Install and upgrade
This package requires Python 3.8 or later (see Python support). It is continuously tested on Linux, and most parts should also work on other operating systems (MacOS, Windows).
I cannot use my system’s Python distribution, what now?
Several Python distributions can co-exist on a single system. If you don’t have access to a recent Python version via your system’s package manager (this might be the case for old operating systems), it is recommended to install the latest version of the Anaconda Python 3 distribution.
Also, there is the possibility to use multiple virtual environments via:
python3 -m virtualenv ENV_NAME source ENV_NAME/bin/activate
where ENV_NAME denotes an individual environment name, if you do not want to mess up the system environment.
Install from PIP
The package can be installed from the Python Package Index PyPI via pip:
pip3 install pypesto
Install from GIT
If you want the bleeding edge version, install directly from github:
pip3 install git+https://github.com/icb-dcm/pypesto.git
If you need to have access to the source code, you can download it via:
git clone https://github.com/icb-dcm/pypesto.git
and then install from the local repository via:
cd pypesto pip3 install .
If you want to upgrade from an existing previous version, replace
ìnstall --upgrade in the above commands.
Install optional packages and external dependencies
pyPESTO includes multiple convenience methods to simplify parameter estimation for models generated using the toolbox AMICI. To use AMICI, install it via pip:
pip3 install amici
or, in case of problems, follow the full instructions from the AMICI documentation.
This package inherently supports optimization using the dlib toolbox. To use it, install dlib via:
pip3 install dlib
All external dependencies can be installed through this shell script.
We adopt the NEP 29 - Recommend Python and NumPy version support as a community policy standard. That means, we adopt a time window based policy for support of Python (and NumPy) versions.