Installation

We will add this project to PyPI to ease installation. For now, a local installation is needed to run the notebooks. There are many ways of installing Python projects locally. We will explain several options here.

Install into virtual environment

TBD

Create a virtual environment

An optional first step is to create a virtual environment. Feel free to skip this if you already have a virtual environment which you want to use:

python3 -m venv oncoexporter-venv
source oncoexporter-venv/bin/activate

The command above will create a new virtual environment at oncoexporter-venv and activate the environment.

Install Oncoexporter

Next, Oncoexporter can be installed into an existing virtual environment by running:

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

pip will install oncoexporter into the active environment. The package is installed in editable mode - any code updates are available after Python restart, instead of having to reinstall.

Use Oncoexporter in Jupyter notebook

To use the kernel in Jupyter notebook, first, make sure you have ipykernel library to allow using the virtual environment as a Jupyter kernel.

python3 -m pip install jupyter ipykernel

Then, we can create a new Jupyter kernel and register the kernel with Jupyter by running:

python -m ipykernel install --user --name oncoexporter_env --display-name "Oncoexporter"

Last, starting from the project directory, we can run Jupyter to work on the notebooks of the Oncoexport repository.

cd notebooks
jupyter-notebook

At this point, a Jupyter page should open in the system browser. Navigate to the notebook or create one and be sure to activate the oncoexporter_env kernel.

mkdocs for documentation.

To run the mkdocs server locally, enter the following code to install prerequisites in the virtual environment

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

and then enter

mkdocs serve

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