Installation¶

sbmlsim requires python >= 3.13 and is available from pypi. It is tested on Linux, macOS and Windows. The simulations run on libroadrunner, which ships binary wheels for all three platforms, so no compiler is needed.

With uv¶

uv is the recommended way to install the package. In a project it is added as a dependency, which resolves and locks it together with the rest of the environment:

uv add sbmlsim

Into an existing virtual environment it is installed through the pip interface of uv:

uv venv --python 3.14
uv pip install sbmlsim

With pip¶

pip install sbmlsim

Development version¶

The current state of the develop branch is installed directly from GitHub:

uv add "sbmlsim @ git+https://github.com/matthiaskoenig/sbmlsim.git@develop"

or, with pip,

pip install git+https://github.com/matthiaskoenig/sbmlsim.git@develop

To work on the repository itself, with the test and documentation tooling, see Development.

Dependencies¶

sbmlsim builds on the packages of the COMBINE ecosystem and the scientific python stack. They are installed with it:

package	used for
libroadrunner	simulation of the SBML models
sbmlutils, python-libsbml	reading, validating and changing SBML models
pymetadata	COMBINE archives of the PEtab problems
numpy, pandas, xarray, scipy, sympy	numerics, data and results
h5netcdf, h5py	the netCDF files of the results
sbmlmath	the math of SBML as sympy expressions
pint, pydantic	units and unit conversions, validated data
petab, pyyaml, SALib	parameter fitting problems, the files of the PEtab test suites and global sensitivity analysis
matplotlib, seaborn, jinja2, rich	plots, reports and the output of scripts

Logging¶

sbmlsim does not configure logging. It logs to loggers below the sbmlsim logger and leaves handlers, levels and formatting to the application, so the messages of the package stay under your control:

import logging

logging.basicConfig(level=logging.INFO)
logging.getLogger("sbmlsim").setLevel(logging.WARNING)

For scripts and interactive work the rich output of the package can be turned on explicitly:

from sbmlsim import log

log.enable_rich_logging()