Software Installation

These instructions explain how to install Anaconda Python 3, Expyriment, Git, a text editor, R and R Studio.

Warnings:

  • You will need to download about 1GB of software from the Internet. Therefore, make sure to have a decent connection.

  • Make sure that you have at least 5GB of free space on your hard drive to unpack the various software.

  • You might need to have administrator rights to install some of the softwares. If you are using a computer from an Institution, this is not always the case. Check with your IT team.

  • If you are using Windows 10, make sure your user name doesn’t include spaces or characters that don’t belong to the English alphabet (accents, ideograms,…). If you do, better create a new user with a simple identifier.

The R statistical software

R is a programming language specialized for statistical data analyses.

Windows

Download and install the latest version of R from https://cran.rstudio.com/bin/windows/base/

MacOS

Download and install the latest version of R from https://cran.rstudio.com/bin/macosx/

Linux

Find the version relevant for your distribution at https://cran.rstudio.com/bin/linux/ and follow the instructions in the README.html file.

Rstudio Desktop

Rstudio is an Integrated Developpement Environment for R which greatly simplifies the use of RMarkdown. You can download and install the latest version of RStudio Desktop from https://www.rstudio.com/products/rstudio/download/. Make sure to select the correct Operating System!

SublimeText code editor

A code editor is a program that allows you to edit pure text files such as Python programs, Markdown or LaTeX documents, etc.

Unless you already master a code editor, we recommend that you download and install Sublime Text. Follow the instructions specific to your Operating System.

[Note: If you prefer to stick to opensource software, you can try Atom, but be aware that it is slower and more buggy than Sublime Text.]

Anaconda Python3 distribution

There exists various Python distributions. Among them, we recommend the Anaconda3 distribution as it already contains most of the packages needed for cognitive science.

  1. Go to <https://www.anaconda.com/products/individual> and click on Download. Then, select the 64-bit installer for your operating system (Windows, MacOS or Linux).

  2. Execute the Anaconda3 installer. During the installation.
    • If you are on a Mac, you can accept all the default for the proposed options.

    • If you are under Windows, pay close attention to the following options:

      • verify that you Install for Just Me (recommended), then click on Next

      • Accept the default Destination folder and click on Next

      • VERY IMPORTANT: Check the boxes in front Add Anaconda to my PATH (ignore the warning that this is not recommended) and Register Anaconda as my default Python and click on Install

      • upon completion, click on Next, then Finish

The Git version control system

Git is a version control tool for software development, an indispensable tool to do reproducible science. To install it:

Linux

execute the command sudo apt install git

MacOSX

Download and install Xcode, either from the App store, or by using the command line xcode-select --install. This will provide git.

Windows

Download the 64 bit version of Git for Windows and launch it.

  1. When the GNU Licence is displayed, press Next;

  2. Accept the default installation folder and press Next;

  3. Accept all the Components selected by default and press Next

  4. Accept the creation of a start menu folder named ‘Git’: press Next;

  5. VERY IMPORTANT: When proposed a default editor, select ‘Use the nano editor’ (unless you want to learn Vim)

  6. VERY IMPORTANT: When proposed to adjust the PATH environment variable, tick the box “Use Git and optional unix tools from the command line prompt”.

You can accept all other defaults.

Now, to finish the installation of git, open a Terminal window as follows:

Windows

Launch Git bash (use the “Search box”)

MacOS

Type terminal in the Spotlight search field (Or, open a Finder window, select the Application folder, then the Utilities folder, then double-click on the Terminal icon)

Linux

launch Terminal from your applications menu (or use Ctrl-Alt-T).

Then, type the following command lines, making sure to replace your_first_and_last_name_here and your_email_here by the relevant personal information:

git config --global user.name "your_first_and_last_names_here"
git config --global user.email your_email_here
git config --global core.editor nano

You can close the Terminal by typing the command exit or, faster, by pressing Ctrl-D, or by just closing its window.

The Pygame and Expyriment python modules

We will rely on the Pygame module to create stimuli and the Expyriment Python Library to program behavorial experiments.

You first need to install the modules 1:

Linux

Open a Terminal (Ctrl-Alt-T) and type:

sudo apt-get install build-essential libsdl-image1.2-dev libsdl-mixer1.2-dev libsdl-ttf2.0-dev libsdl1.2-dev libsmpeg-dev libportmidi-dev ffmpeg libswscale-dev libavformat-dev libavcodec-dev libfreetype6-dev
pip install expyriment[all]
Windows

Start Git bash. This opens a terminal, where you can type pip install expyriment[all]

MacOS
  1. Install XQuartz. Download the .dmg from the official website and open it to install.

  2. Open a Terminal and type /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)" to install Homebrew (which is needed to install SDL).

    • If you see “Password: “, this means the Terminal is prompting you to type your computer’s administrator account password. Type your password and press the return key to continue.

    • If you see an error message such as “Error: /usr/local/Cellar is not writable. You should change the ownership and permissions of /usr/local/Cellar back to your user account: sudo chown -R $(whoami) /usr/local/Cellar”, run in the Terminal the command that was suggested (here sudo chown -R $(whoami) /usr/local/Cellar), and then run the previous command to try installing Homebrew once again

  3. In the same Terminal, type brew install sdl2 sdl2_image sdl2_mixer sdl2_ttf pkg-config to install SDL (which is needed to install expyriment). This may take a while.

  4. In the same Terminal, type pip install "expyriment[all]" to install expyriment.

  5. In the same Terminal, type pip install -U pygame to upgrade pygame (version >= 2.0 is required on recent versions of macOS, but this must be done after installing expyriment otherwise the install of expyriment will fail).

Whatever your operating systems, you now need to test your installation:

  1. To test pygame, run the following command in a Terminal (see below how to open a terminal):

    python -m pygame.examples.aliens
    

    You should see a window with moving spaceships.

  2. To test expyriment, open a Terminal and type ipython.

    Then, after the prompt In [1]:, type the following lines:

    import expyriment
    expyriment.control.run_test_suite()
    

    You should see a screen with Test suite. There are various tests that you can run. Pressing Esc will stop the program.

    To quit ipython, press Ctrl-D, then y.

    To close the Terminal window, press Ctrl-D.

  3. Watch the video at https://www.youtube.com/watch?v=2yhcWvBt7ZE&t and try to perform the activities in it (the insturctions walso work for Mac or Linux: you just need to open a standard Terminal when in Windows you need to start ‘Gih Bash’). Note: the game scripts in python mentioned in the videao ara available at https://github.com/chrplr/PCBS/tree/master/games/games.zip

Do not worry if you do not manage to perform these activies: there will be a training session later on that.

How To open a Terminal

MacOS

Type terminal in the Spotlight search field. Alternatively, you can open a Finder window and select the Application folder, then the Utilities folder, then double-click on the Terminal icon..

Windows

Start Git Bash (This assumes that you have installed Git for windows as described in Instructions for software installation)

  1. Click the Windows or Start icon.

  2. In the Programs list, open the Git folder.

  3. Click the option for Git Bash.

Linux

Launch Terminal from your application menu or use Ctrl-Alt-T (gnome, xfce), or Win+Return (i3)).

To close a Terminal Window, press Ctrl-D

To go further:

Inside a terminal, you interact with a program that expects you to type commands. This program is called a shell (see http://linuxcommand.sourceforge.net/lc3_learning_the_shell.php).

For the moment, you only need to know three commands in order to navigate in the filesystem:

  • ls: list the content of the current working directory

  • pwd: path of current working directory

  • cd: change directory

Read http://linuxcommand.sourceforge.net/lc3_lts0020.php to learn about them.

Other resources to learn more about how to control your computer from a terminal:

Download course materials

This document is available in pdf format at https://pcbs.readthedocs.io/_/downloads/en/latest/pdf/

Once Git is installed on your computer, you can download all the course materials (python scripts, data files, …) from http://github.com/chrplr/PCBS) with the command:

git clone https://github.com/chrplr/PCBS.git

Everything will be downloaded in a subfolder PCBS inside the current working directory .

Be aware that if a folder with that name already exists, git will stop and not download the content of the website. In that case, delete or move the existing PCBS folder before running the git clone command above.

I do often update the materials. To synchronize your local copy with the latest version at http://github.com/chrplr/PCBS), you just need to open a terminal and type:

cd PCBS
git pull

Important: do not manually modify or create new files in the PCBS folder. If you do so, git will notice it and might prevent an automatic upgrade and ask you to ‘resolve conflicts’. If you get such a message, the simplest course of action, for beginners, is to delete the PCBS folder (or move it if you wnat to keep a copy of your modifications) and reissue the git clone command above to reload the full folder.

Potential issues

  • python: command not found: the folder containing anaconda3’s python is missing (or shadowed) from the PATH environment variable that lists all the folders where commands can be located. It is very likely that you did not follow exactly the above installation instructions for either Anaconda3 or Git Bash (Windows only), that is, you did not check the correct options. If you know how to do it, modify the PATH environment variable, else reinstall.

  • expyriment or pygame : module not found. There are many potential causes for that one. Check that you followed the instructions precisely and contat us on the #general channel of the Slask forum.

  • If you see error messages (in red) when importing the expyriment module, it is likely due to issues with the version of Python. If this is the case (and only if this is the case), you should create an [Anaconda environment](https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html) as follows:

    conda create --name expyriment python=3.8
    conda activate expyriment
    pip install expyriment[all]
    

Then, to run python scripts using the expyriment module, you will need to activate this environment with the command:

      conda activate expyriment

Read more about Python Anaconda environments [here](https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html).

Creating a conda environment

1

(advanced students only). To avoid potential clashes betwen modules, it may be a good idea to create a conda environment before installing the modules:

conda create --name pcbs
conda activate pcbs

But then, you must not forget to activate the environment (conda activate pcbs) before working on the materials presented here.

Installing Psychopy and Psychtoolbox on Linux

If you want to install the psychology experiment generators [Psychtoolbox](http://psychtoolbox.org/) and [Psychopy](https://www.psychopy.org) (which we will not use in this course), you can find instruction for Linux at http://www.pallier.org/installing-a-linux-workstation-with-psychtoolbox-psychopy-expyriment.html (For Windows or MacOSX instructions, check their websites)