Contributing to Rclade

Note: GitHub repository at https://github.com/zengzichao/Rclade. Issues and pull requests welcome.

Thank you for your interest in contributing to Rclade!

Reporting Issues

Please submit issues at https://github.com/zengzichao/Rclade/issues.

When reporting a bug, please include: - A minimal reproducible example - Your R session info (sessionInfo()) - The expected vs. actual behavior

Development Setup

# Clone the repository
git clone https://github.com/zengzichao/Rclade.git

# Install development dependencies
install.packages(c("devtools", "testthat", "roxygen2", "knitr", "rmarkdown"))

# Bioconductor dependencies
tryCatch({
  library(BiocManager)
}, error = function(e) {
  install.packages("BiocManager")
})
BiocManager::install(c("ggtree", "treeio", "tidytree"))

# Load the package in development mode
devtools::load_all(".")

# Run tests
devtools::test()

# Check the package
devtools::check()

# Build documentation
devtools::document()

Code Style

• Follow Google’s R Style Guide
• Use snake_case for function names and variables
• Document all exported functions with roxygen2
• Add @keywords internal to non-exported functions
• Run devtools::document() after modifying roxygen comments to keep man/ in sync

Pull Requests

1. Fork the repository
2. Create a feature branch (git checkout -b feature/my-feature)
3. Make your changes
4. Add tests for new functionality
5. Run devtools::check() to ensure no regressions
6. Submit a pull request

Testing

# Run all tests
devtools::test()

# Run specific test file
testthat::test_file("tests/testthat/test-taxonomy.R")

# Check test coverage
covr::package_coverage()

Documentation

• Update both README.EN.md and README.CN.md if user-facing behavior changes.
• Update NEWS.EN.md and NEWS.CN.md for notable changes.
• Regenerate man/ pages with devtools::document() when roxygen comments change.

License

By contributing, you agree that your contributions will be licensed under the MIT License.