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.
- Boost needs to be at least version 1.55.
- If you are using GCC, the oldest supported version is 5.4.
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:
to your ~/.bashrc or ~/.zshrc.
Documentation for Dionysus can be found here.
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