Contributor’s guidelines

This project is a community effort, and everyone is welcome to contribute.

The project is hosted on https://github.com/nservant/HiC-pro

In case you experience issues using this package, do not hesitate to submit a ticket to the GitHub issue tracker. You are also welcome to post feature requests or pull requests.

Our community, our values

We are a community based on openness and friendly, didactic, discussions.

We aspire to treat everybody equally, and value their contributions.

Decisions are made based on technical merit and consensus.

Code is not the only way to help the project. Reviewing pull requests, answering questions to help others on mailing lists or issues, organizing and teaching tutorials, working on the website, improving the documentation, are all priceless contributions.

We abide by the principles of openness, respect, and consideration of others of the R community

Ways to contribute

There are many ways to contribute to HiC-pro, with the most common ones being contribution of code or documentation to the project. Improving the documentation is no less important than improving the library itself. If you find a typo in the documentation, or have made improvements, do not hesitate to send an email to the mailing list or preferably submit a GitHub pull request. Full documentation can be found under the doc/ directory.

But there are many other ways to help. In particular answering queries on the issue tracker, investigating bugs, and reviewing other developers’ pull requests are very valuable contributions that decrease the burden on the project maintainers.

Another way to contribute is to report issues you’re facing, and give a “thumbs up” on issues that others reported and that are relevant to you. It also helps us if you spread the word: reference the project from your blog and articles, link to it from your website, or simply star to say “I use it.”

How to contribute

The preferred way to contribute to HiC-pro is to fork the main repository on GitHub, then submit a “pull request” (PR).

• Create an account on GitHub if you do not already have one.

• Fork the project repository: click on the ‘Fork’ button near the top of the page. This creates a copy of the code under your account on the GitHub user account. For more details on how to fork a repository see this guide.

• Clone your fork of the HiC-pro repo from your GitHub account to your local disk:

    $ git clone git@github.com:YourLogin/HiC-pro.git
    $ cd HiC-pro

• Create a branch to hold your development changes:

  $ git checkout -b my-feature

  and start making changes. Always use a feature branch. It’s good practice to never work on the master branch!

• Develop the feature on your feature branch on your computer, using Git to do the version control. When you’re done editing, add changed files using git add and then git commit files:

    $ git add modified_files
    $ git commit

to record your changes in Git, then push the changes to your GitHub account with:

    $ git push -u origin my-feature

Follow these instructions to create a pull request from your fork. This
will send an email to the committers. You may want to consider sending an
email to the mailing list for more visibility.

If any of the above seems like magic to you, then look up the Git documentation and the Git development workflow on the web, or ask a friend or another contributor for help.

If some conflicts arise between your branch and the master branch, you need to merge master. For that, you first need to fetch the upstream, and then merge its master into your branch:

$ git fetch upstream
$ git merge upstream/master

Subsequently, you need to solve the conflicts. You can refer to the Git documentation related to resolving merge conflict using the command line.

Contributing to related projects

HiC-pro thrives in an ecosystem of several related projects, which also may have relevant issues to work on including:

• iced
• HiTC