lint-changed-lines.yml

Run lintr over the R files a pull request changes, but report only the lints on lines the PR actually added or modified – not whole changed files. This lets lint rules be adopted or tightened incrementally: new and edited code must comply, while untouched legacy code in the same file is left alone until a PR naturally edits it.

Contrast with a whole-file “lint changed files” gate, which fails on function definitions a PR never touched – forcing either a repo-wide reformat or disabling the linter. lint-changed-lines is the incremental alternative. The whole-file, whole-package, and whole-project forms live in lint-changed-files.yml, selected by a scope input; that capability does not fold this one in, because the added-lines diffing here is different machinery.

How it works

The workflow checks out the PR head commit (not the default refs/pull/N/merge ref), sets up R, installs the package (so object_usage_linter can resolve the package’s own functions), then runs lintr on each changed R file and keeps only the lints whose line falls on a line the PR added or modified. Those changed lines are parsed from the GitHub “list PR files” API patch, whose line numbers are relative to the PR head – which is why the checkout is pinned to the head commit, so on-disk line numbers match.

Must be triggered by pull_request (the changed-line set comes from the PR).

Inputs

Input	Type	Default	Description
path	string	'.'	Path to the R package root (the directory holding DESCRIPTION).
install-quarto	boolean	false	Install Quarto when setting up R dependencies.
use-renv	boolean	false	Restore dependencies with renv (setup-renv) instead of DESCRIPTION-based setup-r-dependencies.
renv-cache-version	string	'1'	Cache version suffix passed to setup-renv.
apt-packages	string	''	Extra apt packages to install before setting up dependencies (space-separated).
extra-packages	string	''	Extra R packages to install (space- or comma-separated; passed to setup-r-dependencies, or installed from CRAN under use-renv: true). gh and lintr are always installed.
install-package	boolean	true	Run R CMD INSTALL before linting so object_usage_linter can resolve the package’s own functions. Set false for a repo that is not an installable R package.
fail	boolean	true	Fail the workflow when a lint is found on a changed line (rather than warn only).

Permissions

contents: read and pull-requests: read (to read the PR’s changed-file patches).

Example

# Copy to .github/workflows/lint-changed-lines.yml in your repo.
# Lints only the lines a pull request adds or modifies (not whole changed
# files), so lint rules can be adopted or tightened incrementally.
name: lint-changed-lines

on:
  pull_request:

jobs:
  lint:
    uses: Morrison-Lab/gha/.github/workflows/lint-changed-lines.yml@v2
    # with:
    #   path: '.'               # R package root (holding DESCRIPTION)
    #   use-renv: false         # true to restore dependencies with setup-renv
    #   renv-cache-version: '1' # bump to invalidate renv cache
    #   apt-packages: ''        # system packages required for compilation
    #   extra-packages: ''      # extra R deps (gh + lintr always installed)
    #   install-package: false  # skip R CMD INSTALL for a non-package repo
    #   fail: false             # warn instead of failing on lints

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