check-quarto-manuscript.yml

Bundles the standard check suite for Quarto manuscript and academic paper repositories (such as Morrison-Lab/qmt). Replaces individual workflow files with a single composite action or reusable workflow call.

What it runs

Runs the full Morrison-Lab repository hygiene pass plus manuscript-specific checks:

check-junk-files.yml: OS and editor detritus (.DS_Store, Thumbs.db, .Rhistory, etc.)
check-secrets.yml: Gitleaks scan of git history for committed credentials and tokens
check-non-standard-chars.yml: flags non-standard unicode characters, curly quotes, and smart dashes
check-new-line-breaks.yml: enforces semantic line breaks on modified lines in diffs
check-typos.yml: crate-ci/typos CLI scan for spelling errors on modified files
check-ai-tells.yml: scans narrative prose (*.md, *.qmd) for AI cliches and tells
lint-yaml.yml: yamllint over tracked YAML files
lint-workflows.yml: actionlint and zizmor over GitHub Actions workflows
lint-markdown.yml: markdownlint-cli2 over tracked Markdown files
lint-qmd.yml: markdownlint over prose sections of tracked .qmd files
check-links.yml: lychee link checker across manuscript sections, references, and external links
check-quarto-links.yml: relative links from .qmd/.md/.Rmd sources to pages that do not exist, which Quarto only warns about and lychee does not read out of a .qmd
check-orphaned-images.yml: tracked images that no source file references (warn-only by default)
check-typed-output.yml: typed or faked code output in Quarto sources (warn-only by default)
check-informal-definitions.yml: flags technical concepts defined in running prose rather than formal Quarto definition divs (::: {#def-...}) (warn-only by default)
check-bibliography-dois.yml: validates BibTeX bibliography entries in .bib files
check-equation-renders.yml: crawls rendered HTML manuscript pages to ensure MathJax typesets all equations without errors (active when equation-renders-site-dir is specified)

Every check is enabled by default. Opt out of any specific check by passing its boolean flag as false.

Inputs

Input	Type	Default	Description
`fail`	boolean	`true`	Fail the job on findings (else warn only).
`check-junk-files`	boolean	`true`	Enable junk files check.
`junk-patterns`	string	see `check-junk-files.qmd`	Gitignore patterns naming junk files.
`junk-paths-ignore`	string	`''`	Paths to exempt from junk files scan.
`check-secrets`	boolean	`true`	Enable gitleaks secrets scan.
`secrets-config`	string	`''`	Custom gitleaks config file path.
`secrets-paths-ignore`	string	`''`	Regex paths to exempt from secrets scan.
`check-non-standard-chars`	boolean	`true`	Enable non-standard character check.
`non-standard-chars-extensions`	string	`'.qmd, .md'`	File extensions to check for non-standard characters.
`check-new-line-breaks`	boolean	`true`	Enable semantic line break check.
`new-line-breaks-base-ref`	string	`''`	Base ref for diff-scoping new line breaks.
`new-line-breaks-globs`	string	`''`	Globs to check for new line breaks.
`check-typos`	boolean	`true`	Enable typos check.
`typos-config`	string	`''`	Typos configuration file path.
`typos-base-ref`	string	`''`	Base ref for diff-scoping typo checks.
`check-ai-tells`	boolean	`true`	Enable AI tells check on prose.
`ai-tells-threshold`	string	`'10'`	Maximum allowed tell density (per 1,000 words).
`ai-tells-ignore`	string	`''`	Comma- or space-separated list of tells to ignore.
`lint-yaml`	boolean	`true`	Enable YAML linting.
`yaml-config-file`	string	`''`	Custom yamllint config file path.
`yaml-paths-ignore`	string	`''`	Patterns to exclude from YAML linting.
`lint-workflows`	boolean	`true`	Enable workflow linting.
`workflows-path`	string	`'.'`	Path to workflow files.
`lint-markdown`	boolean	`true`	Enable Markdown linting.
`markdown-config-file`	string	`''`	Markdownlint config file path.
`markdown-globs`	string	`'*.md'`	Git pathspecs of Markdown files to lint.
`markdown-paths-ignore`	string	`''`	Paths to exempt from Markdown linting.
`markdown-base-ref`	string	`''`	Base ref for list-item splice checks.
`lint-qmd`	boolean	`true`	Enable QMD prose linting.
`qmd-config-file`	string	`''`	Markdownlint config file for QMD files.
`qmd-globs`	string	`'*.qmd'`	Pathspecs of QMD files to lint.
`qmd-paths-ignore`	string	`''`	Patterns to skip for QMD linting.
`check-links`	boolean	`true`	Enable lychee link checker.
`lychee-config`	string	`''`	Path to a custom lychee config file.
`lychee-args`	string	`'--exclude-mail'`	Command-line arguments for lychee. Do not pass `--format` or `--output`.
`check-quarto-links`	boolean	`true`	Enable the check for links to missing Quarto pages; blocking or not follows `fail`.
`quarto-links-paths-ignore`	string	`''`	Globs of source files to skip for the Quarto links check.
`check-orphaned-images`	boolean	`true`	Enable the orphaned-images report.
`orphaned-images-paths-ignore`	string	`''`	Globs of images to skip.
`orphaned-images-base-ref`	string	`''`	Base ref so only images added since it are reported; empty examines every image.
`orphaned-images-fail`	boolean	`false`	Fail on an orphaned image; the report warns only by default, whatever `fail` says.
`check-typed-output`	boolean	`true`	Enable the check for typed or faked code output.
`typed-output-globs`	string	`'*.qmd'`	Space-separated git pathspecs of tracked files to check.
`typed-output-paths-ignore`	string	`''`	Patterns to skip for typed output check.
`typed-output-diff-scoped`	boolean	`false`	Report only findings on lines added since `typed-output-base-ref`.
`typed-output-base-ref`	string	`''`	Base ref for diff-scoped typed output check.
`typed-output-fail`	boolean	`false`	Fail on typed code output; the check warns only by default, whatever `fail` says.
`check-informal-definitions`	boolean	`true`	Enable check for informal definitions in prose.
`informal-definitions-globs`	string	`'*.qmd'`	Space-separated git pathspecs of tracked files to check.
`informal-definitions-paths-ignore`	string	`''`	Patterns to skip for informal definitions check.
`informal-definitions-diff-scoped`	boolean	`false`	Report only findings on lines added since `informal-definitions-base-ref`.
`informal-definitions-base-ref`	string	`''`	Base ref for diff-scoped informal definitions check.
`informal-definitions-fail`	boolean	`false`	Fail on informal definitions; the check warns only by default, whatever `fail` says.
`check-bibliography-dois`	boolean	`true`	Enable bibliography DOI validation.
`bib-exclude-keys`	string	`''`	BibTeX keys to skip for DOI validation.
`check-equation-renders`	boolean	`true`	Enable equation render validation.
`equation-renders-site-dir`	string	`''`	Directory of built HTML pages to crawl.

Example

name: Check Quarto manuscript

on:
  push:
    branches: [main]
  pull_request:

jobs:
  check:
    permissions:
      contents: read
    uses: Morrison-Lab/gha/.github/workflows/check-quarto-manuscript.yml@v3