lint-yaml.yml

Lint tracked YAML files with yamllint using a bundled default config (overridable), plus a companion check that flags run: script blocks in workflow/action YAML longer than a configurable line threshold, so they get decomposed into a separate script file the way this repo’s own R/Python capabilities already do.

Inputs

Input	Type	Default	Description
`python-version`	string	`'3.x'`	Python version to set up.
`config-file`	string	`''`	Path (in the caller repo) to a yamllint config file. Falls back to the bundled default when empty or the file does not exist.
`paths-ignore`	string	`''`	Comma/newline-separated glob patterns (relative paths) to skip, for both checks. Supports ``, `?`, and recursive `*`.
`fail`	boolean	`true`	Fail the workflow when yamllint reports an error (not a warning).
`max-script-lines`	string	`'150'`	Flag a `run:` block longer than this many lines. Matches the lab manual’s `<150`-line function-length heuristic.
`fail-on-long-scripts`	boolean	`false`	Fail when a `run:` block exceeds `max-script-lines`. Defaults to warn-only, since the lab manual documents its line-count heuristic as a provisional trigger to reassess decomposition, not a hard constraint.

Permissions

Only contents: read (the default), so no permissions: block is needed.

Example

# Copy to .github/workflows/lint-yaml.yml in your repo.
# Lints tracked YAML files with yamllint (bundled default config), plus a
# companion check that flags long `run:` script blocks in workflow/action
# YAML as decomposition candidates.
# Only contents:read is needed (the default), so no permissions block is required.
name: Lint YAML

on:
  push:
    branches:
      - main
  pull_request:
  workflow_dispatch:

jobs:
  lint:
    uses: Morrison-Lab/gha/.github/workflows/lint-yaml.yml@v2
    # with:
    #   config-file: '.yamllint.yml'   # override the bundled default config
    #   paths-ignore: 'renv/**'        # skip known-vendored paths
    #   fail: false                    # warn instead of failing on yamllint errors

See the examples/ directory for the full caller stub (lint-yaml.yml).