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fail_fast: false

default_language_version:

python: python3

default_stages:

- pre-commit

- pre-push

minimum_pre_commit_version: 2.16.0

repos:

- repo: https://github.com/biomejs/pre-commit

rev: v2.5.3

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

hooks:

- id: pyproject-fmt

- repo: https://github.com/astral-sh/ruff-pre-commit

rev: v0.15.21

hooks:

- id: ruff-check

types_or: [python, pyi, jupyter]

args: [--fix, --exit-non-zero-on-fix]

- id: ruff-format

types_or: [python, pyi, jupyter]

- repo: https://github.com/pre-commit/pre-commit-hooks

rev: v6.0.0

hooks:

- id: detect-private-key

- id: check-ast

- id: end-of-file-fixer

- id: mixed-line-ending

args: [--fix=lf]

- id: trailing-whitespace

- id: check-case-conflict

# Check that there are no merge conflicts (could be generated by template sync)

- id: check-merge-conflict

args: [--assume-in-merge]

- repo: https://github.com/pre-commit/mirrors-mypy

rev: v2.1.0

hooks:

- id: mypy

pass_filenames: false

args: [src/pydeseq2, --ignore-missing-imports]

additional_dependencies: [pandas-stubs, scipy-stubs]

- repo: https://github.com/zizmorcore/zizmor-pre-commit

rev: v1.24.1

hooks:

- id: zizmor

args: [--no-progress, --fix]