https://github.com/pyrates-neuroscience/pycobi
Python package for automated bifurcation analysis and parameter continuations, based on Auto-07p.
https://github.com/pyrates-neuroscience/pycobi
auto-07p bifurcation bifurcation-analysis bifurcation-detection differential-equations dynamical-systems fortran90 parameter-continuation phase-transitions python
Last synced: 6 months ago
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Python package for automated bifurcation analysis and parameter continuations, based on Auto-07p.
- Host: GitHub
- URL: https://github.com/pyrates-neuroscience/pycobi
- Owner: pyrates-neuroscience
- License: gpl-3.0
- Created: 2022-01-14T15:04:19.000Z (almost 4 years ago)
- Default Branch: master
- Last Pushed: 2025-02-28T18:15:08.000Z (8 months ago)
- Last Synced: 2025-04-14T22:16:20.952Z (6 months ago)
- Topics: auto-07p, bifurcation, bifurcation-analysis, bifurcation-detection, differential-equations, dynamical-systems, fortran90, parameter-continuation, phase-transitions, python
- Language: Python
- Homepage: https://pycobi.readthedocs.io/en/latest/
- Size: 688 KB
- Stars: 22
- Watchers: 2
- Forks: 2
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.rst
- License: LICENSE
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README
# PyCoBi
[](https://github.com/pyrates-neuroscience/PyCoBi)
[](https://badge.fury.io/py/pycobi)
[](https://badge.fury.io/py/pycobi)
[](https://circleci.com/gh/pyrates-neuroscience/PyCoBi)
[](https://pycobi.readthedocs.io/en/latest/?badge=latest)
[](https://zenodo.org/badge/latestdoi/448007450)
*PyCoBi* is a **Py**thon tool for parameter **co**ntinuations and automated **bi**furcation 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](https://github.com/pyrates-neuroscience/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](https://github.com/auto-07p/auto-07p).
You can follow these [installation instructions](https://github.com/auto-07p/auto-07p/tree/master/doc) 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.
A typical installation procedure would be the following:
**Step 1:** Clone the *Auto-07p* github repository:
```shell
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
```shell
./configure
```
**Step 3:** Install *Auto-07p*
In the same directory, call
```shell
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*
```shell
python setup.py install
```
**Step 5:** Install *PyCoBi*
Use `pip` to install the latest stable version of *PyCoBi*
```shell
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](https://pycobi.readthedocs.io/en/latest/).
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.