Add R linting config

[ManavalanG]

As R is widely used across the team, we need to add linting for R. Tasks:

1. Which linter to use?
2. What configs to use?

Reached out to the team over slack to get info.

[sdhutchins]

I'm currently using lintr for the mecfs dge analysis repo.

My setup is below. I have turned off warnings as errors with the LINTR_ERROR_ON_LINT: false flag.

# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
on:
  push:
    branches: [main, master]
  pull_request:
    branches: [main, master]

name: run-lintr

jobs:
  lint-project:
    runs-on: ubuntu-latest
    env:
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
    steps:
      - uses: actions/checkout@v3

      - uses: r-lib/actions/setup-r@v2
        with:
          use-public-rspm: true

      - name: Install lintr
        run: install.packages("lintr")
        shell: Rscript {0}

      - name: Lint root directory
        run: lintr::lint_dir()
        shell: Rscript {0}
        env:
          LINTR_ERROR_ON_LINT: false

[ManavalanG]

This would be a fantastic addition. Is there anyone else in our team who use lintr for linting R? We could use another set of eyes on this setup and add this github action to the template repo. Thanks for setting it up and sharing with us :)

[sdhutchins]

Hey @ManavalanG! I decided to add that script here since it fits the scope a bit.

All it does is add/remove some folders/files, but it keeps the key structure.

#!/bin/bash
# ------------------------------------------------------------------
# [Shaurita Hutchins] rproj-setup
#          Script to apply R-specific .gitignore, clean up, and update directories/lintr
#

# R-specific .gitignore content
r_gitignore="# History files
.Rhistory
.Rapp.history

# Session Data files
.RData
.RDataTmp

# User-specific files
.Ruserdata

# Example code in package build process
*-Ex.R

# Output files from R CMD build
/*.tar.gz

# Output files from R CMD check
/*.Rcheck/

# RStudio files
.Rproj.user/

# Produced vignettes
vignettes/*.html
vignettes/*.pdf

# OAuth2 token
.httr-oauth

# knitr/R markdown cache dirs
*_cache/
/cache/

# Temp R markdown files
*.utf8.md
*.knit.md

# R environment variables
.Renviron

# Translation temp files
po/*~

# RStudio Connect folder
rsconnect/"

# Apply .gitignore and remove Python-specific files
{
  echo "$r_gitignore" >.gitignore
  rm -f .pylintrc
  rm -rf notebooks
} && echo ".gitignore and Python cleanup: Done."

# Rename src to analysis
mv src analysis && echo "Renamed src to analysis."

# Create output directory and .gitkeep
mkdir -p output
touch output/.gitkeep
echo "Created output directory and .gitkeep."

# lintr GitHub Actions workflow
lintr_content="# Workflow derived from r-lib/actions
name: run-lintr

on:
  push:
    branches: [main, master]
  pull_request:
    branches: [main, master]

jobs:
  lint-project:
    runs-on: ubuntu-latest
    env:
      GITHUB_PAT: \${{ secrets.GITHUB_TOKEN }}
    steps:
      - uses: actions/checkout@v3

      - uses: r-lib/actions/setup-r@v2
        with:
          use-public-rspm: true

      - name: Install lintr
        run: install.packages(\"lintr\")
        shell: Rscript {0}

      - name: Lint root directory
        run: lintr::lint_dir()
        shell: Rscript {0}
        env:
          LINTR_ERROR_ON_LINT: false
"

mkdir -p .github/workflows
echo "$lintr_content" >.github/workflows/lintr.yml && echo "Created lintr.yml."

# Update README.md structure diagram
if [[ -f "README.md" ]]; then
  # Replace src with analysis
  sed -i '' 's|├── src.*|├── analysis          <- Dir to store analysis code for use in this project|' README.md

  # Add output directory if not listed
  grep -q '├── output' README.md ||
    sed -i '' '/notebooks.*<- Dir to store.*notebooks/a\
├── output            <- Dir to store output files
' README.md

  # Add lintr.yml above linting.yml if not present
  grep -q 'lintr.yml' README.md ||
    sed -i '' '/│       ├── linting.yml/i\
│       ├── lintr.yml             <- GitHub Actions lint workflow for R
' README.md

  # Remove .pylintrc line regardless of spacing
  awk '!/├──[[:space:]]*\.pylintrc[[:space:]]*<- Python linting config/' README.md >tmp && mv tmp README.md

  echo "Updated README.md."
else
  echo "Warning: README.md not found. Skipping update."
fi

echo "All operations completed."

[wilkb777]

Conversation in stand up led us to conclude that updating the .gitignore and adding the GitHub action for rlinting in the template repo should go in and have a PR for review with @ManavalanG and @samuelbharti .