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Contributing

Source: CONTRIBUTING.md

Awesome that you are reading this.

This GitHub follows the Contributor Covenant Code of Conduct.

  • For questions, you can create an Issue
  • Code changes go via Pull Requests

Which package to contribute to?

beautier is part of the babette package suite, which consists out of five packages. Here is how to determine which package is best suited for your contribution:

If you want to contribute to how BEAST2 is run, go to beautier.

If you want to contribute to how BEAST2 output is parsed, go to tracerer

If you want to contribute regarding the BEAST2 package management, go to mauricer

If you want to contribute with an overarching idea, go to babette.

If you want to contribute to the creation of BEAST2 XML input files, you are at the right spot :-)

Submitting use cases

Use cases within the default BEAUti environment are welcomed.

Please send all that is needed to reproduce the use case:

  • the alignment file
  • screenshots of BEAUti settings you’ve changed
  • the resulting XML file
  • (optional) the desired call to beautier

BEAUti plugins are not supported (for now). See ‘Submitting code’ if you’d like beautier to do so.

You can do so by:

  • Add an Issue
  • Send @richelbilderbeek an email (@richelbilderbeek will make an Issue of it)

Submitting code

Submitted code should follow these quality guidelines:

  • All tests pass cleanly/silently
  • Code coverage above 95%
  • Coding style should follow the default style by lintr

These are all checked by Travis CI when submitting a Pull Request.

For BEAUti plugins, there needs to be added:

  • Enough documentation so an example use case can be reproduced
  • Stating that maintenance will be done by the Collaborator

Emails with code will not be accepted.

Submitting bugs

Awesome. These are your options:

  • Add an Issue, with the test that fails
  • Submit a Pull Request, where the test is added to the tests/testthat folder
  • Send @richelbilderbeek an email (@richelbilderbeek will make an Issue of it)

Pull Requests should follow the same guidelines as ‘Submitting code’.

Branching policy

  • The master branch should always build successfully
  • The development branch is for developers

git usage

To get started working on beautier do:

git clone https://github.com/ropensci/beautier

Development is done on the develop branch. To download and checkout the develop branch, first go into the beautier folder (cd beautier), then do:

git checkout develop

Then the workflow is the common git workflow:

git pull
git add --all :/
git commit -m "Did something awesome"
git push