From 920490ad1ad0c883f36537ee12ab3395782f97df Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 3 Aug 2026 16:29:14 +0000
Subject: [PATCH 1/2] chore: Update pre-commit hooks
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.14.7 → v0.16.1](https://github.com/astral-sh/ruff-pre-commit/compare/v0.14.7...v0.16.1)
- [github.com/rbubley/mirrors-prettier: v3.7.3 → v3.9.6](https://github.com/rbubley/mirrors-prettier/compare/v3.7.3...v3.9.6)
---
 .pre-commit-config.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 1ebd4d8..38cb6a9 100644
--- a/.pre-commit-config.yaml
+++ b/.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"]

From 03c72823c438b666966cf319b5c3b651f6792e30 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 3 Aug 2026 16:31:55 +0000
Subject: [PATCH 2/2] style: Pre-commit fixes

---
 src/bioframe/core/arrops.py     | 2 +-
 src/bioframe/sandbox/clients.py | 3 +--
 tests/test_ops.py               | 2 +-
 3 files changed, 3 insertions(+), 4 deletions(-)

diff --git a/src/bioframe/core/arrops.py b/src/bioframe/core/arrops.py
index ab8c752..ad8c2b6 100644
--- a/src/bioframe/core/arrops.py
+++ b/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])
 
 
diff --git a/src/bioframe/sandbox/clients.py b/src/bioframe/sandbox/clients.py
index 4218dcd..9c1f8c5 100644
--- a/src/bioframe/sandbox/clients.py
+++ b/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(
diff --git a/tests/test_ops.py b/tests/test_ops.py
index 66c0fd2..fd4d840 100644
--- a/tests/test_ops.py
+++ b/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