Installation

Note that python versions 3.9 and 3.10 are recommended. Python versions 3.7 and below will not work with more recent versions of StaVia/pyVIA

install using pip

conda create --name ViaEnv python=3.10
pip install pyVIA // tested on linux Ubuntu 16.04 and Windows 10

This usually tries to install hnswlib, produces an error and automatically corrects itself by first installing pybind11 followed by hnswlib. To get a smoother installation, consider installing in the following order after creating a new conda environment:

pip install pybind11
pip install hnswlib
pip install pyVIA

install by cloning repository and running setup.py (ensure dependencies are installed):

git clone https://github.com/ShobiStassen/VIA.git
python3 setup.py install // cd into the directory of the cloned VIA folder containing setup.py and issue this command

MAC installation The pie-chart cluster-graph plot does not render correctly for MACs for the time-being. All other outputs are as expected.:

conda create --name ViaEnv python=3.10
pip install pybind11
conda install -c conda-forge hnswlib
pip install pyVIA

Windows installation:

Note that on Windows if you do not have Visual C++ (required for hnswlib) you can install using this link . You can also subsequently install dependences separately

pip install pybind11, hnswlib, igraph, leidenalg>=0.7.0, umap-learn, numpy>=1.17, scipy, pandas>=0.25, sklearn, termcolor, pygam, phate, matplotlib,scanpy
pip install pyVIA