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]
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.