Machine learning for biomarkers computing
Project description
Biolearn
Biolearn enables easy and versatile analyses of biomarkers of aging data. It provides statistics and machine-learning tools, with instructive documentation and an open science approach.
Important links
Official source code repo: https://github.com/bio-learn/biolearn/
HTML documentation (only development release for the moment): https://bio-learn.github.io/
Install
Latest release
0. Install the right Python version
Biolearn supports Python 3.10, please verify that you have the right Python 3 version before proceeding with the developer setup.
1. Setup a virtual environment
At the moment we do not have a stable release, only a unstable developer version. This means that you should not install the package directly from pypi but always get the source code from github and do a local pip install.
In the following steps we show an installation path we have tested with venv and pip. Other package managers have not been tested and are not supported at the moment.
In linux from inside the repo directory run the following to setup a virtual environment and install dependencies
python3.10 -m venv .venv
make installRemember we do not support a pypi version at the moment, as in (pip install biolearn), the command will work but you will just get a dummy package.
Check installation
You can verify that your setup is working by running the tests
make testIf no error is raised, you have installed biolearn correctly.
You can also run the following to start jupyter lab with the library available
make jupyterimport biolearnDiscord server
The biolearn team has a discord server to answer questions, discuss feature requests, or have any biolearn related discussions.
Dependencies
The required dependencies to use the software are listed in the file pyproject.toml.
Development
Detailed instructions on developer setup and how to contribute are available in the repo
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