chore: Update pre-commit hooks

.pre-commit-config.yaml

@@ -13,7 +13,7 @@ repos:
       - id: check-case-conflict
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.14.7
+    rev: v0.16.1
     hooks:
       - id: ruff-check
         types_or: [python, pyi, jupyter]
@@ -30,7 +30,7 @@ repos:
       - id: text-unicode-replacement-char
 
   - repo: https://github.com/rbubley/mirrors-prettier
-    rev: v3.7.3
+    rev: v3.9.6
     hooks:
       - id: prettier
         args: ["--cache-location=.prettier_cache/cache"]

src/bioframe/core/arrops.py

@@ -7,7 +7,7 @@
 INT64_MAX = np.iinfo(np.int64).max
 
 
-def natsort_key(s, _NS_REGEX=re.compile(r"(\d+)", re.U)):
+def natsort_key(s, _NS_REGEX=re.compile(r"(\d+)", re.UNICODE)):
     return tuple([int(x) if x.isdigit() else x for x in _NS_REGEX.split(s) if x])
 
 

src/bioframe/sandbox/clients.py

@@ -47,8 +47,7 @@ def __init__(self, cachedir, assembly, metadata=None):
                 with requests.get(self.METADATA_URL, stream=True) as r:
                     r.raise_for_status()
                     with open(metadata_path, "wb") as f:
-                        for chunk in r.iter_content(chunk_size=8192):
-                            f.write(chunk)
+                        f.writelines(r.iter_content(chunk_size=8192))
 
             self._meta = pd.read_table(metadata_path, low_memory=False)
             table_assemblies = sorted(

tests/test_ops.py

@@ -5,7 +5,7 @@
 import pytest
 
 import bioframe
-import bioframe.core.checks as checks
+from bioframe.core import checks
 from bioframe.core.construction import make_viewframe
 
 # import pyranges as pr