.github/CONTRIBUTING.md

In devonjkohler/MSstatsTMTPTM: Post Translational Modification (PTM) Significance Analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling

Contributing to MSstatsTMTPTM

Thank you for considering contributing to the MSstatsTMTPTM package. This document aims to help you take the right steps to file a bug report (report an issue), request a new feature, fix a typo or propose code changes.

Code of conduct

As contributors and maintainers of MSstatsTMTPTM 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:

• via the official Google group,

• or via GitHub issues (the preferred way).

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 MSstatsTMTPTM.

Code contributions

We welcome code contributions to the MSstatsTMTPTM. Every contribution should be made via a pull request on GitHub and obey the following rules:

• if the pull request is meant to fix a bug, please start an issue earlier to describe it,
• a separate Git branch should be created for each pull request,
• the pull request must pass checks performed by the continuous integration system,
• the pull request should include relevant tests. We use testthat for writing tets,
• new code should be properly documented. We use roxygen2 and R Markdown for documentation.
• new code should follow the tidyverse style guide with the following exceptions:
  • names of functions and classes should be camelCase,
  • other names should use the underscore _ and lowercase, except already existing names, which should not be changed to ensure backward compatibility.
• when starting a pull request, please add at least one reviewer:
  • Devon Kohler - the main developer of MSstatsTMTPTM,
• before the pull request is merged, please update the NEWS.md file and version of the package, following the conventions of semantic versioning and Bioconductor.

devonjkohler/MSstatsTMTPTM documentation built on Oct. 27, 2021, 7:50 a.m.