From d1db26438b440182496a4dc403c34bbe718a2efe Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 19 Oct 2026 18:17:57 +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: v2.5.3 → v2.5.15](https://github.com/biomejs/pre-commit/compare/v2.5.3...v2.5.15)
- [github.com/tox-dev/pyproject-fmt: v2.25.3 → v2.30.3](https://github.com/tox-dev/pyproject-fmt/compare/v2.25.3...v2.30.3)
- [github.com/astral-sh/ruff-pre-commit: v0.15.21 → v0.17.1](https://github.com/astral-sh/ruff-pre-commit/compare/v0.15.21...v0.17.1)
- [github.com/pre-commit/mirrors-mypy: v2.1.0 → v2.4.0](https://github.com/pre-commit/mirrors-mypy/compare/v2.1.0...v2.4.0)
- [github.com/zizmorcore/zizmor-pre-commit: v1.24.1 → v1.31.1](https://github.com/zizmorcore/zizmor-pre-commit/compare/v1.24.1...v1.31.1)
---
 .pre-commit-config.yaml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 7f4f5560..0c6d9702 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -7,16 +7,16 @@ default_stages:
 minimum_pre_commit_version: 2.16.0
 repos:
   - repo: https://github.com/biomejs/pre-commit
-    rev: v2.5.3
+    rev: v2.5.15
     hooks:
       - id: biome-format
         exclude: ^\.cruft\.json$ # inconsistent indentation with cruft - file never to be modified manually.
   - repo: https://github.com/tox-dev/pyproject-fmt
-    rev: v2.25.3
+    rev: v2.30.3
     hooks:
       - id: pyproject-fmt
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.15.21
+    rev: v0.17.1
     hooks:
       - id: ruff-check
         types_or: [python, pyi, jupyter]
@@ -38,7 +38,7 @@ repos:
         args: [--assume-in-merge]
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v2.1.0
+    rev: v2.4.0
     hooks:
       - id: mypy
         pass_filenames: false
@@ -46,7 +46,7 @@ repos:
         additional_dependencies: [pandas-stubs, scipy-stubs]
 
   - repo: https://github.com/zizmorcore/zizmor-pre-commit
-    rev: v1.24.1
+    rev: v1.31.1
     hooks:
       - id: zizmor
         args: [--no-progress, --fix]

From da672e1699d557e9c1dc2488a8fef01772510dca Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 19 Oct 2026 18:18:32 +0000
Subject: [PATCH 2/2] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 pyproject.toml | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 894c8568..12a04fb8 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -22,6 +22,7 @@ classifiers = [
   "Programming Language :: Python :: 3.12",
   "Programming Language :: Python :: 3.13",
   "Programming Language :: Python :: 3.14",
+  "Programming Language :: Python :: 3.15",
 ]
 dynamic = [ "version" ]
 dependencies = [
@@ -87,6 +88,8 @@ envs.docs.scripts.build = "sphinx-build -M html docs docs/_build -W {args}"
 envs.docs.scripts.clean = "git clean -fdX -- {args:docs}"
 envs.docs.scripts.open = "python -m webbrowser -t docs/_build/html/index.html"
 envs.docs.dependency-groups = [ "doc" ]
+envs.hatch-check-types.scripts.check = [ "mypy src/pydeseq2 --ignore-missing-imports" ]
+envs.hatch-check-types.dependency-groups = [ "typecheck", "test" ]
 envs.hatch-test.matrix = [
   # Test the lowest and highest supported Python versions with normal deps
   { deps = [ "stable" ], python = [ "3.12", "3.14" ] },
@@ -99,8 +102,6 @@ envs.hatch-test.overrides.matrix.deps.env-vars = [
   { value = "allow", key = "UV_PRERELEASE", if = [ "pre" ] },
 ]
 envs.hatch-test.dependency-groups = [ "dev", "test" ]
-envs.hatch-check-types.scripts.check = [ "mypy src/pydeseq2 --ignore-missing-imports" ]
-envs.hatch-check-types.dependency-groups = [ "typecheck", "test" ]
 
 [tool.ruff]
 line-length = 89
@@ -151,11 +152,11 @@ ini_options.filterwarnings = [
 ]
 
 [tool.coverage]
+run.source = [ "pydeseq2" ]
 run.omit = [
   "**/test_*.py",
 ]
 run.patch = [ "subprocess" ]
-run.source = [ "pydeseq2" ]
 
 [tool.cruft]
 skip = [