23", "flake8-builtins==1.5.3"]
+        additional_dependencies: ["flake8-bugbear==22.10.27", "flake8-builtins==2.0.1"]
   - repo: https://github.com/asottile/blacken-docs
     rev: v1.12.1
     hooks:

python/tests/test_drawing.py

@@ -2407,7 +2407,7 @@ def verify_known_svg(self, svg, filename, save=False, **kwargs):
         svg_fn = pathlib.Path(__file__).parent / "data" / "svg" / filename
         if save:
             logging.warning(f"Overwriting SVG file `{svg_fn}` with new version")
-            with open(svg_fn, "wt") as file:
+            with open(svg_fn, "w") as file:
                 file.write(svg)
         with open(svg_fn, "rb") as file:
             expected_svg = file.read()

python/tests/test_lowlevel.py

@@ -2318,22 +2318,26 @@ def test_summary_func_errors(self):
         for exception in [ValueError, TypeError]:
 
             def f(x):
-                raise exception("test")
+                raise exception("test")  # noqa: B023
 
             with pytest.raises(exception):
                 ts.general_stat(W, f, 1, ts.get_breakpoints())
 
         # Wrong output dimensions
         for bad_array in [[1, 1], range(10)]:
             with pytest.raises(ValueError):
-                ts.general_stat(W, lambda x: bad_array, 1, ts.get_breakpoints())
+                ts.general_stat(
+                    W, lambda x: bad_array, 1, ts.get_breakpoints()  # noqa:B023
+                )
         with pytest.raises(ValueError):
             ts.general_stat(W, lambda x: [1], 2, ts.get_breakpoints())
 
         # Bad arrays returned from f
         for bad_array in [["sdf"], 0, "w4", None]:
             with pytest.raises(ValueError):
-                ts.general_stat(W, lambda x: bad_array, 1, ts.get_breakpoints())
+                ts.general_stat(
+                    W, lambda x: bad_array, 1, ts.get_breakpoints()  # noqa:B023
+                )
 
 
 class TestVariant(LowLevelTestCase):