Introduction

XPP is a software by Bard Ermentrout for the analysis of systems of ODEs. pyxpp is a Python wrapper around XPP that allows you to conveniently query information from the ODE file, run integrations, and compute nullclines. The main strength of pyxpp lies in its the usage of PLY, a Python Lex-Yacc implementation, to build a full-fledged XPP lexer, parser, and code generator. This provides easy customisability, and differentiates pyxpp from other XPP Python wrappers such as Py_XPPCALL and xppy.

Features

• Read paramters, initial conditions, auxiliary variables, state variables, RHS of ODEs, and functions.
• Run numerical integrations.
• Compute nullclines (unique to pyxpp, to my knowledge)
• Modify parameters, nullcline options, initial conditions ...

Dependencies

• Python 3
• PLY
• numpy
• XPP 8.0. The latest XPP Ubuntu binary is included as xppaut. You may need to change permissions to executable. Many distros also provide the binaries in their repos, e.g. Debian, Ubuntu, Arch (AUR).

Tutorial

A demo and tutorial can be found here.

TODO

• Convert functions to actual Python lambda expressions.
• Directional fields.
• Add some other commands. The following commands are not yet supported but could be easily implemented: table, bdry, volt, markov, wiener, solv, special, set, derived parameters, numbers, int, block pseudo-arrays

How to Cite pyxpp

If referencing pyxpp in a paper, please use

Olenik, M. PyXPP. 2018. Available at: https://github.com/markolenik/pyxpp.

And as BibTeX:

@Misc{pyxpp,
  author       = {Mark Olenik},
  title        = {pyxpp},
  howpublished = {https://github.com/markolenik/pyxpp},
  year         = {2018--2022}
}