Installation¶

pkpdsim requires python >= 3.14 and is available from pypi. It is tested on Linux, macOS and Windows with python 3.14 and on Linux with python 3.15. It simulates with sbmlsim 0.15 (sbmlsim>=0.15.0,<0.16, installed with it); pkpdsim 0.4 is the version for models on sbmlsim 0.8.

With uv¶

uv is the recommended way to install the package. In a project it is added as a dependency:

uv add pkpdsim

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

uv venv --python 3.14
uv pip install pkpdsim

With pip¶

pip install pkpdsim

AMICI, the second simulator¶

The battery of the checks of a model compares its builds with AMICI when it is installed, see Battery of the builds. AMICI is the optional extra amici; it is built from source and compiles every model, so it needs a C++ compiler (cmake and ninja come with the extra):

uv pip install "pkpdsim[amici]"

Development version¶

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

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

or, with pip,

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

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

Dependencies¶

package	used for
sbmlutils	the factory of the models (creators, units, compartments), the qualifiers of the annotations and the console
libroadrunner	the simulator, the initial values are selections of a roadrunner model

libroadrunner ships binary wheels for Linux (x86_64), macOS and Windows. Its extension links against libpython: an interpreter which uv installs keeps libpython in its lib directory, where the loader of Linux does not look, and import roadrunner fails with libpython3.14.so.1.0: cannot open shared object file. Put the directory on the library search path, e.g. in a project managed by uv:

export LD_LIBRARY_PATH="$(uv run python -c 'import sys; print(sys.base_prefix)')/lib"

An interpreter of the system or of conda is not affected, nor are macOS and Windows. On python 3.15 the wheel of libroadrunner 2.11.0 takes the symbol __jit_debug_register_code from libpython, which only an interpreter built with the experimental JIT defines: the interpreters of uv are, others may not be (deadsnakes on Ubuntu is not), and import roadrunner fails with undefined symbol: __jit_debug_register_code (roadrunner#1406); use an interpreter of uv there.

Logging¶

pkpdsim does not configure logging; it logs to the loggers below the pkpdsim logger and leaves handlers, levels and formatting to the application.