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Code of conduct

As contributors and maintainers of MSstats project, we pledge to follow the Carpentry Code of Conduct.

Instances of abusive, harassing or other unacceptable behavior may be reported by following our reporting guidelines.

Typos

Typos and grammatical errors in documentation can be fixed directly via Github. All changes should be made in the .R or .Rmd files rather than .Rd files in the /man directory.

Bug reports

Bug reports can be filed in two ways:

Before filing a bug report please make sure that:

  • the problem was not solved before (by searching older issues and possibly other sources such as the Google group)

  • you can provide a minimal reproducible example so that the developers can reproduce and understand the problem. The reprex package might be helpful.

To help with describing the bug, we have created an issue template which can be used after starting a new issue.

Feature requests

GitHub issues are meant primarily for bug requests. We suggest to make feature requests via the official Google group of MSstats.

Code contributions

We welcome code contributions to the MSstats. Every contribution should be made via a pull request on GitHub.

Hard Constraints (Required)

These requirements must be met for your pull request to be accepted:

Soft Constraints (Strongly Recommended)

These guidelines should be followed when possible to maintain code quality:

  • For bug fixes: Open an issue first to describe the problem
  • Follow the tidyverse style guide with these exceptions:
    • Function and class names: use camelCase
    • Other names: use lowercase with underscores (snake_case), except for existing names that must remain unchanged for backward compatibility
  • Limit dependencies to keep the package lightweight
  • Maintain backward compatibility when modifying existing functionality
  • Use @inheritParams when functions share parameter documentation
  • Reuse existing functions rather than duplicating code
  • Prefer data.table for data manipulation when appropriate
  • Use match.arg() for argument validation when applicable

🚀 New Developer Setup Guide

This guide is for developers who want to contribute to any VitekLab project. It will walk you through setting up a local development environment to run the app from its source code.

1. Prerequisites 💻

Make sure you have the following software installed:

2. Step-by-Step Setup

Step 1: Clone the Repository (MSstatsShiny Example)

  1. Open your computer's Terminal (Mac/Linux) or Git Bash (Windows).

  2. Navigate to the folder where you want to store the project.

  3. Run the git clone command

    git clone [https://github.com/Vitek-Lab/MSstatsShiny.git](https://github.com/Vitek-Lab/MSstatsShiny.git)

Step 2: Set Up the RStudio Project

  1. Open the RStudio application.
  2. Go to the top menu: File > New Project...
  3. Select Existing Directory.
  4. Click Browse... and navigate to the MSstatsShiny folder you just cloned.
  5. Click Create Project.

Step 3: Install All Dependencies

  1. In RStudio, go to the Console pane.

  2. Install the devtools package:

    install.packages("devtools")

  3. Run the following command to install all project dependencies:

    devtools::install_deps(dependencies = TRUE)

Note: This step can take a long time. You only need to do this once.

3. The Developer Workflow 🧑‍💻

This is the cycle you will follow to make and test changes.

Step 1: Load Your Local Code

In the RStudio Console, run:

library(MSstatsShiny)

Step 2: Edit, Load, and Test!

This is your core workflow:

  1. Edit: Open any project file and make your code changes.
  2. Save: Save the file.
  3. Install: Go to the top right corner and click "Install" to reinstall the package.
  4. Build: Go to the top right corner and click "Build" to run all tests and build the package.

Repeat this Edit > Save > Install > Build cycle as you develop.