This document described guidelines for contributions for projects led by members of the Poisot lab of computational ecology, Université de Montréal. It should be followed by lab members (at all times), as well as people with suggested added features, or willing to contribute enhancement or bug fixes.
Any contribution to the code of a software grants authorship on the next paper
describing this software. Any contribution to a paper hosted as a public
version-controlled repository grants authorship of the paper. For this reason,
it is important to correctly identify yourself. For R packages, this is done
throug the DESCRIPTION file. Whenever a CONTRIBUTORS file is found, add your
name to it as part of the workflow described next. For authorship of papers, the
first and last authors will decide on the position.
This section describes the general steps to make sure that your contribution is integrated rapidly. The general workflow is as follows:
- Fork the repository
- Create an explicitely named branch
- Create a pull request even if you haven't pushed code yet
- Be as explicit as possible on your goals
Creating a pull request before you push any code will signal that you are interested in contributing to the project. Once this is done, push often, and be explicit about what the commits do. This gives the opportunity for feedback during your work, and allow for tweaks in what you are doing.
Most of our repositories undergo continuous integration, and code coverage analysis.
It is expected that:
- Your commits will not break a passing repo
- Your commits can make a breaking repo pass (thank you so much!)
- Your additions or changes will be adequately tested
This information will be given in the thread of your pull request. Most of our repositories are set-up in a way that new commits that decrease coverage by more than 10% won't be pulled.
Don't repeat yourself. If you have to do something more than once, write a function for it.
Check user input, check data structure, and fail often but explicitely.
Any given function must always return an object of the same type.
A function like y = (x) -> x>3?true:x (returns true if x is larger than 3,
else returns x) is not acceptable, as it is hard to predict, hard to debug,
and hard to use.
Comment your code -- comments should not explain what the code does (this is for the documentation), but how it does it.
Be as explicit as possible. Have a look at the rest of the codebase before your start.
Write som. R packages, must be compiled with roxygen, python code must
have docstrings for all documentable objects, and Julia functions must be
commented.
If there is a documentation, add the parts relevant for your changes.
We use semantic versioning (major.minor.patch). Anything that adds
no new feature should increase the patch number, new non-API-breaking changes
should increase minor, and major changes should increase major. Any increase
of a higher level resets the number after it (e.g, 0.3.1 becomes 1.0.0 for
the first major release).
Good stuff. Here's ours: http://khmer.readthedocs.org/en/v1.3/dev/index.html . Main suggestion - link to more docs, like the github flow description, so that people have somewhere to go if they don't understand what you're saying!
Also, contributor guidelines for research papers usually specify intellectual contribution as a requirement for being an author. I think your rules above are a bit too lenient, from that perspective. We have been adding contributors as authors on software papers, but not necessarily on research papers (i.e. we make a distinction between the two).