Installation

The package is designed to work with Python 3.8 or later.

Dependencies

Oncopacket has the following main dependencies: - phenopackets (GA4GH Phenopacket Schema) - cdapython (Cancer Data Aggregator Python library) - hpo-toolkit (Tools for working with the Human Phenotype Ontology) - requests (For API communication)

Installation

1: Create a virtual environment (recommended)

First, create and activate a virtual environment, for example:

python3 -m venv oncopacket-venv
source oncopacket-venv/bin/activate  # On Windows: oncopacket-venv\Scripts\activate

2: Install from GitHub repository

Install the latest version directly from the GitHub repository:

# Ensure you are in the repo folder
cd oncopacket
python3 -m pip install --editable .

The package is installed in editable mode - any code updates are available after Python restart, without needing to reinstall.

3. Using Oncopacket in Jupyter notebooks (optional)

To use Oncopacket in Jupyter notebooks, first install Jupyter and ipykernel:

python3 -m pip install jupyter ipykernel

Then, create a new Jupyter kernel and register it with Jupyter:

python -m ipykernel install --user --name oncopacket_env --display-name "oncopacket"

Start Jupyter to work with the notebooks in the repository:

cd notebooks
jupyter-notebook

At this point, a Jupyter page should open in your browser. Navigate to any notebook (and activate the oncopacket_env kernel if you made one above).

Building the documentation

To run the mkdocs server locally for documentation development:

1. Install the required packages:

pip install mkdocs-material
pip install mkdocs-material[imaging]
pip install mkdocs-material-extensions
pip install pillow cairosvg
pip install mkdocstrings[python]

1. Serve the documentation locally:

mkdocs serve

This will serve the documentation site at http://127.0.0.1:8000/ and dynamically show changes. Merging to the main branch will update the public documentation site.