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Contributing to flotilla

You are an awesome human being for wanting to contribute to the flotilla large-scale RNA-seq open-source software! Check out our guidelines below for how to best format your code and features so your sweet new idea can be added as soon as possible.

Install in development mode

First clone the repository,

git clone [email protected]:YeoLab/flotilla

Change directories to the flotilla directory you just made,

cd flotilla

Now install via pip in "editable" mode, aka "develop" mode:

pip install -e .

Git branching

We use the GitHub-Flow model.

To contribute:

  1. Make a branch off of the master.

  2. Commit updates exclusively to your branch.

  3. When changes on that branch are finished, open a pull request.

  4. Once someone has reviewed and approved of the changes on your branch, you should immediately merge your branch into the master.

Naming conventions

When in doubt, please defer to [Python Enhancement Proposal 8 (aka [PEP8] (http://legacy.python.org/dev/peps/pep-0008/)) and the [Zen of Python] (http://legacy.python.org/dev/peps/pep-0020/)

  • Classes are CamelCase, e.g.: BaseData and PCAViz
  • Functions are lower_case_with_underscores, e.g. go_enrichment and binify
  • Explicit is better than implicit

Docstring conventions

We will attempt to stick to the numpy docstring specification (aka "numpydoc").

To make this easier, I use ["Live Templates" in PyCharm] (http://peter-hoffmann.com/2010/python-live-templates-for-pycharm.html), check out the instructions here for how to install and use them.

Testing

In the source directory (wherever you cloned flotilla to that has this README.md file), do:

make test

This will run the unit test suite.

Coverage

To check coverage of the test suite, run

make coverage

in the source directory.

PEP8 Conventions

To run pep8 and pyflakes over the code, make sure you have [this fork] (pip install https://github.com/dcramer/pyflakes/tarball/master) of pyflakes installed (e.g. via pip install https://github .com/dcramer/pyflakes/tarball/master) and run:

make lint

Pull Request Checklist

When you make a pull request, please copy this text into your first message of the pull request, which will create a checklist, which should be completed before the pull request is merged.

- [ ] Is it mergable?
- [ ] Did it pass the tests?
- [ ] If it introduces new functionality in is it tested?
  Check for code coverage. To run code coverage on only the file you changed,
  for example `flotilla/compute/splicing.py`, use this command: 
  `coverage run --source flotilla --omit=test --module py.test flotilla/test/compute/test_splicing.py`
  which will show you which lines aren't covered by the tests.
- [ ] Do the new functions have descriptive 
  [numpydoc](https://github.com/numpy/numpy/blob/master/doc/HOWTO_DOCUMENT.rst.txt)
  style docstrings?
- [ ] If it adds a new feature, is it documented as an IPython Notebook in 
  `examples/`, and is that notebook added to `doc/tutorial.rst`?
- [ ] If it adds a new plot, is it documented in the gallery, as a `.py` file 
  in `examples/`?
- [ ] Is it well formatted? Look at the output of `make lint`.
- [ ] Is it documented in the doc/releases/?
- [ ] Was a spellchecker run on the source code and documentation after
  changes were made?

Note: This checklist was heavily borrowed from the khmer project.