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AI Assistant Instructions for igvShiny

Source: AGENTS.md

This is an R package for Bioconductor. All code changes must adhere to Bioconductor standards.

Workflow & Standards

  1. Documentation (Roxygen2): Use roxygen2 for all R documentation. When modifying .R files in the R/ directory (adding/changing functions or docs), you must run devtools::document() to update the man/ directory and NAMESPACE file. Do not edit NAMESPACE or .Rd files manually.
  2. Testing: This package uses the testthat framework for testing. Tests are located in tests/testthat/. Any new feature or bug fix must be accompanied by appropriate tests. Run tests via make test or devtools::test() to verify changes.
  3. Continuous Integration / Checking: The preferred method for running comprehensive checks (R CMD check, tests, linters, etc.) is via gDRstyle::checkPackage(). Ensure the package passes these checks before finalizing any commits.
  4. Dependencies: R dependencies are defined in the DESCRIPTION file. If a new package is required, add it to the appropriate section (Imports:, Suggests:, Depends:).
  5. Front-end / JavaScript: As an htmlwidgets package, the JavaScript code is typically located in inst/htmlwidgets/ or a similarly configured directory. Ensure any JS modifications are properly synchronized with the R widget bindings.
  6. General Make Targets: The makefile provides useful targets: make roxy (document), make test (run testthat tests), make demo (run the shiny demo app), and make all.

Automated review — what it does and does not catch

Pull requests are reviewed by CodeRabbit (.coderabbit.yaml, profile assertive). Treat it as editorial review: style, obvious logic slips, missing tests and docs. It reads the diff, so it cannot catch the class of bug that has actually hurt this package — the semantics of the bundled igv.js. Finding those means reading inst/htmlwidgets/lib/igv-*.js directly, and that path is filtered out of review on purpose (~8.7 MB of third-party code).

Two conventions exist for the bot’s benefit:

  • PRs use Related: #NNN, not Fixes #NNN — see .github/pull_request_template.md. Auto-closing has hidden partly-finished work before (#36), but the reference still has to be there or CodeRabbit’s linked-issue checks silently skip.
  • Broken external assets are checked deterministically, not by an AI reviewer: .github/workflows/asset-url-check.yml runs .github/scripts/check-asset-urls.sh weekly and files an issue when a genome, index or demo track URL stops resolving. Run the script by hand after touching any URL in R/, inst/demos/ or inst/htmlwidgets/igvShiny.js.