Setup

This document describes how to install the stable version or the bleeding edge code into your Python environment.

Stable code

Installing GA4GH Phenopacket Core is easy - we publish the releases on PyPi.

Therefore, the latest stable release can be installed by running:

python3 -m pip install ga4gh-phenopacket-core

The bleeding edge code

To access the bleeding edge features, the development version can be installed by:

git clone https://github.com/monarch-initiative/ga4gh-phenopacket-core.git
cd ga4gh-phenopacket-core
git checkout development && git pull
python3 -m pip install .

This will clone the Git repository into your machine, switch to the development branch, and install ga4gh-phenopacket-core into the active Python environment, assuming you have privileges to install packages.

Run tests

The contributors may want to run the unit tests and the integration tests to ensure all features work as expected.

Before running tests, make sure you install GA4GH Phenopacket Core with test dependencies:

python3 -m pip install .[test]

The unit tests, integration tests, doctests, and the tutorial scripts can the be running by invoking the pytest runner:

pytest

Note

The library must be installed in the environment before running all tests.

That’s all for the setup!