| Name | pycobi JSON |
| Version |
0.8.7
JSON |
| download |
| home_page | None |
| Summary | Python tool for parameter continuation and bifurcation analysis |
| upload_time | 2024-03-31 21:57:04 |
| maintainer | None |
| docs_url | None |
| author | Richard Gast |
| requires_python | >=3.6 |
| license | GPL v3 |
| keywords |
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| VCS |
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| bugtrack_url |
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| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
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| coveralls test coverage |
No coveralls.
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# 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)
<img src="PyCoBi_logo_color.png" width="20%" heigth="20%" align="right">
*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.
Raw data
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"description": "# PyCoBi\n\n[](https://github.com/pyrates-neuroscience/PyCoBi)\n[](https://badge.fury.io/py/pycobi)\n[](https://badge.fury.io/py/pycobi)\n[](https://circleci.com/gh/pyrates-neuroscience/PyCoBi)\n[](https://pycobi.readthedocs.io/en/latest/?badge=latest)\n[](https://zenodo.org/badge/latestdoi/448007450)\n\n<img src=\"PyCoBi_logo_color.png\" width=\"20%\" heigth=\"20%\" align=\"right\">\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\n\n",
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