.pre-commit-config.yaml

# If need global exclude:
# exclude: "^docs/conf.py"

# NOTE:
# Where excluding "docs/user_guide", that is because these are auto-generated files.

repos:
- repo: https://github.com/pre-commit/pre-commit-hooks
  rev: v4.5.0
  hooks:
  - id: trailing-whitespace
    args: [
      "--markdown-linebreak-ext=md",
    ]
    exclude: "docs/user_guide"
  - id: check-added-large-files
    args: [
      "--maxkb=1000",
    ]
  - id: check-ast
  - id: check-case-conflict
  - id: check-json
  - id: check-merge-conflict
  - id: check-toml
  - id: check-xml
  - id: check-yaml
  - id: check-executables-have-shebangs
  - id: debug-statements
  - id: end-of-file-fixer
    exclude: "docs/user_guide"
  - id: pretty-format-json
    args: [
      "--autofix",
      "--indent=4",
      "--no-sort-keys",
    ]
    exclude: ".*.ipynb"  # Do not want .ipynb to be treated as JSON.
  - id: requirements-txt-fixer
    exclude: docs/requirements.txt
  - id: mixed-line-ending
    args: [
      "--fix=auto",
    ]

- repo: https://github.com/pycqa/isort
  rev: 5.12.0
  hooks:
  - id: isort

- repo: https://github.com/psf/black
  rev: 23.11.0
  hooks:
  - id: black-jupyter
    language_version: python3
    exclude: "docs/user_guide"

# If like to embrace black styles even in the docs:
- repo: https://github.com/asottile/blacken-docs
  rev: 1.16.0
  hooks:
  - id: blacken-docs
    additional_dependencies: [
      "black",
    ]
    exclude: "docs/user_guide"

# Standard `flake8` run for all Python files:
- repo: https://github.com/PyCQA/flake8
  rev: 6.1.0
  hooks:
  - id: flake8

- repo: https://github.com/pre-commit/mirrors-mypy
  rev: v1.7.0
  hooks:
  - id: mypy
    files: "^src/"
    args: [
      "--config-file=mypy.ini",
    ]
    # NOTE:
    # Re. additional **typed dependencies** and pre-commit mypy: https://stackoverflow.com/a/74291151.
    # The list of typed dependencies below needs to be kept up-to-date with `setup.cfg`  for mypy errors to match
    # the development environment. The typical "mismatched" mypy error that happens if these are not kept in sync is:
    # `error: Unused "type: ignore" comment  [unused-ignore]`.
    additional_dependencies: [
      "dask[dataframe]",
      "hydra-core >=1.3",
      "hyperimpute >= 0.1.17",
      "loguru",
      "optuna >= 2.8.0",
      "pandas >= 1",
      "pandera >= 0.17.0",
      "pydantic >= 2",
      "torch",
      "tsai",
    ]
    # NOTE:
    # src/tempor/models/clairvoyance2/ is excluded via file `# mypy: ignore-errors` comments as otherwise mypy
    # does not appear to ignore this properly.

- repo: https://github.com/PyCQA/bandit
  rev: 1.7.5
  hooks:
  - id: bandit
    args: [
      "-c",
      "pyproject.toml",
      "-q"
    ]
    additional_dependencies: [
      "bandit[toml]",
    ]
    exclude: "^src/tempor/models/clairvoyance2/.*"

- repo: https://github.com/pycqa/pydocstyle
  rev: 6.3.0
  hooks:
  - id: pydocstyle
    additional_dependencies: [
      "tomli",  # To read configuration from pyproject.toml.
    ]
    exclude: |
      (?x)^(
          docs/.*|
          tests/.*|
          src/tempor/models/clairvoyance2/.*
      )$

# `pydoclint` run via `flake8`, with some additional locations ignored.
- repo: https://github.com/PyCQA/flake8
  rev: 6.1.0
  hooks:
  - id: flake8
    name: "pydoclint_via_flake8"
    additional_dependencies: [
      "pydoclint",
    ]
    exclude: |
      (?x)^(
          docs/.*|
          tests/.*|
          src/tempor/models/clairvoyance2/.*
      )$