Update pre-commit

Author: benjeffery

.pre-commit-config.yaml

@@ -1,29 +1,29 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v3.4.0
+    rev: v4.5.0
     hooks:
       - id: check-merge-conflict
       - id: debug-statements
       - id: mixed-line-ending
       - id: check-case-conflict
       - id: check-yaml
   - repo: https://github.com/asottile/reorder_python_imports
-    rev: v2.4.0
+    rev: v3.12.0
     hooks:
       - id: reorder-python-imports
   - repo: https://github.com/asottile/pyupgrade
-    rev: v2.12.0
+    rev: v3.15.0
     hooks:
       - id: pyupgrade
         args: [--py3-plus, --py36-plus]
   - repo: https://github.com/psf/black
-    rev: 20.8b1
+    rev: 23.9.1
     hooks:
       - id: black
         language_version: python3
-  - repo: https://gitlab.com/pycqa/flake8
-    rev: 3.9.1
+  - repo: https://github.com/pycqa/flake8
+    rev: 6.1.0
     hooks:
       - id: flake8
         args: [--config=.flake8]
-        additional_dependencies: ["flake8-bugbear==20.1.4", "flake8-builtins==1.5.3"]
+        additional_dependencies: ["flake8-bugbear==23.9.16", "flake8-builtins==2.1.0"]

tests/test_compression.py

@@ -57,36 +57,36 @@ def test_int16(self):
         self.verify(
             np.int16,
             np.array(
-                [2 ** 15 - 1, -(2 ** 15) + 1, 2 ** 7 + 1, -(2 ** 7) - 1], dtype=np.int64
+                [2**15 - 1, -(2**15) + 1, 2**7 + 1, -(2**7) - 1], dtype=np.int64
             ),
         )
 
     def test_uint16(self):
-        self.verify(np.uint16, np.array([256, 2 ** 16 - 1], dtype=np.uint64))
+        self.verify(np.uint16, np.array([256, 2**16 - 1], dtype=np.uint64))
 
     def test_int32(self):
         self.verify(
             np.int32,
             np.array(
-                [2 ** 31 - 1, -(2 ** 31) + 1, 2 ** 15 + 1, -(2 ** 15) - 1],
+                [2**31 - 1, -(2**31) + 1, 2**15 + 1, -(2**15) - 1],
                 dtype=np.int64,
             ),
         )
 
     def test_uint32(self):
-        self.verify(np.uint32, np.array([2 ** 16 + 1, 2 ** 32 - 1], dtype=np.uint64))
+        self.verify(np.uint32, np.array([2**16 + 1, 2**32 - 1], dtype=np.uint64))
 
     def test_int64(self):
         self.verify(
             np.int64,
             np.array(
-                [2 ** 63 - 1, -(2 ** 63) + 1, 2 ** 31 + 1, -(2 ** 31) - 1],
+                [2**63 - 1, -(2**63) + 1, 2**31 + 1, -(2**31) - 1],
                 dtype=np.int64,
             ),
         )
 
     def test_uint64(self):
-        self.verify(np.uint64, np.array([2 ** 32 + 1, 2 ** 64 - 1], dtype=np.uint64))
+        self.verify(np.uint64, np.array([2**32 + 1, 2**64 - 1], dtype=np.uint64))
 
     def test_float32(self):
         self.verify(np.float32, np.array([0.1, 1e-3], dtype=np.float32))

tszip/compression.py

@@ -107,7 +107,7 @@ def compress(ts, destination, variants_only=False):
         else:
             # Assume that destination is a file-like object open in "wb" mode.
             with open(filename, "rb") as source:
-                chunk_size = 2 ** 10  # 1MiB
+                chunk_size = 2**10  # 1MiB
                 for chunk in iter(functools.partial(source.read, chunk_size), b""):
                     destination.write(chunk)
 
@@ -167,7 +167,6 @@ def compress(self, root, compressor):
 
 
 def compress_zarr(ts, root, variants_only=False):
-
     provenance_dict = provenance.get_provenance_dict({"variants_only": variants_only})
 
     if variants_only:
@@ -345,12 +344,12 @@ def visitor(array):
 
     arrays.sort(key=lambda x: x.nbytes_stored)
     max_name_len = max(len(array.name) for array in arrays)
-    stored = [
+    storeds = [
         humanize.naturalsize(array.nbytes_stored, binary=True) for array in arrays
     ]
-    max_stored_len = max(len(size) for size in stored)
-    actual = [humanize.naturalsize(array.nbytes, binary=True) for array in arrays]
-    max_actual_len = max(len(size) for size in actual)
+    max_stored_len = max(len(size) for size in storeds)
+    actuals = [humanize.naturalsize(array.nbytes, binary=True) for array in arrays]
+    max_actual_len = max(len(size) for size in actuals)
 
     line = "File: {}\t{}".format(
         path, humanize.naturalsize(os.path.getsize(path), binary=True)
@@ -372,7 +371,7 @@ def visitor(array):
         "ratio",
     )
     print(line)
-    for array, stored, actual in zip(arrays, stored, actual):
+    for array, stored, actual in zip(arrays, storeds, actuals):
         ratio = 0
         if array.nbytes > 0:
             ratio = array.nbytes_stored / array.nbytes