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[pre-commit.ci] pre-commit autoupdate #1

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f16c82d
[pre-commit.ci] pre-commit autoupdate
pre-commit-ci[bot] Jan 19, 2026
c94fb0c
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jan 19, 2026
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24 changes: 12 additions & 12 deletions .pre-commit-config.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -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:
Expand All @@ -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
Expand All @@ -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:
Expand All @@ -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:
Expand All @@ -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]
1 change: 1 addition & 0 deletions docs/tools/totalvi.md
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Expand Up @@ -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.