Installation

PIP / PyPI

The easiest way to install PyHPO is via pip

pip install pyhpo

This will install a base version of PyHPO that offers most functionality.

Note

Some features of PyHPO require pandas and scipy. The standard installation via pip will not include pandas or scipy and PyHPO will work just fine. (You will get a warning on the initial import though).

Without installing pandas, you won’t be able to export the Ontology as a Dataframe, everything else will work fine.

Without installing scipy, you won’t be able to use the stats module, especially the enrichment calculations.

If you want to do enrichment analysis, you must also install scipy.

pip install 'pyhpo[scipy]'

If you want to work with PyHPO using pandas dataframes, you can install the pandas dependency

pip install 'pyhpo[pandas]'

Or simply install both together:

# Include all dependencies
pip install 'pyhpo[all]'

From source

You can also install PyHPO from source by cloning the git repository:

git clone https://github.com/Centogene/pyhpo.git

I recommend to use a virtual environment to use PyHPO:

cd pyhpo
virtualenv venv
source ./venv/bin/activate

Install dependencies:

pip install -r requirements.txt

Development / Contributing

If you want to contribute to PyHPO development, first install from source (see above), then install all dev dependencies:

pip install -r requirements_dev.txt

Make sure to install mypy and linter, such as flake8 or ruff.