From dbf01e12a26efbfd10209b73268cfdb82e442a2c Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 16 Mar 2026 21:29:17 +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:
- https://github.com/psf/black → https://github.com/psf/black-pre-commit-mirror
- [github.com/psf/black-pre-commit-mirror: 23.10.1 → 26.3.1](https://github.com/psf/black-pre-commit-mirror/compare/23.10.1...26.3.1)
- [github.com/PyCQA/flake8: 6.1.0 → 7.3.0](https://github.com/PyCQA/flake8/compare/6.1.0...7.3.0)
- [github.com/pycqa/isort: 5.12.0 → 8.0.1](https://github.com/pycqa/isort/compare/5.12.0...8.0.1)
---
 .pre-commit-config.yaml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index df1bae45..46f0b72d 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,14 +1,14 @@
 repos:
-    - repo: https://github.com/psf/black
-      rev: '23.10.1'
+    - repo: https://github.com/psf/black-pre-commit-mirror
+      rev: '26.3.1'
       hooks:
           - id: black
     - repo: https://github.com/PyCQA/flake8
-      rev: 6.1.0
+      rev: 7.3.0
       hooks:
           - id: flake8
     - repo: https://github.com/pycqa/isort
-      rev: 5.12.0
+      rev: 8.0.1
       hooks:
           - id: isort
             name: isort (python)

From c3d531fc0020fb0db9949e794a221473838b126d Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 16 Mar 2026 21:31:09 +0000
Subject: [PATCH 2/2] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 cell2location/distributions/NegativeBinomial.py | 1 +
 cell2location/distributions/transforms.py       | 1 +
 cell2location/plt/RotateCrop.py                 | 1 +
 3 files changed, 3 insertions(+)

diff --git a/cell2location/distributions/NegativeBinomial.py b/cell2location/distributions/NegativeBinomial.py
index 8d42ce0a..772c3a9c 100755
--- a/cell2location/distributions/NegativeBinomial.py
+++ b/cell2location/distributions/NegativeBinomial.py
@@ -104,6 +104,7 @@ class NegativeBinomial(Distribution):
     one parameterization to another.
 
     """
+
     arg_constraints = {
         "mu": constraints.greater_than_eq(0),
         "theta": constraints.greater_than_eq(0),
diff --git a/cell2location/distributions/transforms.py b/cell2location/distributions/transforms.py
index 77b00f63..4ae68a29 100644
--- a/cell2location/distributions/transforms.py
+++ b/cell2location/distributions/transforms.py
@@ -6,6 +6,7 @@ class SoftplusTransform(Transform):
     r"""
     Transform via the mapping :math:`\text{Softplus}(x) = \log(1 + \exp(x))`.
     """
+
     domain = constraints.real_vector
     codomain = constraints.positive
 
diff --git a/cell2location/plt/RotateCrop.py b/cell2location/plt/RotateCrop.py
index 8d61ef9b..fb69d1b6 100644
--- a/cell2location/plt/RotateCrop.py
+++ b/cell2location/plt/RotateCrop.py
@@ -1,4 +1,5 @@
 r"""Class for rotating and cropping images."""
+
 import cv2 as cv
 import numpy as np