Add comprehensive tests for utils.R and improve coverage for low-coverage files #36
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| # GitHub Copilot Environment Setup for lavaanExtra R Package | |
| # This workflow sets up the development environment before Copilot starts working | |
| # Based on: https://docs.github.com/en/copilot/how-tos/use-copilot-agents/coding-agent/customize-the-agent-environment | |
| name: copilot-setup-steps | |
| on: | |
| workflow_dispatch: | |
| # This workflow is automatically triggered by GitHub Copilot | |
| # before the agent starts working in the repository | |
| pull_request: | |
| types: [opened, synchronize] | |
| jobs: | |
| copilot-setup-steps: | |
| # Optional: only run on Copilot agent commits; remove this if you also want your own pushes to trigger it | |
| if: > | |
| github.event_name == 'workflow_dispatch' || | |
| (github.event_name == 'pull_request' && | |
| github.actor == 'github-copilot') | |
| runs-on: ubuntu-latest | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| R_KEEP_PKG_SOURCE: yes | |
| _R_CHECK_CRAN_INCOMING_: false | |
| _R_CHECK_FORCE_SUGGESTS_: false | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 1 | |
| - name: Determine if R setup is needed | |
| id: check_r_needed | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| run: | | |
| set -euo pipefail | |
| echo "Checking if R environment setup is needed..." | |
| R_NEEDED=true | |
| # If this is a PR, use the PR's changed files (authoritative) | |
| if [ "${GITHUB_EVENT_NAME}" = "pull_request" ]; then | |
| PR_NUMBER=$(jq -r '.number' < "$GITHUB_EVENT_PATH") | |
| echo "PR number: $PR_NUMBER" | |
| # Get changed files from the PR | |
| FILES=$(curl -sS -H "Authorization: Bearer ${GITHUB_TOKEN}" \ | |
| -H "Accept: application/vnd.github+json" \ | |
| "${GITHUB_API_URL}/repos/${GITHUB_REPOSITORY}/pulls/${PR_NUMBER}/files?per_page=100" \ | |
| | jq -r '.[].filename') | |
| echo "Files in PR:" | |
| echo "${FILES}" | |
| # If ANY file is not in the "docs/config-only" set -> need R | |
| # Allowed-only set (docs/config): tweak as you like | |
| # Note: use a temporary file to avoid word-splitting issues | |
| echo "${FILES}" > /tmp/pr_files.txt | |
| if grep -E '\.(R|Rmd|Rd)$' /tmp/pr_files.txt >/dev/null || \ | |
| grep -E '^(R/|tests/|man/|vignettes/|src/)' /tmp/pr_files.txt >/dev/null; then | |
| echo "Detected R-related paths in PR." | |
| R_NEEDED=true | |
| else | |
| # Anything outside the allowed docs/config list? Then R is needed. | |
| if grep -v -E '^(\.github/copilot-instructions\.md|\.github/workflows/|README\.md|\.gitignore|\.Rbuildignore|NEWS\.md|CONTRIBUTING\.md|LICENSE|CITATION\.cff|DESCRIPTION|cran-comments\.md|.+\.md$|.+\.ya?ml$)$' /tmp/pr_files.txt | grep -E '.' >/dev/null; then | |
| echo "Changes go beyond docs/config-only." | |
| R_NEEDED=true | |
| else | |
| echo "PR is docs/config-only." | |
| R_NEEDED=false | |
| fi | |
| fi | |
| else | |
| # No PR context (Copilot run, pushes, etc.) | |
| # Fallback: fast probe + light heuristics | |
| echo "No PR context; using probe/heuristics." | |
| # Example probe: if R already present and renv/cache present, skip | |
| if command -v R >/dev/null 2>&1 && [ -f "renv.lock" ] && [ -d "~/.cache/R" ]; then | |
| echo "R and cache present; likely no heavy setup needed." | |
| R_NEEDED=false | |
| else | |
| # Last-commit heuristic (with full history available) | |
| # Compare against the immediate parent only, to avoid "recent history" bias | |
| if git rev-parse --verify HEAD~1 >/dev/null 2>&1; then | |
| CHANGED=$(git diff --name-only HEAD~1...HEAD || true) | |
| else | |
| CHANGED=$(git ls-files) # first run in a new repo clone | |
| fi | |
| echo "${CHANGED}" > /tmp/changed.txt | |
| if grep -E '\.(R|Rmd|Rd)$' /tmp/changed.txt >/dev/null || \ | |
| grep -E '^(R/|tests/|man/|vignettes/|src/)' /tmp/changed.txt >/dev/null; then | |
| R_NEEDED=true | |
| else | |
| if grep -v -E '^(\.github/copilot-instructions\.md|\.github/workflows/|README\.md|\.gitignore|\.Rbuildignore|NEWS\.md|CONTRIBUTING\.md|LICENSE|CITATION\.cff|DESCRIPTION|cran-comments\.md|.+\.md$|.+\.ya?ml$)$' /tmp/changed.txt | grep -E '.' >/dev/null; then | |
| R_NEEDED=true | |
| else | |
| R_NEEDED=false | |
| fi | |
| fi | |
| fi | |
| fi | |
| echo "R_NEEDED=${R_NEEDED}" | tee -a "$GITHUB_OUTPUT" | |
| echo "" | |
| echo "=== FINAL DECISION ===" | |
| if [ "$R_NEEDED" == "true" ]; then | |
| echo "✓ R setup WILL be run" | |
| echo "Reason: Analysis indicates R functionality is needed" | |
| else | |
| echo "✓ R setup WILL BE SKIPPED" | |
| echo "Reason: Only documentation/config files detected" | |
| fi | |
| echo "Decision: R_NEEDED=$R_NEEDED" | |
| - name: Setup R | |
| if: steps.check_r_needed.outputs.R_NEEDED == 'true' | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: 'release' | |
| use-public-rspm: true | |
| - name: Setup pandoc (required for building vignettes and reprex) | |
| if: steps.check_r_needed.outputs.R_NEEDED == 'true' | |
| uses: r-lib/actions/setup-pandoc@v2 | |
| - name: Install system dependencies | |
| if: steps.check_r_needed.outputs.R_NEEDED == 'true' | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y \ | |
| libcurl4-openssl-dev \ | |
| libssl-dev \ | |
| libxml2-dev | |
| - name: Setup R user library | |
| if: steps.check_r_needed.outputs.R_NEEDED == 'true' | |
| run: | | |
| mkdir -p ~/R/library | |
| echo 'R_LIBS_USER=~/R/library' >> ~/.Renviron | |
| shell: bash | |
| - name: Install R dependencies using pak | |
| if: steps.check_r_needed.outputs.R_NEEDED == 'true' | |
| uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| # Use stable pak for reliable dependency resolution | |
| dependencies: '"hard"' | |
| # Install core package dependencies and essential development tools | |
| extra-packages: | | |
| local::. | |
| any::testthat | |
| any::lintr | |
| any::styler | |
| any::roxygen2 | |
| any::devtools | |
| any::reprex | |
| any::knitr | |
| any::rmarkdown | |
| any::clipr | |
| needs: check | |
| # Let r-lib/actions handle caching automatically (more efficient than manual cache) | |
| # NOTE: Suggested packages are NOT installed during setup to save time. | |
| # Only core dependencies (Imports/Depends) and essential development tools are installed. | |
| # Additional packages are installed on-demand based on specific PR requirements. | |
| # See copilot-instructions.md for targeted installation guidance. | |
| # NOTE: The local package (lavaanExtra) is automatically built and installed | |
| # by setup-r-dependencies@v2 when using 'local::.', eliminating the need | |
| # for manual build/install steps | |
| - name: Verify R installation and packages | |
| if: steps.check_r_needed.outputs.R_NEEDED == 'true' | |
| run: | | |
| cat("=== R Version ===\n") | |
| print(R.version.string) | |
| cat("\n=== Core Development Packages ===\n") | |
| required_packages <- c("lavaan", "insight", "testthat", "lintr", "styler", "roxygen2", "reprex") | |
| for (pkg in required_packages) { | |
| if (requireNamespace(pkg, quietly = TRUE)) { | |
| cat("✓", pkg, "- version", as.character(packageVersion(pkg)), "\n") | |
| } else { | |
| cat("✗", pkg, "- NOT AVAILABLE\n") | |
| } | |
| } | |
| cat("\n=== lavaanExtra Package (auto-installed by setup-r-dependencies) ===\n") | |
| if (requireNamespace("lavaanExtra", quietly = TRUE)) { | |
| library(lavaanExtra) | |
| cat("✓ lavaanExtra - version", as.character(packageVersion("lavaanExtra")), "\n") | |
| } else { | |
| cat("✗ lavaanExtra - NOT AVAILABLE\n") | |
| } | |
| shell: Rscript {0} | |
| - name: Test core lavaanExtra functionality | |
| if: steps.check_r_needed.outputs.R_NEEDED == 'true' | |
| run: | | |
| library(lavaanExtra) | |
| cat("=== Testing Core Functions ===\n") | |
| # Test basic data function | |
| test_data <- data.frame(id = c(1,1,2,3), val = c(1,2,3,4)) | |
| duplicates <- extract_duplicates(test_data, id = "id") | |
| cat("✓ extract_duplicates() works\n") | |
| # Basic verification that package loads correctly | |
| cat("✓ lavaanExtra package loads and core functions work\n") | |
| cat("=== Core Function Tests Complete ===\n") | |
| shell: Rscript {0} | |
| - name: Display environment summary | |
| run: | | |
| echo "=== GitHub Copilot Environment Setup Complete ===" | |
| echo "" | |
| if [ "${{ steps.check_r_needed.outputs.R_NEEDED }}" == "true" ]; then | |
| echo "✓ Optimized R development environment configured using pak:" | |
| echo " - R and essential system dependencies installed" | |
| echo " - Core package dependencies (Imports/Depends) installed via setup-r-dependencies" | |
| echo " - lavaanExtra package automatically built and installed" | |
| echo " - Essential development tools (lintr, styler, roxygen2, devtools)" | |
| echo " - reprex dependencies ready (reprex + knitr + rmarkdown + pandoc)" | |
| echo " - Efficient pak-based dependency resolution with automatic caching" | |
| echo " - Suggested packages NOT installed (install as needed per PR)" | |
| echo " - Minimal testing performed for faster setup" | |
| echo "" | |
| echo "The environment is ready for R package development work." | |
| echo "Copilot can now build, test, lint, and create reproducible examples." | |
| else | |
| echo "✓ Minimal environment configured:" | |
| echo " - Repository checked out and ready" | |
| echo " - R setup SKIPPED - only documentation/config changes detected" | |
| echo "" | |
| if [ "${GITHUB_EVENT_NAME:-}" = "pull_request" ]; then | |
| echo "Decision based on PR file analysis using GitHub API" | |
| else | |
| echo "Decision based on git diff analysis" | |
| fi | |
| echo "The environment is ready for documentation and configuration work." | |
| echo "Perfect for version bumps, NEWS.md updates, and text editing tasks." | |
| fi | |
| shell: bash |