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CONTRIBUTING.md

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Contributing

Contributions are welcome, and they are greatly appreciated! Every little bit helps, and credit will always be given.

You can contribute in many ways:

Types of Contributions

Report Bugs

Report bugs at https://github.com/kundajelab/bpnet/issues.

If you are reporting a bug, please include:

  • Your operating system name and version.
  • Any details about your local setup that might be helpful in troubleshooting.
  • Detailed steps to reproduce the bug.

Fix Bugs

Look through the GitHub issues for bugs. Anything tagged with “bug” and “help wanted” is open to whoever wants to implement it.

Implement Features

Look through the GitHub issues for features. Anything tagged with “enhancement” and “help wanted” is open to whoever wants to implement it.

Write Documentation

BPNet could always use more documentation, whether as part of the official BPNet docs, in docstrings, or even on the web in blog posts, articles, and such.

Submit Feedback

The best way to send feedback is to file an issue at https://github.com/kundajelab/bpnet/issues.

If you are proposing a feature:

  • Explain in detail how it would work.
  • Keep the scope as narrow as possible, to make it easier to implement.
  • Remember that this is a volunteer-driven project, and that contributions are welcome :)

Workflow

  • make an issue for the thing you want to implement
  • create the corresponding branch
  • develop
  • write units tests in tests/
  • write documentation in markdown (see other functions for example)
  • push the changes
  • make a pull request
  • once the pull request is merged, the issue will be closed

Get Started!

Ready to contribute? Here’s how to set up BPNet for local development.

  1. Fork the BPNet repo on GitHub.

  2. Clone your fork locally:

    $ git clone [email protected]:your_name_here/bpnet.git

  3. Install your local copy into a conda environment. Assuming you have conda installed, this is how you set up your fork for local development:

    $ conda create -n bpnet python=3.6
$ cd bpnet/
$ source activate bpnet
$ pip install -e '.[develop]'

  4. Create a branch for local development:

    $ git checkout -b name-of-your-bugfix-or-feature

    Now you can make your changes locally.

  5. When you’re done making changes, check that your changes pass the tests:

    $ py.test tests/ -n 4

Where -n 4 will use 4 cores in parallel to run tests.

  1. Commit your changes and push your branch to GitHub:

    $ git add .
$ git commit -m "Your detailed description of your changes."
$ git push origin name-of-your-bugfix-or-feature

  2. Submit a pull request through the GitHub website.

Pull Request Guidelines

Before you submit a pull request, check that it meets these guidelines:

  1. The pull request should include tests.
  2. If the pull request adds functionality, the docs should be updated. Put your new functionality into a function with a docstring.
  3. The pull request should work for Python 3.6.