Install and upgrade

Requirements

This package requires Python 3.11 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 PyPI

The package can be installed from the Python Package Index PyPI via pip:

pip3 install pypesto

Install from GitHub

If you want the bleeding edge version, install directly from GitHub:

pip3 install git+https://github.com/icb-dcm/pypesto.git@develop

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 .

Upgrade

If you want to upgrade from an existing previous version, replace install by 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.

Install and run Docker container

We provide a pyPESTO OCI image through the Docker.io registry.

A docker image build is triggered on changes/commits in the develop branch of pyPESTO. The container is built and pushed via a GHA to the Docker.io registry with the tag corresponding to latest.

The image can be obtained by a pull from the Docker.io registry: docker pull docker.io/stephanmg/pypesto:latest

The Docker image can also be built locally using the Dockerfile found here: https://github.com/ICB-DCM/pyPESTO/tree/main/docker

If you require to transfer the docker image manually, build the container using the Dockerfile, then export your docker image to .tar by: docker save -o pypesto.tar pypesto:latest. The .tar file can then be transfered (e.g. with scp) to a remote location.

To run the pyPESTO container and print the current pyPESTO version: docker run --rm pypesto python3 -c 'import pypesto; print(f"pyPESTO version: {pypesto.__version__}")'.

Python support

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.