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CONTRIBUTING.md

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How to contribute to ADAM

Thank you in advance for contributing to ADAM!

It would be great if you could introduce yourself to the community on one of the following channels but it is not required. You can just let your code do the talking for you if you like.

Join the ADAM Gitter channel

The primary mechanism for communication between ADAM developers and users is the ADAM Gitter channel.

Join the ADAM IRC channel

If you prefer IRC, you can often find ADAM developers and users on Libera.Chat in the #adamdev room.

Join the ADAM developers mailing list

The ADAM project also hosts a developers mailing list, see http://bdgenomics.org/mail/ for details.

Search the Github issue tracker and pull requests

Before you write too much code, check the open issues in the ADAM issue tracker and ADAM open pull requests to see if someone else is already working on it. If the issue is a new one, and you have already written the code to address the issue, simply submit a pull request. If you haven't written any code but plan to, go ahead and open a new issue and assign it to yourself to socialize your work. When you submit your PR, please reference this pull request so that it will be automatically closed when the PR is merged.

The issue tracker has a list of "pick me up!" issues that are good tasks to help you get familiar with ADAM; they don't require an understanding of genomics and are fairly limited in scope.

Submit your pull request

Github provides a nice overview on how to create a pull request.

Some general rules to follow:

  • Do your work in a fork of the ADAM repo.
  • Create a branch for each feature/bug in ADAM that you're working on. These branches are often called "feature" or "topic" branches.
  • Use your feature branch in the pull request. Any changes that you push to your feature branch will automatically be shown in the pull request. If your feature branch is not based off the latest master, you will be asked to rebase it before it is merged. This ensures that the commit history is linear, which makes the commit history easier to read.
  • Remember to reference any issues that your pull request fixes in the commit message. This will ensure that the issue is automatically closed when the PR is merged.
  • Run the ./scripts/format-source script in order to format the code and ensure correct license headers 
    $ ./scripts/format-source
  • Please alphabetize your imports. We follow the following approach: first, alphabetize by package name (e.g., org.apache.spark should be before org.bigdatagenomics.adam). Within a project, "lower level" packages should be sorted ahead (e.g., org.apache.spark.SparkContext should be before org.apache.spark.rdd.RDD). Within a single package, sort alphabetically, but put object implicit imports first (e.g., put org.apache.spark.SparkContext._ before org.apache.spark.Logging, and org.apache.spark.Logging before org.apache.spark.SparkContext).
  • Keep your pull requests as small as possible. Large pull requests are hard to review. Try to break up your changes into self-contained and incremental pull requests, if need be, and reference dependent pull requests, e.g. "This pull request builds on request #92. Please review #92 first."
  • The first line of commit messages should start by referencing the issue number they fix (i.e., "[ADAM-307]" indicates that this commit fixes ADAM issue #307), followed by a short (<80 character) summary, followed by an empty line and then, optionally, any details that you want to share about the commit.
  • Include unit tests with your pull request. We love tests and use Jenkins to check every pull request and commit. Just look for files in the ADAM repo that end in "*Suite.scala", e.g. ADAMContextSuite.scala, to see examples of how to write tests. You might also want to glance at the ./scripts/jenkins-test script for more end-to-end tests.

We appreciate your contribution!