@hivehub/rulebook 2.1.0 → 3.0.0

package/templates/skills/languages/r/SKILL.md

@@ -0,0 +1,360 @@
+---
+name: "R"
+description: "Execute these commands after EVERY implementation (see AGENT_AUTOMATION module for full workflow)."
+version: "1.0.0"
+category: "languages"
+author: "Rulebook"
+tags: ["languages", "language"]
+dependencies: []
+conflicts: []
+---
+<!-- R:START -->
+# R Project Rules
+
+## Agent Automation Commands
+
+**CRITICAL**: Execute these commands after EVERY implementation (see AGENT_AUTOMATION module for full workflow).
+
+```bash
+# Complete quality check sequence:
+Rscript -e 'styler::style_pkg(dry="on")'  # Format check
+Rscript -e 'lintr::lint_package()'  # Linting
+R CMD check .             # Full check
+Rscript -e 'devtools::test()'  # All tests
+
+# Security audit:
+Rscript -e 'pak::pkg_deps_explain()'  # Dependency check
+```
+
+## R Configuration
+
+**CRITICAL**: Use R 4.2+ with modern package development tools.
+
+- **Version**: R 4.2+
+- **Recommended**: R 4.3+
+- **Style Guide**: tidyverse style guide
+- **Testing**: testthat 3.x
+- **Documentation**: roxygen2
+
+### DESCRIPTION File Requirements
+
+```
+Package: yourpackage
+Type: Package
+Title: Your Package Title
+Version: 0.1.0
+Author: Your Name
+Maintainer: Your Name <you@example.com>
+Description: A comprehensive description of what your package does.
+License: MIT + file LICENSE
+Encoding: UTF-8
+LazyData: true
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.2.3
+Depends: 
+    R (>= 4.2)
+Imports:
+    dplyr (>= 1.1.0),
+    ggplot2 (>= 3.4.0)
+Suggests: 
+    testthat (>= 3.0.0),
+    knitr,
+    rmarkdown
+VignetteBuilder: knitr
+```
+
+## Code Quality Standards
+
+### Mandatory Quality Checks
+
+**CRITICAL**: After implementing ANY feature, you MUST run these commands in order.
+
+**IMPORTANT**: These commands MUST match your GitHub Actions workflows to prevent CI/CD failures!
+
+```bash
+# Pre-Commit Checklist (MUST match .github/workflows/*.yml)
+
+# 1. Format check (matches workflow - use dry="on"!)
+Rscript -e "styler::style_pkg(dry = 'on')"
+
+# 2. Lint (MUST pass with no warnings - matches workflow)
+Rscript -e "lintr::lint_package()"
+
+# 3. Run all tests (MUST pass 100% - matches workflow)
+Rscript -e "devtools::test()"
+
+# 4. Check package (matches workflow - strict CRAN checks)
+R CMD build .
+R CMD check *.tar.gz --as-cran --no-manual
+
+# 5. Check coverage (MUST meet threshold)
+Rscript -e "covr::package_coverage()"
+
+# 6. Build documentation (matches workflow)
+Rscript -e "devtools::document()"
+
+# If ANY fails: ❌ DO NOT COMMIT - Fix first!
+```
+
+**If ANY of these fail, you MUST fix the issues before committing.**
+
+**Why This Matters:**
+- Running different commands locally than in CI causes "works on my machine" failures
+- CI/CD workflows will fail if commands don't match
+- Example: Using `styler::style_pkg()` locally but `dry='on'` in CI = failure
+- Example: Missing `--as-cran` flag = CRAN submission fails
+- Example: Skipping lintr locally = CI catches style violations
+
+### Formatting
+
+- Use `styler` for consistent code style
+- Based on tidyverse style guide
+- Configuration in `.lintr` file
+
+Example `.lintr`:
+```
+linters: linters_with_defaults(
+  line_length_linter(100),
+  object_name_linter = NULL,
+  cyclocomp_linter(25)
+)
+exclusions: list(
+  "tests/testthat.R"
+)
+```
+
+### Documentation
+
+- Use roxygen2 for function documentation
+- All exported functions must be documented
+- Include examples in documentation
+
+Example roxygen2 documentation:
+```r
+#' Process Data
+#'
+#' This function processes input data and returns cleaned results.
+#'
+#' @param data A data.frame with input data
+#' @param threshold Numeric threshold value (default: 0.5)
+#' @param verbose Logical; if TRUE, print progress messages
+#'
+#' @return A data.frame with processed data
+#' @export
+#'
+#' @examples
+#' data <- data.frame(x = 1:10, y = rnorm(10))
+#' result <- process_data(data, threshold = 0.7)
+process_data <- function(data, threshold = 0.5, verbose = FALSE) {
+  if (!is.data.frame(data)) {
+    stop("data must be a data.frame")
+  }
+  
+  if (verbose) {
+    message("Processing data...")
+  }
+  
+  # Implementation
+  return(data)
+}
+```
+
+### Testing
+
+- **Framework**: testthat 3.x
+- **Location**: `/tests/testthat` directory
+- **Coverage**: Must meet threshold (80%+)
+- **File naming**: `test-*.R` for test files
+
+Example test structure:
+```r
+# tests/testthat/test-process.R
+
+test_that("process_data handles valid input", {
+  data <- data.frame(x = 1:5, y = 1:5)
+  result <- process_data(data)
+  
+  expect_s3_class(result, "data.frame")
+  expect_equal(nrow(result), 5)
+})
+
+test_that("process_data errors on invalid input", {
+  expect_error(
+    process_data("not a dataframe"),
+    "data must be a data.frame"
+  )
+})
+
+test_that("process_data respects threshold parameter", {
+  data <- data.frame(x = 1:10, y = rnorm(10))
+  result <- process_data(data, threshold = 0.7)
+  
+  expect_true(all(result$y >= 0.7 | result$y <= -0.7))
+})
+```
+
+## Package Development
+
+### Package Structure
+
+```
+yourpackage/
+├── DESCRIPTION          # Package metadata
+├── NAMESPACE            # Auto-generated by roxygen2
+├── LICENSE              # License file
+├── README.md            # Package overview
+├── NEWS.md              # Changelog
+├── R/
+│   ├── package.R        # Package-level documentation
+│   ├── data.R           # Data documentation
+│   └── functions.R      # Function implementations
+├── man/                 # Auto-generated documentation
+├── tests/
+│   ├── testthat.R
+│   └── testthat/
+│       ├── test-functions.R
+│       └── test-data.R
+├── data/                # Package data
+├── inst/                # Installed files
+└── vignettes/           # Long-form documentation
+```
+
+### Development Workflow
+
+```r
+# Load package for development
+devtools::load_all()
+
+# Run tests
+devtools::test()
+
+# Check package
+devtools::check()
+
+# Generate documentation
+devtools::document()
+
+# Build package
+devtools::build()
+
+# Install locally
+devtools::install()
+```
+
+## Dependencies
+
+### CRAN vs GitHub Packages
+
+```r
+# From CRAN
+install.packages("dplyr")
+
+# From GitHub
+devtools::install_github("tidyverse/dplyr")
+
+# Specify in DESCRIPTION:
+Imports:
+    dplyr (>= 1.1.0)
+Remotes:
+    github::tidyverse/dplyr@main
+```
+
+## Best Practices
+
+### DO's ✅
+
+- **USE** tidyverse principles
+- **DOCUMENT** all exported functions
+- **TEST** all functionality
+- **CHECK** inputs with `stopifnot()` or custom validation
+- **RETURN** consistent types
+- **NAMESPACE** use explicit `::` for external functions
+- **VECTORIZE** operations when possible
+
+### DON'Ts ❌
+
+- **NEVER** use `T` or `F` (use `TRUE` and `FALSE`)
+- **NEVER** use `attach()` or `<<-` in packages
+- **NEVER** modify global options
+- **NEVER** use `library()` inside functions
+- **NEVER** leave `browser()` or `print()` debug code
+- **NEVER** assume working directory
+
+Example code style:
+```r
+# ✅ GOOD: Proper function structure
+process_data <- function(data, threshold = 0.5) {
+  # Input validation
+  stopifnot(
+    is.data.frame(data),
+    is.numeric(threshold),
+    threshold >= 0, threshold <= 1
+  )
+  
+  # Use explicit namespace
+  result <- dplyr::filter(data, value > threshold)
+  
+  return(result)
+}
+
+# ❌ BAD: Poor practices
+process_data <- function(data, threshold = 0.5) {
+  library(dplyr)  # DON'T load packages in functions!
+  attach(data)    # NEVER use attach()!
+  
+  result <- filter(data, value > threshold)  # Unclear where filter comes from
+  result <<- result  # DON'T use global assignment!
+  
+  print(result)  # Don't print inside functions
+}
+```
+
+## CI/CD Requirements
+
+Must include GitHub Actions workflows:
+
+1. **Testing** (`r-test.yml`):
+   - Test on ubuntu-latest, windows-latest, macos-latest
+   - R versions: release, devel
+   - Use R CMD check --as-cran
+   - Upload coverage to Codecov
+
+2. **Linting** (`r-lint.yml`):
+   - Run lintr checks
+   - Check style with styler
+   - Verify roxygen2 documentation
+
+3. **CRAN Check** (`r-cran.yml`):
+   - R CMD check with --as-cran
+   - Verify no NOTEs, WARNINGs, or ERRORs
+
+## Publishing to CRAN
+
+### Pre-Submission Checklist
+
+- ✅ All tests passing
+- ✅ R CMD check --as-cran passes with 0 NOTEs
+- ✅ Package documentation complete
+- ✅ NEWS.md updated
+- ✅ README.md current
+- ✅ Examples run successfully
+- ✅ Vignettes build correctly
+- ✅ Valid LICENSE file
+- ✅ No submission policy violations
+
+### Submission Process
+
+```r
+# 1. Final check
+devtools::check(cran = TRUE)
+
+# 2. Build package
+devtools::build()
+
+# 3. Submit to CRAN
+devtools::submit_cran()
+
+# 4. Respond to CRAN feedback promptly
+```
+
+<!-- R:END -->