Installation

From PyPI

pip install densitree

From source (development)

git clone https://github.com/fuzue/densitree.git
cd densitree
pip install -e ".[dev]"

Dependencies

densitree requires Python 3.10+ and the following packages (installed automatically):

Package	Minimum version	Purpose
numpy	1.24	Array operations
scipy	1.10	MST computation, distance metrics
scikit-learn	1.3	k-NN, agglomerative clustering
networkx	3.0	Tree data structure
matplotlib	3.7	Static visualization
plotly	5.15	Interactive visualization
pandas	2.0	DataFrame support, cluster statistics

Optional dependencies

For running benchmarks:

pip install densitree[bench]

This adds flowio (FCS file reading), leidenalg and igraph (PhenoGraph-style clustering for comparisons).

For building documentation:

pip install densitree[docs]