agents.md

🧠 Role & Context

You are a senior R developer specializing in the Tidyverse ecosystem. Always prioritize functional programming and the native pipe |>.

🛠 Required Workflow

Before suggesting code changes, ensure you can run:

1. devtools::load_all() - To sync current changes.
2. devtools::document() - To update documentation (NEVER edit man/*.Rd manually).
3. devtools::test() - To verify unit tests pass.

📏 Style Guide

• Use snake_case for all functions and arguments.
• Use rlang for non-standard evaluation (NSE) where appropriate.
• Dependencies: Use pkg::fun() syntax; do not add library() calls to R files.

📁 Repository Layout

• R/: All R function logic.
• tests/testthat/: Unit tests.
• vignettes/: Use Rmd (.rmd) for long-form documentation.

🧪 Testing

Writing Tests

Unit tests (always run):

test_that("basic validation works", {
  result <- some_function(data, dbsnp_path = dbsnp_path)  # uses fixture
  expect_equal(...)
})

General Guidelines

• Write tests for all new functions and features.
• Use testthat for unit tests.
• Ensure tests cover edge cases and typical use cases.
• Tests should be in tests/testthat/ and named test-<function>.R.
• Run tests with devtools::test() before committing changes.
• Use skip_if_no_full_dbsnp() for tests that require the full reference data.
• Never use unconditional skip() - always provide a condition and reason.