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Contributing to immunarch

This document outlines how to propose a change to immunarch.

How to contribute?

There are three general ways to contribute to the package.

  1. Code contribution via pull requests. Helps us improve the codebase of the package, add new features or fix bugs and typos in the documentation.
  2. Bug reports and feature requests via GitHub issues. Helps us notice important issues and improvements to address.
  3. Helping others by answering tickets in GitHub issues. Greatly helps build the community and accelerates the immune repertoire research progress.

Code contribution via pull requests

Prerequisites

Before you make a substantial pull request, you should always file an issue and make sure someone from the team agrees that it's a problem. If you've found a bug, create an associated issue and illustrate the bug with a minimal reprex. If you need to send a data and can't do that via GitHub, please note it in the issue.

Pull request process

  • Always start by forking the dev branch from here to make sure you have the latest pre-release version of immunarch. Name it accordingly to your contributions. repClonality refactor or fix-issue-12 would work.

  • We recommend that you create a Git branch for each pull request (PR).

  • We follow the following guidelines for commit naming.

  • New code should follow our style guide that is the tidyverse style guide You can use the styler package to

    apply these styles, but please don't restyle code that has nothing to do with

    your PR.

  • We use roxygen2 for documentation.

  • We use testthat. Contributions

    with test cases included are easier to accept.

  • Look at the CI (Continuous Integration) build status before and after making changes.

    The README should contain badges for any continuous integration services used

    by the package.

Fixing typos

Small typos or grammatical errors in documentation may be edited directly using the GitLab web IDE functionality / GitHub web interface, so long as the changes are made in the source file. Please make sure to create a Pull Request instead of commiting directly to the master branch.

  • YES: you edit a roxygen comment in a .R file below R/.
  • NO: you edit an .Rd file below man/.

Version naming

We employ Major.Minor.Patch. E.g., 0.4.0.

Hotfixes: Major.Minor.Patch → Major.Minor.(Patch + 1)

Guidelines: http://r-pkgs.had.co.nz/release.html

Commit naming

We follow the following guidelines for commit naming.

Commit types

There are eight types of commits: chore, docs, feat, fix, refactor, test, perf, style. Most used are feat for implementation of a new feauture, docs for updating the documentation, fix for fixing a bug.

Commit name examples: feat(diversity): added the Chao1 method for diversity estimations, fix(clonality): fixed a bug in clonality computations #12, where #12 is a link to the issue on the immunarch issue page.

Commit scopes

  • Changes in analysis- and visualisation-specific functions: diversity, overlap, pub-rep, clonality, gene-usage, explore, kmers, spectratype, dynamics, tools, single-cell.
  • General changes in visualisation functions (e.g., replace one package with another, or change a non-specific visualisation function such as vis_bar): vis
  • Changes in parsing: io
  • Changes in databases support: db
  • Changes in additional functions such as general statistics functions: utility
  • Changes in data: data
  • Changes in NAMESPACE, DESCRIPTION, citations, ISSUE_TEMPLATE.md, etc., without README: upkeep
  • Changes in README and vignettes: vignette
  • Changes in Continuous Integration: ci
  • Changes in Shiny applications: shiny

Bug reports and feature requests

How to create an Issue

We have a rich list of templates for Issues here. Go to the GitHub Issues page for immunarch and create a new Issue ticket from there.

Helping others by answering tickets

Got to GitHub Issues page and find Issues that you are familiar with to answer.

Code of Conduct

Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.

(adapted from dplyr contribution guide)