Lightly reviewed community code snippets for Hail.
Browse the current submissions here:
Although the flexibility and functionality of the core Hail repository is growing quickly, the amount of useful functionality produced by Hail users is growing far faster. This repository is an attempt to make it easier for Hail users to share their hard work, which will hopefully lead to more rapid progress on both the software and the science for the whole community.
What do we expect make its way here? Utility functions, complete pipelines, visualization methods, and more!
A website that indexes these submissions and makes them searchable will be created at a later date.
We deploy to the Python Package Index (PyPI).
This means that you can install or upgrade hailc with pip:
pip install hailc --upgrade
Each contributor creates a package inside the hailc subdirectory corresponding
to the correct version of Hail, which can be imported as follows:
import hailc.v01.tpoterba as tpThe correct import statement should be listed at the top of each contributor's README.md file.
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Version control process. Make pull requests from forked copies of the main repository. Here's a useful walkthrough about how to do that. Take a look at GitHub help for even more assistance!
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Approval process. Initially, Hail team members and collaborators will review new submissions. As this experiment matures, we will be happy to grant review authority to anyone who is an active and productive participant in the Hail community!
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Naming guidelines. Your package should either be named after your GitHub username, or your name (first initial and last name, for example).
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README is required! Tests and extensive documentation are not. This repository is only minimally reviewed -- it is a resource for the community, and should be maintained by the community. The README is the only requirement -- this is how people can look at the various modules present. It would be nice to include at least minimal documentation about your submissions and describe how you tested them, but submissions will not be rejected without these.
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No automatic monkey-patching! This is the only code rule -- don't automatically modify Hail classes or methods at import time. However, you can include an explicit
patchfunction to do this, as long as you document it in your README. To a user, the patching will look something like this:import hailc.v01.tpoterba as tp tp.patch() -
Example submission. If you're wondering what a submission might look like, take a look at the example. From the repository head, you can copy this into a new folder for your package from the command line:
cp -r example hailc/v01/mypkg -
Style. Try to follow PEP 8. You may be asked to reformat egregiously unreadable code, but otherwise feel free to submit code as you use it yourself.