From 3afcc741a0875ff0d9aea62d2a6569b5cba23fb4 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 21 Sep 2026 17:57:45 +0000
Subject: [PATCH 1/2] [pre-commit.ci] pre-commit autoupdate
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

updates:
- [github.com/biomejs/pre-commit: 992342fc7460b8fe94b98b7e2f3e811d0bebdc5c → 221fa73eac76e0540995318b44e2efb2774af990](https://github.com/biomejs/pre-commit/compare/992342fc7460b8fe94b98b7e2f3e811d0bebdc5c...221fa73eac76e0540995318b44e2efb2774af990)
- [github.com/astral-sh/ruff-pre-commit: e8f7d69b957a30acb2c875078d5fd012de24b64c → 2eeb5678de71a00c0902cbda7105d328432f72cb](https://github.com/astral-sh/ruff-pre-commit/compare/e8f7d69b957a30acb2c875078d5fd012de24b64c...2eeb5678de71a00c0902cbda7105d328432f72cb)
---
 .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 9113eb7..95440e8 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -7,7 +7,7 @@ default_stages:
 minimum_pre_commit_version: 2.16.0
 repos:
   - repo: https://github.com/biomejs/pre-commit
-    rev: 992342fc7460b8fe94b98b7e2f3e811d0bebdc5c  # frozen: v2.5.13
+    rev: 221fa73eac76e0540995318b44e2efb2774af990  # frozen: v2.5.14
     hooks:
       - id: biome-format
         exclude: ^\.cruft\.json$ # inconsistent indentation with cruft - file never to be modified manually.
@@ -16,7 +16,7 @@ repos:
     hooks:
       - id: pyproject-fmt
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: e8f7d69b957a30acb2c875078d5fd012de24b64c  # frozen: v0.16.7
+    rev: 2eeb5678de71a00c0902cbda7105d328432f72cb  # frozen: v0.16.8
     hooks:
       - id: ruff-check
         types_or: [python, pyi, jupyter]

From 8dba8ba09b3831cd487eac1c225684d3187afb06 Mon Sep 17 00:00:00 2001
From: Ilia Kats <ilia-kats@gmx.net>
Date: Mon, 21 Sep 2026 20:16:24 +0200
Subject: [PATCH 2/2] silence anndata Zarr format deprecation warning

---
 src/mudata/_core/io.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/src/mudata/_core/io.py b/src/mudata/_core/io.py
index 848ca06..8107e30 100644
--- a/src/mudata/_core/io.py
+++ b/src/mudata/_core/io.py
@@ -14,7 +14,7 @@
 import re
 from contextlib import ExitStack
 from pathlib import Path
-from warnings import warn
+from warnings import catch_warnings, filterwarnings, warn
 
 import anndata as ad
 import h5py
@@ -131,7 +131,9 @@ def write_zarr(
 
     from .. import __anndataversion__, __mudataversion__, __version__
 
-    zarr_format = getattr(ad.settings, "zarr_write_format", 2)
+    with catch_warnings():
+        filterwarnings("ignore", message="This setting will be removed", category=DeprecationWarning)
+        zarr_format = getattr(ad.settings, "zarr_write_format", 3)
 
     if isinstance(data, AnnData):
         adata = data