Skip to content

Latest commit

 

History

History
130 lines (103 loc) · 4.24 KB

CONTRIBUTING.md

File metadata and controls

130 lines (103 loc) · 4.24 KB

Contributing to RcppML

Thank you for your interest in contributing to RcppML! This document provides guidelines and instructions for contributing to the project.

RcppML v1.0.0 was written in early 2026 in VSCode with GitHub Copilot and Claude Opus 4.6 Agent mode. A similar development IDE is recommended for further contributions due to the large number of backends, algorithms, and optimization branches that are difficult to trace manually. Please ensure all pull requests are as narrow in scope as possible.

Getting Started

  1. Fork and clone the repository:

    git clone https://github.com/zdebruine/RcppML.git
cd RcppML

  2. Install dependencies:

    install.packages(c("Rcpp", "RcppEigen", "Matrix", "testthat", "devtools", "roxygen2", "knitr", "rmarkdown"))

  3. Build and test:

    devtools::document()
devtools::test()
devtools::check()

Project Structure

Directory Contents
R/ R source files (roxygen documented)
src/ C++ Rcpp bridge files (RcppFunctions*.cpp, sparsepress_bridge.cpp)
inst/include/RcppML/ Header-only C++ library (core NNLS, clustering)
inst/include/FactorNet/ NMF/SVD engine, GPU kernels, factor graph fitting
inst/include/streampress/ StreamPress I/O (rANS coding)
inst/include/sparsepress/ SparsePress compression
tests/testthat/ Unit tests (testthat)
vignettes/ Package vignettes
man/ Auto-generated — do NOT edit
NAMESPACE Auto-generated — do NOT edit

Development Workflow

Editing R Code

  1. Edit files in R/ with roxygen2 comments (#' @param, #' @export, etc.)
  2. Regenerate documentation: 
    devtools::document()
  3. Fix the Rcpp info bug: 
    bash tools/fix_rcpp_info_bug.sh
  4. Run tests: 
    devtools::test()

Editing C++ Code

All C++ algorithm code lives in inst/include/ as a header-only library (subdivided into RcppML/, FactorNet/, streampress/, and sparsepress/). The src/ directory contains Rcpp bridge files (RcppFunctions*.cpp) that provide // [[Rcpp::export]] wrappers, plus sparsepress_bridge.cpp for StreamPress I/O.

After changing // [[Rcpp::export]] annotations, run:

devtools::document()  # Also runs Rcpp::compileAttributes()

Then:

bash tools/fix_rcpp_info_bug.sh

Auto-Generated Files (NEVER Edit Manually)

File(s) Generator
NAMESPACE roxygen2 via devtools::document()
man/*.Rd roxygen2 via devtools::document()
src/RcppExports.cpp Rcpp::compileAttributes() via devtools::document()
R/RcppExports.R Rcpp::compileAttributes() via devtools::document()

Code Style

R Code

  • Follow standard R style (snake_case for functions, PascalCase for S4 classes)
  • All exported functions must have complete roxygen documentation including @return and @examples
  • Use stop() for user-facing errors with clear messages

C++ Code

  • Namespace: RcppML (PascalCase) for all new code
  • Templates: use Scalar as the floating-point type parameter
  • Headers must be Rcpp-free — use RCPPML_LOG_INFO() instead of Rcpp::Rcout
  • Sparse matrices: expect Eigen::SparseMatrix<Scalar> in CSC format
  • Internal W is stored transposed (k × m) for cache efficiency

Testing

Running Tests

devtools::test()                                    # All tests
testthat::test_file("tests/testthat/test_nmf.R")    # Single file

Writing Tests

  • Place test files in tests/testthat/ named test_*.R
  • Use skip_if_not_installed() for optional dependencies
  • Use skip_if(Sys.getenv("RCPPML_SKIP_GPU") == "true") for GPU tests
  • Ground truth recovery tests should use multi-restart for robustness

GPU Tests

GPU tests require a CUDA-capable GPU and the compiled GPU library.

Submitting Changes

  1. Create a feature branch: git checkout -b feature/my-feature
  2. Make your changes with tests
  3. Ensure devtools::check() passes with no errors
  4. Push and open a Pull Request against main

Reporting Issues

Open an issue at https://github.com/zdebruine/RcppML/issues with:

  • A minimal reproducible example
  • R session info (sessionInfo())
  • Expected vs actual behavior