.pre-commit-config.yaml

default_language_version:
  python: python3

# Define common configuration variables
default_stages: [pre-commit]

repos:
  # Standard pre-commit hooks
  - repo: https://github.com/pre-commit/pre-commit-hooks
    rev: v5.0.0 # Updated version
    hooks:
      - id: trailing-whitespace
      - id: end-of-file-fixer
      - id: check-docstring-first
      - id: check-yaml
      - id: debug-statements
      - id: detect-private-key
      - id: check-executables-have-shebangs
      - id: check-toml
      - id: check-case-conflict
      - id: check-added-large-files
      - id: check-merge-conflict # Added: catches merge conflict markers
      - id: check-json # Added: validate JSON files

  # Python code formatting
  - repo: https://github.com/psf/black
    rev: 25.1.0 # Updated version
    hooks:
      - id: black
        args: [--line-length, "299"]

  # Python import sorting
  - repo: https://github.com/PyCQA/isort
    rev: 6.0.1
    hooks:
      - id: isort
        args: ["--profile", "black", "--filter-files"]

  # Python upgrading syntax to newer version
  - repo: https://github.com/asottile/pyupgrade
    rev: v3.19.1 # Updated version
    hooks:
      - id: pyupgrade
        args: [--py38-plus]

  # Python docstring formatting
  - repo: https://github.com/myint/docformatter
    rev: eb1df347edd128b30cd3368dddc3aa65edcfac38 # Don't autoupdate until https://github.com/PyCQA/docformatter/issues/293 is fixed
    hooks:
      - id: docformatter
        args:
          [
            --in-place,
            --wrap-summaries=99,
            --wrap-descriptions=99,
            --style=sphinx,
            --black,
          ]

  # Python docstring coverage checking
  - repo: https://github.com/econchick/interrogate
    rev: 1.7.0
    hooks:
      - id: interrogate
        args:
          [
            --verbose,
            --fail-under=100,
            --ignore-init-module,
            --ignore-init-method,
            --ignore-module,
            --ignore-nested-functions,
            -vv,
          ]
        exclude: "^tests/"

  - repo: https://github.com/astral-sh/ruff-pre-commit
    rev: v0.11.5
    hooks:
      - id: ruff
        args: ["--fix", "--line-length=299"]

  # Type checking with mypy (fixed)
  - repo: https://github.com/pre-commit/mirrors-mypy
    rev: v1.16.0
    hooks:
      - id: mypy
        # Removed problematic types-all and added specific type stubs
        additional_dependencies:
          [
            types-requests,
            types-PyYAML,
            types-toml,
            types-setuptools,
            types-tqdm,
            types-seaborn,
          ]
        exclude: "^tests/"

  # Python security linter
  - repo: https://github.com/PyCQA/bandit
    rev: "1.8.3"
    hooks:
      - id: bandit
        # Skip B101 (assert statements), B603/B607 (subprocess with trusted git commands)
        args: ["-s", "B101,B603,B607"]

  # yaml formatting
  - repo: https://github.com/pre-commit/mirrors-prettier
    rev: v4.0.0-alpha.8 # Updated version
    hooks:
      - id: prettier
        types: [yaml]
        exclude: "environment.yaml"

  # shell scripts linter
  - repo: https://github.com/shellcheck-py/shellcheck-py
    rev: v0.10.0.1 # Updated version
    hooks:
      - id: shellcheck

  # md formatting
  - repo: https://github.com/executablebooks/mdformat
    rev: 0.7.22 # Updated version
    hooks:
      - id: mdformat
        args: ["--number"]
        additional_dependencies:
          - mdformat-gfm==0.3.7
          - mdformat-tables
          - mdformat_frontmatter

  # word spelling linter
  - repo: https://github.com/codespell-project/codespell
    rev: v2.4.1 # Updated version
    hooks:
      - id: codespell
        args:
          - --skip=logs/**,data/**,*.ipynb,*.bib
          - --ignore-words-list=fro,ser,SER,Tung,ans,Wehn

  # jupyter notebook cell output clearing
  - repo: https://github.com/kynan/nbstripout
    rev: 0.8.1
    hooks:
      - id: nbstripout

  # jupyter notebook linting
  - repo: https://github.com/nbQA-dev/nbQA
    rev: 1.9.1 # Updated version
    hooks:
      - id: nbqa-black
        args: ["--line-length=299"]
      - id: nbqa-isort
        args: ["--profile=black"]
      - id: nbqa-ruff # Changed from flake8 to ruff
        args: ["--line-length=299"]

  # Documentation style checker
  #- repo: https://github.com/pycqa/doc8
  #  rev: v1.1.1
  #  hooks:
  #    - id: doc8
  #      args: ["--ignore=D001"] # Ignore line length for documentation
  #      exclude: "docs/_build/|docs/generated/"

  # Validate GitHub Actions workflows (new)
  - repo: https://github.com/python-jsonschema/check-jsonschema
    rev: 0.33.0
    hooks:
      - id: check-github-workflows
        files: ^\.github/workflows/

  # Check commit message format (new)
  - repo: https://github.com/commitizen-tools/commitizen
    rev: v4.6.0
    hooks:
      - id: commitizen
        stages: [commit-msg]

  # Local hooks for project automation
  - repo: local
    hooks:
      - id: install-requirements
        name: Install requirements.txt
        entry: pip install -r requirements.txt
        language: system
        always_run: true
        pass_filenames: false
        stages: [pre-commit]
      - id: generate-changelog
        name: Generate changelog.rst from CHANGELOG.md
        entry: python scripts/generate_changelog.py
        language: system
        files: ^CHANGELOG\.md$
        pass_filenames: false
      - id: generate-api-reference
        name: Generate API reference documentation
        entry: python scripts/generate_api_reference.py docs/api_reference.rst
        language: system
        files: ^kaira/.*\.py$
        pass_filenames: false
      - id: generate-example-indices
        name: Generate example gallery index files
        entry: python scripts/generate_example_indices.py
        language: system
        files: ^examples/.*\.py$
        pass_filenames: false