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.
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-buildon 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-07pStep 2: Configure the installation scripts
Go to the directory that you cloned the Auto-07p repository into and call
./configureStep 3: Install Auto-07p
In the same directory, call
makeStep 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 pycobiAlternatively, 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).
A full API, documentation, and use examples can be found at readthedocs.
[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.