.pre-commit-config.yaml

---
exclude: (pipelines/report-.*)|(pipelines/.*.txt)|(data_model/src/linkml_crystalia/datamodel/.*.py)

repos:
  - repo: https://github.com/pre-commit/pre-commit-hooks
    rev: v5.0.0
    hooks:
      # General
      - id: check-added-large-files
      - id: check-case-conflict
      - id: check-executables-have-shebangs
      - id: check-merge-conflict
      - id: check-symlinks
      - id: check-toml
      - id: check-xml
      - id: check-yaml
      - id: detect-private-key
      - id: end-of-file-fixer
      - id: fix-byte-order-marker
      - id: mixed-line-ending # Replaces or checks mixed line ending.
      - id: trailing-whitespace

      # Json
      - id: check-json
      - id: pretty-format-json # Checks that all your JSON files are pretty.
        args: ['--indent', '2', '--autofix']
        exclude: \.ipynb

      # Python
      - id: check-ast # Check whether files parse as valid python.
      - id: check-builtin-literals # Require literal syntax when initializing empty or zero Python builtin types.
      - id: check-docstring-first
      - id: debug-statements # Check for debugger imports and py37+ breakpoint() calls in python source.
      - id: name-tests-test # Assert that files in tests/ end in _test.py, or optionally test*.py
        args: [--pytest-test-first]
      - id: requirements-txt-fixer
  - repo: https://github.com/Yelp/detect-secrets
    rev: v1.5.0
    hooks:
      - id: detect-secrets
        args: ['--baseline', '.secrets.baseline']
        exclude: package.lock.json
  - repo: https://github.com/pryorda/dockerfilelint-precommit-hooks
    rev: v0.1.0
    hooks:
      - id: dockerfilelint


  - repo: https://github.com/hadolint/hadolint
    rev: v2.13.0-beta
    hooks:
      - id: hadolint

  - repo: https://github.com/executablebooks/mdformat
    rev: 0.7.14
    hooks:
      - id: mdformat
        additional_dependencies:
          - mdformat-beautysh
          - mdformat-black
          - mdformat-config
          - mdformat-deflist
          # - mdformat-frontmatter  # Breaks.
          - mdformat-footnote
          - mdformat-gfm
          - mdformat-shfmt
          - mdformat-tables
          - mdformat-toc
  - repo: https://github.com/ikamensh/flynt/
    rev: '1.0.1'
    hooks:
      - id: flynt
  - repo: https://github.com/asottile/add-trailing-comma
    rev: v3.1.0
    hooks:
      - id: add-trailing-comma
        args:
          - --py36-plus

  - repo: https://github.com/hadialqattan/pycln
    rev: v2.4.0 # Possible releases: https://github.com/hadialqattan/pycln/releases
    hooks:
      - id: pycln

  - repo: https://github.com/MarcoGorelli/absolufy-imports
    rev: v0.3.1
    hooks:
      - id: absolufy-imports

  - repo: https://github.com/astral-sh/ruff-pre-commit
    rev: 'v0.6.2'
    hooks:
      - id: ruff
        args: [--fix, --exit-non-zero-on-fix]
        types_or: [python, pyi] # Run on notebooks too.
        exclude: ^(tests)/
      - id: ruff-format
        types_or: [python, pyi] # Run on notebooks too.
  # YAML

  - repo: https://github.com/adrienverge/yamllint
    rev: v1.35.1
    hooks:
      - id: yamllint
        args: [-c=.yamllint.yml]
  - repo: https://github.com/zricethezav/gitleaks
    rev: v8.18.4
    hooks:
      - id: gitleaks

  - repo: https://github.com/rhysd/actionlint
    rev: v1.7.1
    hooks:
      - id: actionlint
        args: ['--ignore', 'is always evaluated to true']

  - repo: https://github.com/streetsidesoftware/cspell-cli
    rev: v8.13.3
    hooks:
      - id: cspell