Installation

Python Version and Environment

Note that due to some of our dependencies we’re currently limited to python version 3.7. Please make sure you set up a virtual environment with that version before trying to install this library. If you’re unsure how to do that please have a look at conda or pyenv.

If you are part of the Blue Brain Project and are working on the BB5 you can find the correct python version in the archive modules between archive/2020-02 and archive/2020-12 (inclusive). Here’s an example of a set of commands that will set up your environment on the BB5:

module purge
module load archive/2020-12
module load python
python -m venv venv
. ./venv/bin/activate
python --version

We also recommend that you make sure that pip is up-to-date and that the packages wheel and setuptools are installed:

pip install --upgrade pip wheel setuptools

Install “Atlas Interpolation”

In order to access the data and the example scripts a local clone of this repository is required. Run these commands to get it:

git clone https://github.com/BlueBrain/atlas-interpolation
cd atlas-interpolation

The “Atlas Interpolation” package can now be installed directly from the clone we just created:

pip install '.[data, optical]'