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README.md

Description

This package provides wrappers for using various persistent homology and other Topological Data Analysis software packages through python.

The code is an compilation of work done by Elizabeth Munch along with her students and collaborators. People who have contributed to teaspoon include:

Locations

Requirements

Please note that this code is still pre-alpha, so many things are not fully up and running yet.

Bugs reports and feature reqests can be posted on the github issues page.

In order to use all wrappers in teaspoon.TDA, the following need to be installed so they can be run command line.

  • Ripser. Code by Ulrich Bauer for computing persistent homology of a point cloud or distance matrix.
  • Perseus. Code by Vidit Nanda for computing persistent homology of point clouds, cubical complexes, and distance matrices.
  • Hera. Code by Michael Kerber, Dmitriy Morozov, and Arnur Nigmetov for computing bottleneck and Wasserstein distances.

Warning: the teaspoon installation will not install nor check for the install of these packages. In particular, perseus should be installed so that typing perseus in a terminal runs it, even though the default perseus installation for some operating systems ends up with an executable with a different name.

Installation

Warning:

This code is still pre-alpha. In particular, using the pip install seems to be finicky at best.
If you are having installation issues, please make a note of what you've done, including copying error message outputs, as a comment into the installation issue on github so we can start figuring out what is up with this system.

Installing using pip:

So far, the most success has been had with pip installation. Run the following commands to clone and install teaspoon. In particular, the pip install . command needs to be run in the folder with the setup.py file.

git clone https://github.com/lizliz/teaspoon.git
cd teaspoon
pip install .

Installing using python:

According to the internet, the pip version of install appears to be better. However, if you don't use pip, another option is to cd into the teaspoon directory and run:

python setup.py install

Alternatively, just add the folder to the python path.

If the above aren't working, add the following line to your .bashrc file.

export PYTHONPATH="${PYTHONPATH}:/path/to/teaspoon"

Documentation

Documentation is done using doxygen. The most recent version of the teaspoon documentation is hosted here.
Further info on documentation can be found in the contributing page.

Contributing

See the contributing page for more information on workflows.

Contact

Liz Munch: muncheli@egr.msu.edu.

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