Fix and update pre-commit

Author: Ben Jeffery

.pre-commit-config.yaml

@@ -1,30 +1,30 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.1.0
+    rev: v4.4.0
     hooks:
       - id: check-merge-conflict
       - id: debug-statements
       - id: mixed-line-ending
       - id: check-case-conflict
       - id: check-yaml
   - repo: https://github.com/benjeffery/pre-commit-clang-format
-    rev: c21a74d089aaeb86c2c19df371c7e7bf40c07207
+    rev: '1.0'
     hooks:
     - id: clang-format
       exclude: avl
       verbose: true
   - repo: https://github.com/asottile/reorder_python_imports
-    rev: v3.0.1
+    rev: v3.9.0
     hooks:
       - id: reorder-python-imports
         args: [ --unclassifiable-application-module=_tsinfer ]
   - 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
@@ -35,9 +35,9 @@ repos:
         args: [--skip-errors]
         additional_dependencies: [black==22.3.0]
         language_version: python3
-  - repo: https://gitlab.com/pycqa/flake8
-    rev: 3.9.2
+  - repo: https://github.com/pycqa/flake8
+    rev: 6.0.0
     hooks:
       - id: flake8
         args: [--config=.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"]

tests/test_cli.py

@@ -403,7 +403,7 @@ def test_infer(self):
     )
     def test_map(self):
         ratemap = os.path.join(self.tempdir.name, "ratemap.txt")
-        with open(ratemap, "wt") as map:
+        with open(ratemap, "w") as map:
             print("Chromosome  Position(bp)  Rate(cM/Mb)  Map(cM)", file=map)
             print("chr1 0 0.1 0", file=map)
             print("chr1 1 0.2 0.002", file=map)
@@ -428,7 +428,7 @@ def test_fails_on_bad_map(self):
         sd = tsinfer.load(self.sample_file)
         last_pos = sd.sites_position[-1]
         assert last_pos > 2
-        with open(ratemap, "wt") as map:
+        with open(ratemap, "w") as map:
             print("Chromosome  Position(bp)  Rate(cM/Mb)  Map(cM)", file=map)
             print("chr1 0 0.1 0.0", file=map)
             print(f"chr1 {int(last_pos) - 1} 0.2 0.001", file=map)