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CONTRIBUTING.md

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Contributing

MIToS is a Open Source project, and you can contribute to it in different ways. Please use GitHub issues to report errors/bugs or to ask for new features. We welcome contributions in the form of pull requests. For your code to be considered it must meet the following guidelines.

  • By making a pull request, you agree to license your code under an MIT license.
  • Types and functions must be documented using Julia's docstrings.
  • All significant codes must be tested.

Style

  • Type names are camel case, with the first letter capitalized. E.g. MultipleSequenceAlignment.
  • Function names, apart from constructors, are all lowercase. Include underscores between words only if the name would be hard to read without. E.g. frequencies, read_file.
  • Names of private (unexported) functions begin with an underscore, for example _load_sequences.
  • Separate logical blocks of code with blank lines.

Code

MIToS has a .JuliaFormatter.toml file, so that JuliaFormatter can be used to automatically format the code following the described style.

  • Generally, keep lines below 92 columns.
  • Try to use a 4 spaces indentation.

Documentation

  • Please include examples or jldoctest blocks if possible.

References

Please include references to the papers where the algorithms are described. MIToS uses DocumenterCitations to include references in the documentation. All the references are stored in the docs/src/refs.bib using the BibTeX format. When storing a new reference to the refs.bib file:

  • Please include the DOI of the paper so that the reference can have a link to the paper.
  • Use the paper's DOI as the reference key (citekey).

To include a reference in the documentation, use the @cite or the @citet macro. The first will be rendered as a number, and the second as the author's name and the number. For example, to include the reference to the MIToS paper as [1], use [10.1093/bioinformatics/btw646](@cite) in the documentation—please note that the DOI is the citekey. To include it as Zea et al. [1], use [10.1093/bioinformatics/btw646](@citet).

If the reference is placed in a docstring, to ensure that the reference is well rendered in the REPL, please add it by hand using the first author's last name. Format it using italic, for example, *Zea et al.*. Then add at the end of the docstring the # References header, followed by a list of the references in MLA format. The whole reference should link to the references section in the documentation. Use [MLA](@cite DOI) to achieve that. For example:

# References

  - [Zea, Diego J., et al. "MIToS. jl: mutual information tools for protein sequence 
    analysis in the Julia language." Bioinformatics 33.4 (2017): 
    564-565.](@cite 10.1093/bioinformatics/btw646)

Conduct

We adhere to the Julia community standards.