.pre-commit-config.yaml

# pre-commit install
# pre-commit run --all-files
# See https://pre-commit.com for more information
# See https://pre-commit.com/hooks.html for more hooks
ci:
  autoupdate_commit_msg: "chore(deps): update pre-commit hooks"
  autofix_commit_msg: "style: pre-commit fixes"
  autoupdate_schedule: "quarterly"
  skip:
    - uv-lock
    - pip-compile
default_install_hook_types:
  - pre-commit
  - commit-msg
repos:
  # * meta hooks
  - repo: meta
    hooks:
      - id: check-hooks-apply
      - id: check-useless-excludes

  # * sync dependencies
  - repo: https://github.com/wpk-nist-gov/sync-pre-commit-hooks
    rev: v0.5.1
    hooks:
      - id: forbidden-files
      - id: sync-pre-commit-deps
      - id: sync-uv-build-deps
      - id: sync-uv-dependency-groups

  # * Top level
  - repo: https://github.com/pre-commit/pre-commit-hooks
    rev: v6.0.0
    hooks:
      - id: check-added-large-files
        exclude: ^uv[.]lock|.*\.ipynb
      - id: check-case-conflict
      - id: check-merge-conflict
        args: [--assume-in-merge]
      - id: check-symlinks
        exclude: SRS_data$|SWF_Adsorption_data$
      - id: check-yaml
      - id: check-json
      - id: check-toml
      - id: trailing-whitespace
      - id: end-of-file-fixer
      - id: mixed-line-ending

  # * toml/pyproject.toml
  # ** format
  - repo: https://github.com/ComPWA/taplo-pre-commit
    rev: v0.9.3
    hooks:
      - id: taplo-format
        # exclude: (^|/)pyproject\.toml$
      - id: taplo-lint
        args: ["--no-schema"]
  - repo: https://github.com/tox-dev/pyproject-fmt
    rev: v2.21.1
    hooks:
      - id: pyproject-fmt
  # ** validate (schema-store)
  - repo: https://github.com/henryiii/validate-pyproject-schema-store
    rev: 2026.04.21
    hooks:
      - id: validate-pyproject
        name: validate-pyproject-schema-store
        stages: [manual]
  # ** repo review
  - repo: https://github.com/scientific-python/cookie
    rev: 2026.04.04
    hooks:
      - id: sp-repo-review
        stages: [manual]

  # * Prettier
  - repo: https://github.com/rbubley/mirrors-prettier
    rev: v3.8.3
    hooks:
      - id: prettier
        alias: markdownlint
        stages: [pre-commit, manual]
        args:
          - "--cache"
          - "--cache-location=.prettier_cache/cache"

  # * Markdown
  - repo: https://github.com/DavidAnson/markdownlint-cli2
    rev: v0.22.1
    hooks:
      - id: markdownlint-cli2
        alias: markdownlint
        args: [--style, prettier]

  # Just
  - repo: https://github.com/wpk-nist-gov/just-pre-commit
    rev: v1.50.0
    hooks:
      - id: justfile-format

  # * Linting
  - repo: https://github.com/astral-sh/ruff-pre-commit
    rev: v0.15.11
    hooks:
      - id: ruff-check
        alias: ruff
        args: [--fix, --show-fixes]
        types_or: &ruff_types [python, pyi, jupyter, markdown]
      - id: ruff-format
        alias: ruff
        types_or: *ruff_types

  # * Spelling
  # ** typos
  - repo: https://github.com/adhtruong/mirrors-typos
    rev: v1.45.1
    hooks:
      - id: typos
        exclude_types: [jupyter]
        exclude: ^uv[.]lock$|^requirements|^\.copier-answers\.ya?ml$

  # * Dependencies
  # ** pyproject2conda
  - repo: https://github.com/usnistgov/pyproject2conda
    rev: v0.22.1
    hooks:
      - id: pyproject2conda-project
        alias: requirements
        args:
          - "--custom-command=prek run pyproject2conda-project --all-files"
  # ** uv
  - repo: https://github.com/astral-sh/uv-pre-commit
    rev: 0.11.7
    hooks:
      - id: uv-lock
        alias: requirements
        args: [--locked]
      - id: pip-compile
        alias: requirements
        entry: python tools/requirements_lock.py
        pass_filenames: true
        files: ^requirements/[^/]*\.txt$

  # * Commit message
  - repo: https://github.com/commitizen-tools/commitizen
    rev: v4.13.10
    hooks:
      - id: commitizen
        stages: [commit-msg]

  # * Actions
  - repo: https://github.com/python-jsonschema/check-jsonschema
    rev: 0.37.1
    hooks:
      - id: check-github-workflows
        alias: actions
        priority: 0
      - id: check-github-actions
        alias: actions
  - repo: https://github.com/rhysd/actionlint
    rev: v1.7.12
    hooks:
      - id: actionlint
        alias: actions
        stages: [manual]
        args:
          - "-ignore=SC2129" # ignorable stylistic lint from shellcheck
          - "-ignore=SC2016" # another shellcheck lint: seems to have false positives?
        language: golang # means renovate will also update `additional_dependencies`
        additional_dependencies:
          # actionlint has a shellcheck integration which extracts shell scripts in `run:` steps from GitHub Actions
          # and checks these with shellcheck. This is arguably its most useful feature,
          # but the integration only works if shellcheck is installed
          - "github.com/wasilibs/go-shellcheck/cmd/shellcheck@v0.11.1"
        # see https://github.com/rhysd/actionlint/issues/46
        exclude: ^\.github/actions
        priority: 0
  - repo: https://github.com/zizmorcore/zizmor-pre-commit
    # Zizmor version.
    rev: v1.24.1
    hooks:
      # Run the linter.
      - id: zizmor
        alias: actions

  # * Notebook specific --------------------------------------------------------
  # * Strip out metadata from notebooks
  - repo: https://github.com/kynan/nbstripout
    rev: 0.9.1
    hooks:
      - id: nbstripout
        args:
          - "--keep-output"
          - "--keep-count"
          - "--extra-keys"
          - "metadata.kernelspec metadata.kernel_spec"

  - repo: https://github.com/nbQA-dev/nbQA
    rev: 1.9.1
    hooks:
      # ** typos
      - id: nbqa
        name: nbqa-typos
        alias: typos
        additional_dependencies: &typos-deps
          - typos==1.45.1
        args:
          - typos
          - --force-exclude
          - --no-check-filenames
          - --write-changes
          - --nbqa-shell
      - id: nbqa
        name: nbqa-typos-markdown
        alias: typos
        additional_dependencies: *typos-deps
        args:
          - typos
          - --force-exclude
          - --no-check-filenames
          - --write-changes
          - --nbqa-shell
          - --nbqa-md

  # ** symlink in notebooks from example/usage to docs/example/usage
  - repo: local
    hooks:
      - id: symlink-docs-examples-notebooks
        name: symlink-docs-examples-notebooks
        entry: python tools/symlink_docs_examples_notebooks.py
        language: python
        files: ^docs/examples/.*\.md$
        pass_filenames: false

  #  * Other tools --------------------------------------------------------------