Persistent Homology Python Packages

gudhi

The GUDHI library is a generic open source C++ library, with a Python interface, for Topological Data Analysis (TDA) and Higher Dimensional Geometry Understanding.

ripser

A Lean Persistent Homology Library for Python

cripser

Persistent homology calculation for 1D (scalar time series), 2D (image), and 3D, 4D (voxel) arrays

multipers

Python library for multiparameter persistence

lophat

Lockfree Persistent Homology Algorithm Toolkit

pyflagser

Python bindings and API for the flagser C++ library (https://github.com/luetge/flagser).

teaspoon

Topological Signal Processing in Python

chromatic-tda

Tool to compute six-packs of persistence diagrams for chromatic point clouds [packaged on PyPI]

pynerve

Pynerve: Topological Data Analysis library for Python and C++

petls-pytorch

PyTorch-native persistent topological Laplacians for TDA, with GPU-compatible spectral computations.

topp

Exact persistence-diagram Bottleneck and Wasserstein distances

treegraphduals

PyPI package for graph-theoretic time series analysis ; level set trees and their duals- horizontal tunnelability graphs

topapprox

Package for computing topological approximation using Persistent Homology in various settings.

genpath-pph

GenPath-PPH: Python package for integrating gene expression and KEGG pathway networks via Persistent Path Homology to detect disease-relevant pathway dysregulation. Available on PyPI: pip install genpath-pph

pervect

Vectorization of persistence diagrams and approximate Wasserstein distance

topoconscious

Persistent homology pipeline for detecting neural correlates of consciousness from fMRI — H0/H1/H2, Wasserstein + Müller-Lyer timelines, HMM decoding, topological transfer entropy.

topogeoml

Topology-aware ML toolkit plus preregistered graph-classification study; honest negative result, statistical harness, reproducible evidence.

groupoid

Pre-alpha groupoid/sheaf/Riemannian aggregation prototype for federated learning; tested math components, not production FL.

topologyx

Topological Data Analysis Routines

quaternion-monoid-algebra

Compositional algebra over fixed-width quaternionic-symbolic state packets. A monoid (closed, associative, with two-sided identity) plus empirical topology preservation. MIT licensed.

diagram2vec

Vector Representations of Persistence Diagrams

steenroder

Computation of persistence Steenrod barcodes

shapr-torch

SHAPR: Code for "Capturing Shape Information with Multi-Scale Topological Loss Terms for 3D Reconstruction"

topsimp

Package for computing topological approximation using Persistent Homology in various settings.