pydstool | PyDSTool main development repo

by robclewley Python Version: Current License: Non-SPDX

X-Ray Key Features Code Snippets Community Discussions(3)Vulnerabilities Install Support

kandi X-RAY | pydstool Summary

pydstool is a Python library. pydstool has no bugs, it has no vulnerabilities, it has build file available and it has low support. However pydstool has a Non-SPDX License. You can download it from GitHub.

PyDSTool main development repo

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Quality

Security

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Support

pydstool has a low active ecosystem.

It has 135 star(s) with 55 fork(s). There are 25 watchers for this library.

It had no major release in the last 6 months.

There are 39 open issues and 44 have been closed. On average issues are closed in 191 days. There are 4 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of pydstool is current.

Quality

pydstool has 0 bugs and 0 code smells.

Security

pydstool has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

pydstool code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

pydstool has a Non-SPDX License.

Non-SPDX licenses can be open source with a non SPDX compliant license, or non open source licenses, and you need to review them closely before use.

Reuse

pydstool releases are not available. You will need to build from source code and install.

Build file is available. You can build the component from source.

pydstool saves you 51502 person hours of effort in developing the same functionality from scratch.

It has 59713 lines of code, 3154 functions and 291 files.

It has high code complexity. Code complexity directly impacts maintainability of the code.

Top functions reviewed by kandi - BETA

kandi has reviewed pydstool and discovered the below as its top functions. This is intended to give you an instant insight into pydstool implemented functionality, and help decide if they suit your requirements.

Execute the ODE system
Searches through the model
Return True if val is contained in interval
Set f_params
Generate nullclines for nullclines
Compile the shared library
Create a new curve
Loads the shared library
Performs an ODE system
Performs an ODE computation
R Finds the saddleman manifold
Compute the model for a given trajectory
Initialize the autocore module
Calculate statistics for a covered array
Sample from the trajectory
Generate a dictionary of auxiliary functions
Create a ZeroEvent expression
Convert a qexpr expression into a function
Generate self - auxiliary functions
Compute latent variables
Compute a trajectory segment
Searches for an event
Generate an adjoint PRC
Create a spiffyodel object
Given a list of criteria and a set of criteria return a dictionary of transition intervals
Make channel rates

Get all kandi verified functions for this library.

pydstool Key Features

No Key Features are available at this moment for pydstool.

pydstool Examples and Code Snippets

No Code Snippets are available at this moment for pydstool.

Community Discussions

Trending Discussions on pydstool

Simultaneous event detection using solve_ivp

Python library or package for bifurcation analysis in ordinary differential equations

PyDSTool do not recognize SciPy version

QUESTION

Simultaneous event detection using solve_ivp

Asked 2020-Feb-09 at 17:46

I'm trying to couple several Quadratic integrate-and-fire neurons.

My script works successfully with two neurons, but when I modified the script for 3 neurons, I noticed that the voltage of the third neuron suddenly explodes and therefore, the integration fails.

I did some basic analysis, and looking at the solution array, my guess is that the event detection of scipy.solve_ivp can't detect when two neurons fire at the same time. My reason for saying this is that the 2nd and 3rd neurons' firing rate should be identical, since they only neuron with an external current is the 1st one.

However, while they both fire together, the event detection only detects one event, and therefore fails to reset the voltage of the other one, hence the exponential growth.

My ultimate goal would be to couple this with other types of neurons, but since many of those have intrinsic repolarization dynamics, event handling of QIFs is the crucial part of scaling the network.

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ANSWER

Answered 2020-Feb-09 at 17:46

You are indeed correct, solve_ivp does not detect additional events that happen at the same time (outside of situations where you duplicate a component as here it is highly unlikely to arrive at such a situation in a numerical simulation). You can test this manually, as an event is a root of the event function. So set

Source https://stackoverflow.com/questions/60136367

QUESTION

Python library or package for bifurcation analysis in ordinary differential equations

Asked 2019-Aug-23 at 12:27

What are libraries packages available in Python for the simulation and bifurcation study of dynamical systems?

I want to study the bifurcation phenomenon in ordinary differential equations. I know that there is AUTO in Fortran. I also found PyDSTool in Pyhton. The issue with PyDSTool is that it has some incompatibilities with 64-bit systems and Python 3 (and also numpy, etc.). I was wondering if there is any state-of-the-art library in Python for this purpose. Thanks.

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ANSWER

Answered 2019-Aug-23 at 12:27

I don't think there is anything available in Python (except for PyDSTools and its interface with AUTO). You might check out the bifurcation suite in JULIA (which is also well suited to simulate and model dynamical systems): http://docs.juliadiffeq.org/latest/analysis/bifurcation.html It is also built around PyDstools though but you might be able to circumvent your incompatibility problems.

Source https://stackoverflow.com/questions/56296010

QUESTION

PyDSTool do not recognize SciPy version

Asked 2019-Apr-17 at 15:42

I have installed PyDSTool package :

...

ANSWER

Answered 2018-Mar-20 at 10:33

The PyDSTool project homepage at sourceforge is down: http://pydstool.sourceforge.net/ points to http://www.ni.gsu.edu/~rclewley/PyDSTool/FrontPage.html that returns "file not found".

The project has moved to GitHub: https://github.com/robclewley/pydstool

There are several issues in line with yours there. The problem is that, currently, the development of SciPy's integrate module has broken the calls from PyDSTool.

One solution: use an older version of SciPy. The alternatives are either to find yourself the points of failure or to use the fork here: https://github.com/tkf/pydstool/tree/tkf

Source https://stackoverflow.com/questions/49369299

Community Discussions, Code Snippets contain sources that include Stack Exchange Network

Vulnerabilities

No vulnerabilities reported

Install pydstool

You can download it from GitHub.
You can use pydstool like any standard Python library. You will need to make sure that you have a development environment consisting of a Python distribution including header files, a compiler, pip, and git installed. Make sure that your pip, setuptools, and wheel are up to date. When using pip it is generally recommended to install packages in a virtual environment to avoid changes to the system.

Support

For any new features, suggestions and bugs create an issue on GitHub. If you have any questions check and ask questions on community page Stack Overflow .

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