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Contributing to msPCA

Source: CONTRIBUTING.md

Thank you for your interest in contributing to msPCA. This document covers everything you need to get the development environment running and submit high-quality changes.

Table of contents

  1. Development setup
  2. Running tests
  3. Code style
  4. Documentation
  5. Submitting changes
  6. Reporting issues

Development setup

Prerequisites

  • R ≥ 4.1 (tested on release and devel)
  • A C++14-capable compiler (GCC ≥ 7, Clang ≥ 5, or MSVC 2017+)
  • The following R packages:
install.packages(c("Rcpp", "RcppEigen", "devtools", "testthat", "covr"))

Clone and install

git clone https://github.com/jeanpauphilet/msPCA.git
cd msPCA
# From the R console, inside the package directory:
devtools::install(dependencies = TRUE)

Compile C++ code after edits

devtools::load_all()   # recompiles src/ and sources R/ in one step

Running tests

devtools::test()
# or equivalently:
testthat::test_local()

All tests live in tests/testthat/. The test files are:

File What it covers
test-mspca.R mspca() output structure, Sigma and X paths, real-data smoke tests
test-tpm.R tpm() output structure, both input paths
test-validators.R Error paths for invalid inputs (non-square, non-PSD, non-finite, …)
test-s3methods.R print.mspca, summary.mspca, and helper functions

Coverage report

covr::report()   # opens an HTML coverage report in the browser

The project targets ≥ 90% line coverage.

Code style

R

  • Follow tidyverse style for R code.
  • Exported functions and helpers must have roxygen2 documentation blocks.
  • All roxygen directives use Markdown (enabled via Roxygen: list(markdown = TRUE) in DESCRIPTION).
  • Run devtools::document() after any change to roxygen comments.

C++

  • Standard: C++14.
  • Match the existing brace and spacing style in src/.
  • Every source file (*.cpp, *.h) must carry the SPDX header:
// SPDX-License-Identifier: MIT
// Copyright (C) 2025 Ryan Cory-Wright, Jean Pauphilet

R source files

# SPDX-License-Identifier: MIT
# Copyright (C) 2025 Ryan Cory-Wright, Jean Pauphilet

Auto-generated files (R/RcppExports.R, src/RcppExports.cpp) are excluded from the header requirement — do not edit them by hand.

Documentation

Rebuild Rd files after changing roxygen comments:

devtools::document()

Rebuild the pkgdown site (requires pkgdown):

pkgdown::build_site()

The docs/ folder is committed to main and served as GitHub Pages — do not delete it.

Submitting changes

  1. Fork the repository and create a branch from main:

    git checkout -b fix/my-bugfix

  2. Make your changes and add or update tests as appropriate.

  3. Ensure devtools::check() passes with no new errors, warnings, or notes (the CI matrix runs R CMD check --as-cran on Linux, macOS, and Windows).

  4. Push your branch and open a pull request against main.

  5. Fill in the pull request description, referencing any related issues.

Reporting issues

Please use the GitHub issue templates:

  • Bug report — for reproducible errors or unexpected behaviour.
  • Feature request — for suggestions or ideas.

For security vulnerabilities, contact the maintainer directly by e-mail rather than opening a public issue.