broadinstitute / ukbb_qc

QCing the UKBB
1 stars 0 forks source link

Add build configuration #226

Closed nawatts closed 2 years ago

nawatts commented 2 years ago

This adds build configuration that makes it possible to pip install ukbb_qc. This does not include uploading ukbb_qc to PyPI, but allows pip installing from a local copy, a GitHub URL, etc.

More information about the configuration files added here:

The motivation for this was broadinstitute/gnomad_qc#218, which adds some imports from ukbb_qc. This will make it easier to install ukbb_qc in gnomad_qc's PR check workflows, which will let us check gnomad_qc's usage of it using Pylint. This will also let us install ukbb_qc on Dataproc clusters using hailctl dataproc's --packages argument.

A few limitations... this does not list dependencies, so they will not be automatically installed. Similar to gnomad_methods, we don't want to automatically install Hail because it causes issues when installing on a cluster using hailctl dataproc.

This also adds a .gitignore file, copied from GitHub's Python example. This is included here to ignore build outputs (build, ukbb_qc.egg-info).

nawatts commented 2 years ago

Discussion in Slack resulted in deciding to remove ukbb_qc imports from gnomad_qc, so there's no longer a need for this.