Installation

⚙️ Installation

(optional) Creating a conda environment

It is common practice creating a separate conda environment to avoid dependencies mixing. You can create the new environment named vitrum with minimal amount of required packages with the following command:

conda create -n vitrum python=3.11
conda activate vitrum

Installation of vitrum

To install vitrum:

pip install directly from this repository. (Make sure you have git installed)

pip install "vitrum @ git+https://github.com/R-Chr/vitrum.git"

To update package to the most current version

pip install --force-reinstall --no-deps "vitrum @ git+https://github.com/R-Chr/vitrum.git"

(optional) To install dependencies for batch_active (BALACE framework):

pip install "vitrum[batch_active] @ git+https://github.com/R-Chr/vitrum.git"

(optional) Dionysus and Diode

For persistent homology analsysis these packages are required.

pip install dionysus
pip install git+https://github.com/mrzv/diode.git

DioDe uses CGAL to generate alpha shapes filtrations in a format that Dionysus understands. For DioDe to work CGAL is required (Only important for persistent homology).