dionysus 2.1.0

Library for computing persistent homology

Dionysus is a computational topology package focused on persistent homology. It is written in C++, with Python bindings. The second version (previous version) is re-written from scratch, which helps it accomplish a few goals:

• Modified BSD license (because GPL causes too many problems in academic software).

• No dependency on Boost.Python; Dionysus 2 uses (and includes) PyBind11 instead, which greatly simplifies installation.

• Cleaner, more consistent internal design (for example, all algorithms support arbitrary fields).

• Some new algorithms, e.g., omni-field persistence and Wasserstein and bottleneck distance computation from Hera.

• A few plotting routines, based on Matplotlib.

• Better integration with NumPy.

Features that haven’t (yet) made it over from Dionysus 1 include vineyards. Alpha shape filtrations are available via DioDe.

Dependencies:

• Boost, although Dionysus 2 doesn’t link any of its libraries, so it’s considerably easier to build the project.

• (Optional) SciPy for the LSQR routine used in circular coordinates.

• (Optional) Matplotlib for plotting.

Requirements:

• Boost needs to be at least version 1.55.

• If you are using GCC, the oldest supported version is 5.4.

Contact:

• please use the dionysus mailing list for all questions and discussion related to the library;

• GitHub’s issue tracker is a central location for bug reports and feature requests.

Get, Build, Install

The simplest way to install Dionysus, as a Python package, is from PyPI:

pip install --verbose dionysus

Pass --upgrade to pip, if you have already installed some version of Dionysus.

Alternatively, you can install it directly from the development repository (this gives you the latest version):

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

Alternatively, you can clone and build everything by hand. To get Dionysus 2, either clone its repository:

git clone https://github.com/mrzv/dionysus.git

or download it as a Zip archive.

To build the project:

mkdir build
cd build
cmake ..
make

To use the Python bindings, either launch Python from .../build/bindings/python or add this directory to your PYTHONPATH variable, by adding:

export PYTHONPATH=.../build/bindings/python:$PYTHONPATH

to your ~/.bashrc or ~/.zshrc.

Documentation

Documentation for Dionysus can be found here.