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Contributing to ClassiPyR

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

Getting Started

Prerequisites

  • R (>= 4.0.0)
  • devtools package for development
  • Python with scipy (required for saving .mat annotation files)

Setting Up the Development Environment

  1. Fork the repository on GitHub

  2. Clone your fork locally:

    git clone https://github.com/YOUR-USERNAME/ClassiPyR.git
cd ClassiPyR

  3. Install the package in development mode:

    devtools::install_deps(dependencies = TRUE)
devtools::load_all()

  4. Set up Python environment (required for saving .mat annotation files):

    library(iRfcb)
ifcb_py_install(envname = "./venv")

Running the App During Development

# From the repository root
shiny::runApp()

# Or run from inst/app
shiny::runApp("inst/app")

Package Structure

ClassiPyR/
├── R/                      # Package functions (exported)
│   ├── run_app.R           # App launcher
│   ├── utils.R             # Utility functions
│   ├── sample_loading.R    # Sample loading logic
│   └── sample_saving.R     # Sample saving logic
├── inst/
│   ├── app/                # Shiny application
│   │   ├── app.R           # Entry point
│   │   ├── global.R        # Initialization
│   │   ├── server.R        # Server logic
│   │   └── ui.R            # User interface
│   └── CITATION            # Citation info
├── tests/testthat/         # Test suite
├── vignettes/              # Documentation articles
├── man/                    # Function documentation (auto-generated)
└── docs/                   # pkgdown site (auto-generated)

How to Contribute

Reporting Bugs

Before submitting a bug report:

  • Check existing issues to avoid duplicates
  • Collect information about the bug (R version, OS, error messages)

When submitting a bug report, please include:

  • A clear, descriptive title
  • Steps to reproduce the issue
  • Expected vs actual behavior
  • R session info (sessionInfo() output)
  • Screenshots if applicable

Suggesting Features

Feature suggestions are welcome! Please:

  • Check existing issues for similar suggestions
  • Describe the feature and its use case
  • Explain how it would benefit IFCB researchers

Submitting Changes

  1. Create a new branch for your feature or fix:

    git checkout -b feature/your-feature-name

  2. Make your changes following the code style guidelines below

  3. Run tests and checks:

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

  4. Commit your changes with a descriptive message:

    git commit -m "feat: add support for new classification format"

  5. Push to your fork:

    git push origin feature/your-feature-name

  6. Open a Pull Request against the main branch

Code Style Guidelines

R Code

  • Use meaningful variable and function names
  • Document exported functions with roxygen2 comments
  • Keep functions focused and modular
  • Follow tidyverse style guide where applicable
  • Aim for >80% test coverage on new code

Commit Messages

Use conventional commit format:

  • feat: new features
  • fix: bug fixes
  • docs: documentation changes
  • test: test additions or modifications
  • refactor: code refactoring

Testing

Run the test suite before submitting:

devtools::test()

Check for R CMD check issues:

devtools::check()

Tests are located in tests/testthat/. When adding new functionality, please include appropriate tests.

Documentation

  • Function documentation uses roxygen2 (in R/ files)
  • User guides are in vignettes/ as R Markdown
  • The pkgdown site is built automatically via GitHub Actions

To preview documentation locally:

devtools::document()
pkgdown::build_site()

Pull Request Process

  1. Ensure all tests pass (devtools::test())
  2. Ensure R CMD check passes (devtools::check())
  3. Update documentation if needed
  4. Describe your changes clearly in the PR description
  5. Link any related issues
  6. Be responsive to review feedback

Questions?

Feel free to open an issue for any questions about contributing.

License

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