TDAPNRG

Dependancies:

• numpy
• scipy
• Cython
• scitkit-tda
• matplotlib.
• scikit-learn
• plotly
• GF2Matrix

Cython should be the only one required before installation. Due to setuptools not specifying order of installation, you may need to install Cython before setup, which can be done by running

pip install Cython

This may also occur for numpy.

Windows users: If you are using a Windows machine, you will also need to install MinGW on your system.

To setup for development use:

# TDAPNRG/python-implementation/
python setup.py develop

Or for install:

# TDAPNRG/python-implementation/
python setup.py install

Running with Docker

To build:

#path/to/TDAPNRG
sudo docker build --tag=randology .

To run as a single container, the run.sh shell script is provided for convenience. This handles the locations that files need to be mounted.

sudo bash ./run.sh relative/path/to/output_directory relative/path/to/config_file.json

For infomation on writing config files, see config-syntax.md

The output of the program will then be stored in the output directory mounted.

The random sequence files for running can be found here.