Chapter 12 Contributing

12.1 Contributing to this book

This book is created using bookdown.

Each chapter is an Rmarkdown (.Rmd) file. While reading this book, click on the Edit button in the top navigation bar, which will bring you to the source file for that chapter. You can then make an edit right there in your browser, or you can clone down the repo and make a change locally, then send a pull request.

The source for this book lives at https://github.com/ropenscilabs/taxize-book

12.2 Contributing to taxize

12.2.1 Bugs?

  • Submit an issue on the Issues page - be sure to include R session information and a reproducible example.

12.2.2 Code contributions

12.2.2.1 Broad overview of contributing workflow

  • Fork this repo to your Github account
  • Clone your version on your account down to your machine from your account, e.g,. git clone https://github.com/<yourgithubusername>/taxize.git
  • Make sure to track progress upstream (i.e., on our version of taxize at ropensci/taxize) by doing git remote add upstream https://github.com/ropensci/taxize.git. Before making changes make sure to pull changes in from upstream by doing either git fetch upstream then merge later or git pull upstream to fetch and merge in one step
  • Make your changes (bonus points for making changes on a new feature branch)
  • Please do write a test(s) for your changes if they affect code and not just docs (see Tests below)
  • Push up to your account
  • Submit a pull request to home base at ropensci/taxize

12.2.2.2 Tests

To add tests, go to the folder tests/testthat/. Tests are generally organized as individual files for each exported function from the package (that is, listed as an export in the NAMESPACE file). If you are adding a new exported function, add a new test file. If you are changing an existing function, work in the tests file for that function, unless it doesn’t have tests, in which case make a new test file.

The book R packages book provides a chapter on testing in general. Do consult that first if you aren’t familiar with testing in R.

The easiest set up to run tests is from within an R session:

To test an individual test file

To run all tests

If you are running tests that have skip_on_cran() in them, set Sys.setenv(NOT_CRAN = "true") prior to running tests.

12.2.2.3 Making changes

In addition to changing the code, do make sure to udpate the documentation if applicable. The R packages book book has a chapter on documentation you should read if you aren’t familiar.

After code and documentation has been changed, update documentation by running either devtools::document() or roxygen2::roxygenise().

Make sure if you change what packages or even functions within packages are imported, most likely add the package to Imports in the DESCRIPTION file and list what functions are imported in the taxize-package.R file.

Be conservative about adding new dependencies.

12.2.2.4 Style

  • Make sure code, documentation, and comments are no more than 80 characters in width.
  • Use <- instead of = for assignment
  • Always use snake_case (and all lowercase) instead of camelCase