CMGDB 1.0.4

CMGDB (Conley Morse Graph Database) Python Extension

CMGDB

Conley Morse Graph Database

Overview

This project uses combinatorial and topological methods to compute dynamics of discrete dynamical systems.

Dependencies and Installation

The dependencies and install instructions on a Mac using Homebrew are listed below.

Boost and GMP

Install Boost and GMP

brew install boost
brew install gmp

SDSL

Install the Succinct Data Structure Library (SDSL)

git clone https://github.com/simongog/sdsl-lite.git
cd sdsl-lite
./install.sh /usr/local/

It is also possible to intall the sdsl-lite library with Homebrew using this repository with the commands

brew tap Brewsci/bio
brew install sdsl-lite

Eigen3

Install Eigen3

brew install eigen

graphviz

Install graphviz

brew install graphviz

CMake

Install CMake

brew install cmake

jupyter and graphviz

Install the jupyter and graphviz Python packages

python -m pip install jupyter graphviz

Install CMGDB

git clone https://github.com/marciogameiro/CMGDB.git
cd CMGDB
./install.sh

Documentation and Examples

To get started on how to run the code see the examples in the Jupyter notebooks in the examples folder.

In particular the notebooks Examples.ipynb, Gaussian_Process_Example.ipynb, and Conley_Index_Examples.ipynb present basic examples on how to run the code and are a good starting point.

Here is an old survey and a talk that might be useful.