ontograph/.pre-commit-config.yaml at main · saezlab/ontograph · GitHub

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# pre-commit-config.yaml
# See https://pre-commit.com for docs and https://pre-commit.com/hooks.html for available hooks

# ======================================================
# =======        pre-commit configuration       ========
# ======================================================
fail_fast: false
minimum_pre_commit_version: 3.0.0
default_language_version:
    python: python3
default_stages:
-   pre-commit
-   pre-push

# ======================================================
# =======            repository hooks           ========
# ======================================================
# UPDATE all the hooks regularly by running in the
# terminal:
#   pre-commit autoupdate

repos:
    # Fast Python linter and formatter with auto-fix support
-   repo: https://github.com/astral-sh/ruff-pre-commit
    rev: v0.12.7
    hooks:
    -   id: ruff-check
        args: [--fix, --show-fixes]
        stages: [pre-commit]
        files: \.py$
    -   id: ruff-format
        stages: [pre-commit]
        files: \.py$

    # Go code cleaner (removes unused exports)
#-   repo: https://github.com/deeenes/unexport
#    rev: 0.4.0-patch0-3
#    hooks:
#    -   id: unexport
#        args: [--refactor, --single_quotes]
#        exclude: __init__.py$

    # Official pre-commit-hooks for general checks
-   repo: https://github.com/pre-commit/pre-commit-hooks
    rev: v5.0.0    # Check for updates regularly
    hooks:
    -   id: check-added-large-files
        stages: [pre-commit, pre-push]
    -   id: check-ast
        stages: [pre-commit]
    -   id: check-case-conflict
        stages: [pre-commit]
    -   id: check-merge-conflict
        stages: [pre-commit, pre-push]
    -   id: check-symlinks
        stages: [pre-commit]
    -   id: check-yaml
        args: [--unsafe]
        stages: [pre-commit]
        files: \.ya?ml$
    -   id: detect-private-key
        stages: [pre-commit]
    -   id: end-of-file-fixer
        stages: [pre-commit]
    -   id: mixed-line-ending
        args: [--fix=lf]
        exclude: ^docs/make.bat$
        stages: [pre-commit]
    -   id: requirements-txt-fixer
        stages: [pre-commit]

    # Format code blocks in documentation files
-   repo: https://github.com/asottile/blacken-docs
    rev: 1.19.1
    hooks:
    -   id: blacken-docs
        stages: [pre-commit]
        files: \.(md|rst)$

  # Format TOML and YAML files with pretty-format hooks
-   repo: https://github.com/macisamuele/language-formatters-pre-commit-hooks
    rev: v2.15.0
    hooks:
    -   id: pretty-format-toml
        args:
        -   --autofix
        -   --indent
        -   '4'
        stages: [pre-commit]
        files: \.toml$
    -   id: pretty-format-yaml
        args:
        -   --autofix
        -   --indent
        -   '4'
        stages: [pre-commit]
        files: \.ya?ml$

# clean output from jupyter notebooks
-   repo: https://github.com/kynan/nbstripout
    rev: 0.8.1
    hooks:
    -   id: nbstripout