For Software Developers

Hail is an open-source project. We welcome contributions to the repository.

Requirements

See the requirements for non-pip installations in Getting Started

Building Hail

The Hail source code is hosted on GitHub:

git clone https://github.com/hail-is/hail.git
cd hail/hail

By default, Hail uses pre-compiled native libraries that are compatible with recent Mac OS X and Debian releases. If you’re not using one of these OSes, set the environment (or Make) variable HAIL_COMPILE_NATIVES to any value. This variable tells GNU Make to build the native libraries from source.

Build and install a wheel file from source with local-mode pyspark:

make install HAIL_COMPILE_NATIVES=1

As above, but explicitly specifying the Spark version:

make install HAIL_COMPILE_NATIVES=1 SPARK_VERSION=2.4.1

Building the Docs and Website

Build without testing the documentation examples:

make docs-no-test

Build while testing the documentation examples (significantly slower):

make docs

Serve the built website on http://localhost:8000/

(cd build/www && python3 -m http.server)

Running the tests

A couple Hail tests compare to PLINK 1.9 (not PLINK 2.0 [ignore the confusing URL]):

Execute every Hail test using at most 8 parallel threads:

make -j8 test

Contributing

Chat with the dev team on our Zulip chatroom if you have an idea for a contribution. We can help you determine if your project is a good candidate for merging.

Keep in mind the following principles when submitting a pull request:

  • A PR should focus on a single feature. Multiple features should be split into multiple PRs.
  • Before submitting your PR, you should rebase onto the latest master.
  • PRs must pass all tests before being merged. See the section above on Running the tests locally.
  • PRs require a review before being merged. We will assign someone from our dev team to review your PR.
  • When you make a PR, include a short message that describes the purpose of the PR and any necessary context for the changes you are making.