.pre-commit-config.yaml

# Canonical pre-commit configuration for ClimaAtmos.jl.
#
# Works with either `prek` (https://prek.j178.dev, recommended) or the original
# `pre-commit`. Install the git hooks once with `prek install`, then the hooks
# below run automatically on `git commit` against your staged files. For manual
# runs, `prek run` uses normal hook file matching; use
# `prek run --all-files` for a whole-repo sweep.
#
# Setup instructions live in docs/src/contributor_guide.md ("Pre-commit hooks").
exclude: .*docs/dev-guides.*|\.github.*
repos:
  - repo: https://github.com/pre-commit/pre-commit-hooks
    rev: v5.0.0
    hooks:
      - id: check-added-large-files
      - id: check-case-conflict
      - id: check-merge-conflict
      - id: check-symlinks
      - id: check-toml
      - id: check-yaml
      - id: end-of-file-fixer
      - id: mixed-line-ending
      # JuliaFormatter does not strip all trailing whitespace (e.g., in non-.jl
      # files), so trim it here. This includes markdown: the pinned
      # JuliaFormatter (=2.10.1) leaves no trailing whitespace of its own, so
      # the two hooks agree. JuliaFormatter 1.x did not, and the two would undo
      # each other on every run -- see the `julia-formatter` hook below.
      - id: trailing-whitespace

  - repo: local
    hooks:
      - id: markdown-link-ambiguity
        name: Documenter link ambiguity ([units] followed by parentheses)
        # Documenter parses `[text](target)` as a link, and its parser allows
        # any whitespace -- including a newline -- between `]` and `(`. Units
        # in brackets followed by a parenthetical therefore become links and
        # break the docs build with a :cross_references error. Most docstrings
        # are not rendered (checkdocs = :exports), so these stay latent until
        # the symbol is added to a page; catch them at commit time instead.
        entry: .dev/check_markdown_link_ambiguity.py
        language: system
        types_or: [julia, markdown]
        pass_filenames: true

      - id: julia-formatter
        name: JuliaFormatter (matches CI)
        # Uses the pinned .dev/format environment so the formatting matches the
        # julia-actions/julia-format CI check regardless of the JuliaFormatter
        # version in your base environment. Requires `julia` on your PATH.
        # `Pkg.resolve()` runs first because .dev/format/Manifest.toml is
        # gitignored: a manifest resolved before the compat bound in
        # .dev/format/Project.toml was last bumped still pins the old version,
        # and `Pkg.instantiate` honors it instead of re-resolving, silently
        # formatting with the wrong major version. `resolve` errors rather than
        # re-resolving in that case, so fall back to `Pkg.update()`, which
        # re-resolves against the bound. Both are near no-ops once the
        # environment matches.
        entry: julia --startup-file=no --project=.dev/format -e 'using Pkg; try Pkg.resolve(; io = devnull) catch; Pkg.update(; io = devnull) end; Pkg.instantiate(; io = devnull); using JuliaFormatter; format(ARGS)'
        language: system
        types_or: [julia, markdown]
        pass_filenames: true
        require_serial: true