Installation und Upgrading

Preparation

This package requires Python 3.6 or later. The package is tested on Linux (using Travis continuous integration).

Not all of the package’s functionality is available for Microsoft Windows. As some of the multi-core parallelizations rely on forking, these won’t work on Windows. However, most other parts of the package should work on Windows as well.

My system’s Python distribution is outdated, what now?

Several Python distributions can coexist 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 Debian or Ubuntu operating systems), it is recommended to install the latest version of the Anaconda Python 3 distribution. See also: Installing Anaconda on a Cluster environment.

PIP Installation

Install with root rights into you system’s Python distribution

The package can be installed via pip.:

pip install pyabc

into your system’s Python distribution. This requires usually root access.

GIT Installation

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

pip install git+https://github.com/icb-dcm/pyabc.git

Upgrading

If you want to upgrade from a previous pyABC version, use:

pip install --upgrade pyabc

instead of pip install. You can also consult the pip documentation on how to manage packages. If you installed pyABC into your home directory with pip install --user pyabc, then upgrade also with the --user flag:

pip install --upgrade --user pyabc

Installing Anaconda on a Cluster environment

We’re assuming you’re on a Linux environment. Use the most recent Anaconda Python 3.x distribution. As of writing this documentation, this is the Anaconda Python 3.6 distribution. To install it, run:

wget https://repo.continuum.io/archive/Anaconda3-4.4.0-Linux-x86_64.sh

to download the installer. To execute the installer run:

bash Anaconda3-4.4.0-Linux-x86_64.sh

and follow the guided installation process (i.e. approve the license and tell the installer where to install it to). You might want to replace the “4.4.0” by the most recent version of Anaconda. Find out on the Anaconda Download page which one it is.

Note

The Anaconda installer asks you at the end of the installation whether you want to use Anaconda Python as your default Python:: bash

Do you wish the installer to prepend the Anaconda3 install location to PATH in your /home/username/.bashrc ? [yes|no] [no] >>>

If you answer yes, the path to the Anaconda installation is prepended to your PATH environment variable and subsequent calls to pip (see below) use the Anaconda Python pip (check with the command which pip). If you answer no, you need to ensure manually, that the correct Python installation is used. Just saying “yes” here might safe you from some difficulties later on.

Optional dependencies

pyABC has an optional interface to the R language. To enable it install pyabc via pip install pyabc[R]. All Python based features will work just fine if R is not installed. See also pyABC’s external API.

pyABC optionally uses git to store commit hashed in its database leveraging the gitpython package. This feature can be installed via pip install pyabc[git].