Dionysus 2

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

• Modified BSD license <https://github.com/mrzv/dionysus/blob/master/LICENSE.txt>_ (because GPL causes too many problems in academic software).
• No dependency on Boost.Python; Dionysus 2 uses (and includes) PyBind11 <https://github.com/pybind/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 <http://mrzv.org/software/dionysus2/tutorial/omni-field.html#omni-field> and Wasserstein and bottleneck distance computation <http://mrzv.org/software/dionysus2/tutorial/basics.html#diagram-distances> from Hera <https://bitbucket.org/grey_narn/hera>_.
• A few plotting <http://mrzv.org/software/dionysus2/tutorial/plotting.html#plotting> routines, based on Matplotlib <https://matplotlib.org/>.
• Better integration with NumPy <http://www.numpy.org/>_.

Features that haven't (yet) made it over from Dionysus 1 <http://mrzv.org/software/dionysus> include vineyards. Alpha shape filtrations are available via DioDe <https://github.com/mrzv/diode>.

Dependencies:

• Boost <http://www.boost.org/>_, although Dionysus 2 doesn't link any of its libraries, so it's considerably easier to build the project.
• (Optional) SciPy <https://www.scipy.org/> for the LSQR routine used in circular coordinates <http://mrzv.org/software/dionysus2/tutorial/cohomology.html#circular>.
• (Optional) Matplotlib <https://matplotlib.org/>_ 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 <https://groups.io/g/dionysus/>_ for all questions and discussion related to the library;
• GitHub's issue tracker <https://github.com/mrzv/dionysus/issues>_ 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 <https://pypi.org/project/dionysus/>_:

.. parsed-literal::

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):

.. parsed-literal::

pip install --verbose `git+https://github.com/mrzv/dionysus.git <https://github.com/mrzv/dionysus.git>`_

Alternatively, you can clone and build everything by hand. To get Dionysus 2, either clone its repository <https://github.com/mrzv/dionysus>_:

.. parsed-literal::

git clone `<https://github.com/mrzv/dionysus.git>`_

or download it as a Zip archive <https://github.com/mrzv/dionysus/archive/master.zip>_.

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 <http://mrzv.org/software/dionysus2/>_.