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Compartmental modelling Python package

Project description

comod

Github release PyPI

license MIT

Build Status Documentation Status

Compartmental modelling Python package

Preview

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Check the docs to see more.

Features

  • Define a model with simple rules as strings or with custom functions.
  • Pre-defined models like SIR, SIS, SEIR, ...
  • Community-extensions of models.
  • Solve numerically for fixed or time-dependent parameters.
  • Best-fit to existing data, posibly using time windows.
  • Create compartment graphs.
  • Export LaTeX.
  • Export to Wolfram Language (Mathematica).

Installation

Assuming you have a Python3 distribution with pip, the latest pypi release can be installed with:

pip3 install comod

To install the optional dependencies you can run

pip3 install 'comod[extras]'

Mind the quotes.

Developer information

Instalation

To install a development version, cd to the directory with this file and:

pip3 install -e '.[test]'

As an alternative, a virtualenv might be used to install the package:

# Prepare a clean virtualenv and activate it
virtualenv -p /usr/bin/python3.6 venv
source venv/bin/activate
# Install the package
pip3 install -e '.[test]'

Documentation

To generate the documentation, the docs extra dependencies must be installed.

To generate an html documentation with sphinx run:

make docs

To generate a PDF documentation using LaTeX:

make pdf

Test

To run the unitary tests:

make test

Project details


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Files for comod, version 0.2.0
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