PolyRound 0.1.4

A python package for rounding polytopes.

Efficient random sampling in convex polytopes relies on a ‘rounding’ preprocessing step, in which the polytope is rescaled so that the width is as uniform as possible across different dimensions. PolyRound rounds polytopes on the general form:

 with matrices  and  and vectors  and .

This formulation often arises in Systems Biology as the flux space of a metabolic network.

As output, PolyRound produces a polytope on the form  where  and the zero vector is a stricly interior point. For transforming points back to the original space, it also provides a matrix  and a vector , so that .

Currently, PolyRound is supported for python 3.7 and 3.8.

PolyRound no longer depends on a Gurobi installation and uses optlang (https://github.com/opencobra/optlang) to delegate linear programs to GLPK in case Gurobi is not installed. However, PolyRound is more reliable with Gurobi. Free Gurobi licenses for academic use can be obtained at https://www.gurobi.com/. Once the license is installed, the easiest way to get gurobi to work in python is through Anaconda https://www.anaconda.com/. Installation of gurobi in a conda environment is done with “conda install -c gurobi gurobi”.

An easy example of how to get started is presented in the jupyter notebook “example_usage”.