protein-quest/.pre-commit-config.yaml at main · haddocking/protein-quest · GitHub

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# Keeping pytest and pyrefly out of pre-commit as they need full venv.
# To run needs docker and nodejs installed.

# Do not check or fix downloaded files
exclude: ^tests/.*(\.yaml|\.pdb)$

repos:
  - repo: https://github.com/adamchainz/blacken-docs
    rev: "1.20.0"
    hooks:
      - id: blacken-docs
        additional_dependencies: [black==25.*]

  - repo: https://github.com/pre-commit/pre-commit-hooks
    rev: "v6.0.0"
    hooks:
      - id: check-added-large-files
      - id: check-case-conflict
      - id: check-merge-conflict
      - id: check-symlinks
      - id: check-yaml
      - id: debug-statements
      - id: end-of-file-fixer
      - id: mixed-line-ending
      - id: name-tests-test
        args: ["--pytest-test-first"]
      - id: requirements-txt-fixer
      - id: trailing-whitespace

  - repo: https://github.com/pre-commit/pygrep-hooks
    rev: "v1.10.0"
    hooks:
      - id: rst-backticks
      - id: rst-directive-colons
      - id: rst-inline-touching-normal

  - repo: https://github.com/rbubley/mirrors-prettier
    rev: "v3.7.4"
    hooks:
      - id: prettier
        types_or: [yaml, markdown, html, css, scss, javascript, json]
        args: [--prose-wrap=always]

  - repo: https://github.com/astral-sh/ruff-pre-commit
    rev: "v0.14.10"
    hooks:
      - id: ruff-check
        args: ["--fix", "--show-fixes"]
      - id: ruff-format

  - repo: https://github.com/codespell-project/codespell
    rev: "v2.4.1"
    hooks:
      - id: codespell
        additional_dependencies:
          - tomli; python_version<'3.11'

  - repo: https://github.com/shellcheck-py/shellcheck-py
    rev: "v0.11.0.1"
    hooks:
      - id: shellcheck

  - repo: https://github.com/python-jsonschema/check-jsonschema
    rev: "0.36.0"
    hooks:
      - id: check-github-workflows
      - id: check-citation-file-format
      # Not checking mkdocs.yml as hook does not support custom YAML tags like !!python/....
      # see https://github.com/python-jsonschema/check-jsonschema/issues/489
      # mkdocs schema exists at https://www.schemastore.org/mkdocs-1.6.json

  # Tried to use official jscpd repo, but got jscpd not found error
  - repo: local
    hooks:
      - id: jscpd
        name: jscpd code duplication checker
        entry: npx jscpd
        language: node
        args: ["--gitignore", "--exitCode=1", "src"]
        types: [text]
        pass_filenames: false

  - repo: https://github.com/DavidAnson/markdownlint-cli2
    rev: v0.20.0
    hooks:
      - id: markdownlint-cli2
        args: ["--fix"]