https://github.com/mrzv/dionysus

Library for computing persistent homology
https://github.com/mrzv/dionysus

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Library for computing persistent homology

• Host: GitHub
• URL: https://github.com/mrzv/dionysus
• Owner: mrzv
• License: other
• Created: 2017-07-14T19:02:35.000Z (over 7 years ago)
• Default Branch: master
• Last Pushed: 2023-07-06T22:32:04.000Z (over 1 year ago)
• Last Synced: 2024-03-30T23:02:01.634Z (8 months ago)
• Language: C++
• Homepage: http://mrzv.org/software/dionysus2
• Size: 2.98 MB
• Stars: 138
• Watchers: 8
• Forks: 30
• Open Issues: 7
• Metadata Files:
  • Readme: README.rst
  • License: LICENSE.txt

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README

        
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 `_)

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 `_:

.. 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 `_

Alternatively, you can clone and build everything by hand.

To get Dionysus 2, either clone its `repository `_:

.. parsed-literal::

    git clone ``_

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 `_.