.pre-commit-config.yaml

default_stages: [commit, push]
exclude: (^.github/|^docs/site/|^images/)

repos:
  - repo: https://github.com/executablebooks/mdformat
    # Do this before other tools "fixing" the line endings
    rev: 0.7.17
    hooks:
      - id: mdformat
        name: Format Markdown
        entry: mdformat # Executable to run, with fixed options
        language: python
        types: [markdown]
        args: [--wrap, "80", --number]
        additional_dependencies:
          - mdformat-mkdocs
          - mdformat-toc
          - mdformat-beautysh
          - mdformat-config
          - mdformat-black
          - mdformat-web
          - mdformat-gfm

  - repo: https://github.com/pre-commit/pre-commit-hooks
    rev: v4.5.0
    hooks:
      - id: check-toml
      - id: check-yaml
        args: [--unsafe]
      - id: end-of-file-fixer
      - id: mixed-line-ending
        args: ["--fix=lf"]
        description: Forces to replace line ending by the UNIX 'lf' character.
      - id: trailing-whitespace
      - id: debug-statements
      - id: check-added-large-files # prevent giant files from being committed
      # - id: check-builtin-literals
      - id: check-merge-conflict
      - id: check-executables-have-shebangs
      - id: check-shebang-scripts-are-executable
      - id: check-docstring-first
      - id: check-case-conflict
      - id: fix-byte-order-marker

  - repo: https://github.com/adrienverge/yamllint.git
    rev: v1.33.0
    hooks:
      - id: yamllint
        args:
          - --no-warnings
          - -d
          - "{extends: relaxed, rules: {line-length: {max: 80}}}"

  - repo: https://github.com/charliermarsh/ruff-pre-commit
    rev: v0.1.6
    hooks:
      - id: ruff
        args: [
          "--exclude", "./notebooks/py_scripts/",
          "--ignore", "F401,E402,E501"
        ]
        # F401: Unused import - May flag tables in DataJoint foreign keys
        # E402: Module level import not at top of file - May want lazyloading
        # E501: Line too long - Allow longer lines in table definitions

  - repo: https://github.com/PyCQA/autoflake
    rev: v2.2.1
    hooks:
      - id: autoflake

  - repo: https://github.com/codespell-project/codespell
    rev: v2.2.6
    hooks:
      - id: codespell
        args: [--toml, pyproject.toml]
        additional_dependencies:
          - tomli

  - repo: https://github.com/ambv/black
    rev: 24.1.1
    hooks:
      - id: black
        language_version: python3.9