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Installation

This package requires Python 3.6 or later. Miniconda provides a small installation.

Install from PyPI

Install yaml2sbml from PyPI via:

pip install yaml2sbml

Install from GitHub

To work with the latest development version, install yaml2sbml from GitHub via:

pip install https://github.com/yaml2sbml-dev/yaml2sbml/archive/develop.zip

or clone the repository and install from local via:

git clone https://github.com/yaml2sbml-dev/yaml2sbml
cd yaml2sbml
git checkout develop
pip install -e .

where -e is short for --editable and links the installed package to the current location, such that changes there take immediate effect.

Additional dependencies for running the examples

The notebooks come with additional dependencies. Information on the installation of the ODE simulator AMICI is given in its installation guide. Further dependencies can be installed via:

pip install yaml2sbml[examples]