Installation of anaconda for beginners

Here is the procedure to install Anaconda which allows to deal with different python enviroments but any other python editor can be used.

First, install anaconda: https://docs.anaconda.com/anaconda/install/.

Then, Unix and Mac users have to open a Terminal. Window users must instead open the anaconda prompt (type anaconda prompt in the search tool).

in the prompt, users have to create a new anaconda virtual environment which will be used for ExTrack with the following command: conda create --name pyExTrack python=3.9.

Then the user need to go in the environment to install ExTrack and to use it: conda activate pyExTrack.

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Installing ExTrack

We then need to install the ExTrack package in our virtual environment pyExTrack. The easiest way is to use the pip command:

Installation with pip

pip install extrack

Installation from this GitHub repository

if the installation from pip cannot be used for a reason, one can install the package from the GitHub repository instead:

python -m pip install git+https://github.com/vanTeeffelenLab/ExTrack.git

Installing jupyter notebook

In the section, we will see how to install jupyter notebook from the virtual environment pyExTrack to be able to follow ExTrack tutorial. First make sure you are in the virtual environment pyExTrack. You know you are in this environment if the current line of the Terminal starts with (pyExTrack) and not (base). if the current line do not starts with (pyExTrack), use the command conda activate pyExTrack to navigate to the environment pyExTrack).

Then you can install jupyter notebook in the ExTrack environment:

conda install jupyter notebook

Once installed, you can open a jupyter notebook with the command jupyter notebook (make sure you use this command from the pyExTrack environment as descrived above).

Following the ExTrack Tutorial

In order to follow the ExTrack tutorial you need to download and unzip the ExTrack folder if this has not been already done. You can do this by using the command git clone https://github.com/vanTeeffelenLab/ExTrack.git or by manual download from the source code page