From f16c82dbb32345df1b754af1b704872e26b9fb0d Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 19 Jan 2026 16:40:07 +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: 22.12.0 → 26.1.0](https://github.com/psf/black-pre-commit-mirror/compare/22.12.0...26.1.0)
- [github.com/pre-commit/mirrors-prettier: v3.0.0-alpha.4 → v4.0.0-alpha.8](https://github.com/pre-commit/mirrors-prettier/compare/v3.0.0-alpha.4...v4.0.0-alpha.8)
- [github.com/asottile/blacken-docs: v1.12.1 → 1.20.0](https://github.com/asottile/blacken-docs/compare/v1.12.1...1.20.0)
- [github.com/PyCQA/isort: 5.11.4 → 7.0.0](https://github.com/PyCQA/isort/compare/5.11.4...7.0.0)
- [github.com/asottile/yesqa: v1.4.0 → v1.5.0](https://github.com/asottile/yesqa/compare/v1.4.0...v1.5.0)
- [github.com/pre-commit/pre-commit-hooks: v4.4.0 → v6.0.0](https://github.com/pre-commit/pre-commit-hooks/compare/v4.4.0...v6.0.0)
- [github.com/PyCQA/autoflake: v2.0.0 → v2.3.1](https://github.com/PyCQA/autoflake/compare/v2.0.0...v2.3.1)
- [github.com/PyCQA/flake8: 6.0.0 → 7.3.0](https://github.com/PyCQA/flake8/compare/6.0.0...7.3.0)
- [github.com/asottile/pyupgrade: v3.3.1 → v3.21.2](https://github.com/asottile/pyupgrade/compare/v3.3.1...v3.21.2)
---
 .pre-commit-config.yaml | 24 ++++++++++++------------
 1 file changed, 12 insertions(+), 12 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index a563d02..47403cb 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -2,28 +2,28 @@ fail_fast: false
 default_language_version:
   python: python3
 default_stages:
-  - commit
-  - push
+  - pre-commit
+  - pre-push
 minimum_pre_commit_version: 2.16.0
 repos:
-  - repo: https://github.com/psf/black
-    rev: 22.12.0
+  - repo: https://github.com/psf/black-pre-commit-mirror
+    rev: 26.1.0
     hooks:
       - id: black
   - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: v3.0.0-alpha.4
+    rev: v4.0.0-alpha.8
     hooks:
       - id: prettier
   - repo: https://github.com/asottile/blacken-docs
-    rev: v1.12.1
+    rev: 1.20.0
     hooks:
       - id: blacken-docs
   - repo: https://github.com/PyCQA/isort
-    rev: 5.11.4
+    rev: 7.0.0
     hooks:
       - id: isort
   - repo: https://github.com/asottile/yesqa
-    rev: v1.4.0
+    rev: v1.5.0
     hooks:
       - id: yesqa
         additional_dependencies:
@@ -34,7 +34,7 @@ repos:
           - flake8-bugbear
           - flake8-blind-except
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v6.0.0
     hooks:
       - id: detect-private-key
       - id: check-ast
@@ -45,7 +45,7 @@ repos:
       - id: trailing-whitespace
       - id: check-case-conflict
   - repo: https://github.com/PyCQA/autoflake
-    rev: v2.0.0
+    rev: v2.3.1
     hooks:
       - id: autoflake
         args:
@@ -54,7 +54,7 @@ repos:
           - --remove-unused-variable
           - --ignore-init-module-imports
   - repo: https://github.com/PyCQA/flake8
-    rev: 6.0.0
+    rev: 7.3.0
     hooks:
       - id: flake8
         additional_dependencies:
@@ -65,7 +65,7 @@ repos:
           - flake8-bugbear
           - flake8-blind-except
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.3.1
+    rev: v3.21.2
     hooks:
       - id: pyupgrade
         args: [--py3-plus, --py38-plus, --keep-runtime-typing]

From c94fb0ce25d2b37ad2d8123f1ce83f374ebcc9bc Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 19 Jan 2026 16:40:26 +0000
Subject: [PATCH 2/2] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 docs/tools/totalvi.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/docs/tools/totalvi.md b/docs/tools/totalvi.md
index f028df1..d9ee06b 100644
--- a/docs/tools/totalvi.md
+++ b/docs/tools/totalvi.md
@@ -13,4 +13,5 @@ TotalVI: A transformative algorithm, Berkeley Engineering News, https://engineer
 ## References
 
 [^ref1]: Gayoso, A., Steier, Z., Lopez, R., Regier, J., Nazor, K. L., Streets, A., & Yosef, N. (2021). Joint probabilistic modeling of single-cell multi-omic data with totalVI. Nature Methods, 18(3), 272-282.
+
 [^ref2]: Stoeckius, M., Hafemeister, C., Stephenson, W., Houck-Loomis, B., Chattopadhyay, P. K., Swerdlow, H., … & Smibert, P. (2017). Simultaneous epitope and transcriptome measurement in single cells. Nature methods, 14(9), 865-868.