{"id":20589826,"url":"https://github.com/pyrates-neuroscience/pycobi","last_synced_at":"2025-04-14T22:16:34.489Z","repository":{"id":116414241,"uuid":"448007450","full_name":"pyrates-neuroscience/PyCoBi","owner":"pyrates-neuroscience","description":"Python package for automated bifurcation analysis and parameter continuations, based on 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PyCoBi\n\n[![License](https://img.shields.io/github/license/pyrates-neuroscience/PyCoBi.svg)](https://github.com/pyrates-neuroscience/PyCoBi)\n[![Python](https://img.shields.io/pypi/pyversions/pycobi.svg?style=plastic)](https://badge.fury.io/py/pycobi)\n[![PyPI version](https://badge.fury.io/py/pycobi.svg)](https://badge.fury.io/py/pycobi)\n[![CircleCI](https://circleci.com/gh/pyrates-neuroscience/PyCoBi.svg?style=svg)](https://circleci.com/gh/pyrates-neuroscience/PyCoBi)\n[![Documentation Status](https://readthedocs.org/projects/pycobi/badge/?version=latest)](https://pycobi.readthedocs.io/en/latest/?badge=latest)\n[![DOI](https://zenodo.org/badge/448007450.svg)](https://zenodo.org/badge/latestdoi/448007450)\n\n\u003cimg src=\"PyCoBi_logo_color.png\" width=\"20%\" heigth=\"20%\" align=\"right\"\u003e\n\n*PyCoBi* is a **Py**thon tool for parameter **co**ntinuations and automated **bi**furcation analysis.\nIt provides a Python interface to *Auto-07p* [1], allowing for a more intuitive usage of *Auto-07p* commands within Python scripts. \nIt provides direct access to solutions, branches, and their properties (i.e. special solutions, eigenvalues, etc.) as well as a range of plotting \nfunctions to visualize bifurcation diagrams and solutions.\nFinally, it allows to automatically generate the user-supplied Fortran routines via [PyRates](https://github.com/pyrates-neuroscience/PyRates),\nsuch that *Auto-07p* can be fully used/controlled from within a single Python script, \nwithout the need to supply additional non-Python files.\n\nInstallation\n============\n\nTo use *PyCoBi*, it is required to install [Auto-07p](https://github.com/auto-07p/auto-07p).\nYou can follow these [installation instructions](https://github.com/auto-07p/auto-07p/tree/master/doc) for detailed \ninformation on how to install *Auto-07p* in your specific setup.\nNote that it is not required to manually set any path variables, since *PyAuto* will take care of that for you.  \nA typical installation procedure would be the following:\n\n**Step 1:** Clone the *Auto-07p* github repository:\n\n```shell\ngit clone https://github.com/auto-07p/auto-07p\n```\n\n**Step 2:** Configure the installation scripts\n\nGo to the directory that you cloned the *Auto-07p* repository into and call\n\n```shell\n./configure\n```\n\n**Step 3:** Install *Auto-07p*\n\nIn the same directory, call\n\n```shell\nmake\n```\n\n**Step 4:** Install the Python version of *Auto-07p*\n\nAfter that, in the same directory, execute the following call from within the Python environment that you would like to use for *PyAuto*\n\n```shell\npython setup.py install\n```\n\n**Step 5:** Install *PyCoBi*\n\nUse `pip` to install the latest stable version of *PyCoBi*\n\n```shell\npip install pycobi\n```\n\nAlternatively, the development version of *PyCoBi* can be installed by cloning the github \nrepository and using the `setup.py` for installation (see steps 1 and 4). \n\nDocumentation\n=============\n\nA full API, documentation, and use examples can be found at [readthedocs](https://pycobi.readthedocs.io/en/latest/).\n\nReferences\n==========\n \n[1] E.J. Doedel, T.F. Fairgrieve, B. Sandstede, A.R. Champneys, Y.A. Kuznetsov and W. Xianjun (2007) *Auto-07p:\n       Continuation and bifurcation software for ordinary differential equations.* Technical report,\n       Department of Computer Science, Concordia University, Montreal, Quebec.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpyrates-neuroscience%2Fpycobi","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fpyrates-neuroscience%2Fpycobi","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpyrates-neuroscience%2Fpycobi/lists"}