Setup

The document describes how to install Phenopacket Store Toolkit into your environment.

Stable release

Installing the toolkit is easy - we publish releases on Python Package Index (PyPi).

Run the following to install the latest stable release:

python3 -m pip install phenopacket-store-toolkit

Latest release

The latest release can be installed by cloning the GitHub repository:

git clone https://github.com/monarch-initiative/phenopacket-store-toolkit.git
cd phenopacket-store-toolkit

# Switch to `develop` branch to access the latest features
git checkout develop

python3 -m pip install .

The code above will clone the source code from GitHub repository, switch to the develop branch with the latest features, and install the library into the current Python (virtual) environment.

Run tests

Running tests can be done as an optional step after installation. However, some additional libraries are required to run tests, hence we must do one more install, this time with test option enabled:

python3 -m pip install .[test]

Then, running the tests is as simple as:

pytest

That’s all about testing!