Package Requirements

BioJulia package guidelines

All code in all packages in the BioJulia ecosystem should follow the BioJulia code style guide.

Documentation

Docstrings

Types and functions must be documented using Julia's docstrings.

Documentation regarding specific implementation details that aren't relevant to users should be in the form of comments.

Documentation may be omitted if the function is not exported (i.e. only used internally) and is short and obvious. E.g. cube(x) = x^3.

However, please consider that what may be obvious to you as the write of the code, may not be obvious to others. Therefore, we do recommend documenting as much as possible, to help out fellow julia coders and biologists when they are reading and understanding the code. We are trying to make BioJulia packages as easy as possible to use, understand, and code with for everyone :)

Documenter.jl generated manuals and documentation

In addition to documenting code in the source files through docstrings, we encourage contributers to create documentation which is more akin to a manual, complete with comprehensive explanations and examples of how to use the package.

We use Documenter.jl and mkdocs, to generate such documentation and host it on the web. The source markdown files for such manuals are kept in the docs/src/man folder of each BioJulia package/repository.

Tests

All significant code must be tested. Tests should be organized into contexts, and into separate files based on module.

Files for tests for a module go into an appropriately named folder, within the test folder in the git repo.

Version compatibility

All code contributed should be compatible with the latest stable version of Julia.

If your contribution to a BioJulia package introduces a method which is shared among submodules, they should be declared in the top level module, and then extended by the submodules. For example, in Bio.jl, the method seqname was defined in Bio.Seq and overloaded by Bio.Intervals and Bio.Align. Therefore the declaration of the method was moved to Bio, and the three submodules extend the declared method.