pycobi 1.0.0

Python tool for parameter continuation and bifurcation analysis

PyCoBi

PyCoBi is a Python tool for parameter continuations and automated bifurcation analysis. It provides a Python interface to Auto-07p [1], allowing for a more intuitive usage of Auto-07p commands within Python scripts. It provides direct access to solutions, branches, and their properties (i.e. special solutions, eigenvalues, etc.) as well as a range of plotting functions to visualize bifurcation diagrams and solutions. Finally, it allows to automatically generate the user-supplied Fortran routines via PyRates, such that Auto-07p can be fully used/controlled from within a single Python script, without the need to supply additional non-Python files.

Installation

To use PyCoBi, it is required to install Auto-07p. You can follow these installation instructions for detailed information on how to install Auto-07p in your specific setup. Note that it is not required to manually set any path variables, since PyAuto will take care of that for you.
Additionally, you need to have ninja-build installed, which can be done via

apt install ninja-build

on Ubuntu. A typical installation procedure would proceed the following:

Step 1: Clone the Auto-07p github repository:

git clone https://github.com/auto-07p/auto-07p

Step 2: Configure the installation scripts

Go to the directory that you cloned the Auto-07p repository into and call

./configure

Step 3: Install Auto-07p

In the same directory, call

make

Step 4: Install the Python version of Auto-07p

After that, in the same directory, execute the following call from within the Python environment that you would like to use for PyAuto

pip install ./

Step 5: Install PyCoBi

Use pip to install the latest stable version of PyCoBi

pip install pycobi

Alternatively, the development version of PyCoBi can be installed by cloning the github repository and using the setup.py for installation (see steps 1 and 4).

Documentation

A full API, documentation, and use examples can be found at readthedocs.

References

[1] E.J. Doedel, T.F. Fairgrieve, B. Sandstede, A.R. Champneys, Y.A. Kuznetsov and W. Xianjun (2007) Auto-07p: Continuation and bifurcation software for ordinary differential equations. Technical report, Department of Computer Science, Concordia University, Montreal, Quebec.