For Software Developers
Hail is an open-source project. We welcome contributions to the repository.
Java 8 or 11 JDK. Note: it must be Java 8 or Java 11. Hail does not support versions 9-10 or 12+ due to our dependency on Spark.
The Python and non-pip installation requirements in Getting Started. Note: These instructions install the JRE but that is not necessary as the JDK should already be installed which includes the JRE.
If you are setting HAIL_COMPILE_NATIVES=1, then you need the LZ4 library header files. On Debian and Ubuntu machines run: apt-get install liblz4-dev.
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
make install HAIL_COMPILE_NATIVES=1
As above, but explicitly specifying the Scala and Spark versions:
make install HAIL_COMPILE_NATIVES=1 SCALA_VERSION=2.11.12 SPARK_VERSION=2.4.5
Building the Docs and Website
Install build dependencies listed in the docs style guide.
Build without testing the documentation examples:
Build while testing the documentation examples (significantly slower):
Serve the built website on http://localhost:8000/
(cd build/www && python3 -m http.server)
Running the tests
Install development dependencies:
make -C .. install-dev-requirements
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
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 main.
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.
For user facing changes (new functions, etc), include “CHANGELOG” in the commit message or PR title. This helps identify what should be included in the change log when a new version is released.