Setup for the course

Setup for the course#

There are a few things you need to get working on your machine in order to follow this course. However, don’t worry as it’s all gonna be open source, won’t require a lot of storage and will be explained in detail.

Note

Importantly, some of the content on this page is outdated because it uses more complex environments like Git, etc. In the 2024 version of the course, we will focus more on Python itself rather than IDE environments. So, don’t stress too much about all this information—just focus on the 2024 section.

General things 2024#

There are a few computing requirements for the course that are absolutely necessary (beyond the few software packages you should install, described below):

Laptop You must have administrator access to your computer (i.e., you must be able to install things yourself without requesting IT approval).
Operating Systems: Windows, macOS, or Linux
Python version: Anaconda comes with its own Python installation, so no need to pre-install Python
Disk Space: At least 3 GB of free disk space for the base installation
Internet Access: Required for downloading the installer

Note

If you don’t have a laptop or strugle significantly with instalation process find the section below and contact your instructor

If you foresee any of these being a problem please reach out to one of the instructors and enquire what steps you can take to ensure your setup is ready for the course.

Required software 2024#

To get the most out of the course, we ask that you arrive with the following software already installed:

Discord (for communication purposes)
A modern web-browser
Python 3 via Anaconda
PsychoPy (https://www.psychopy.org/) (we will need much later)

The rest of this page provides more detail on installation procedures for each of the above elements, with separate instructions for each of the three major operating systems (Windows, Mac OS, and Linux).

Discord 2024#

Go to https://discord.com/ and download and install Discord. Please note, that you can also use Discord through your browser if you don’t want to download it. This will be the main channel of communication for the course.

Modern web browser 2024#

Install Firefox or Chrome. (Safari will also work.)

Anaconda Installation with Jupyter Notebook 2024#

Installation Instructions#

Windows Installation

Step 1: Download Anaconda

Go to the Anaconda website.
Download link version 2024.06
Click on the “Download” button and choose the Windows version that matches your system architecture (64-bit recommended).

Step 2: Run the Installer

Locate the downloaded .exe installer and double-click it to run.
Click “Next” and accept the default installation settings.
Choose whether to install Anaconda for “Just Me” or “All Users.” For most cases, “Just Me” is sufficient.
Important: You will be prompted to add Anaconda to your system’s PATH. It is recommended not to check this option. Anaconda will manage the environment for you.

Step 3: Complete the Installation

Once installed, open the “Anaconda Navigator” from the Start Menu or search for it.

Step 4: Launch Jupyter Notebook

In Anaconda Navigator, locate “Jupyter Notebook” and click “Launch.” This will open Jupyter Notebook in your browser.

macOS Installation

Step 1: Download Anaconda

Go to the Anaconda website and download the macOS installer.
Download link for 64-Bit Apple silicon version 2024.06
Download link for 64-Bit Intel chip version 2024.06

Step 2: Install Anaconda

Open the downloaded .pkg file and follow the on-screen instructions.
During the installation, the installer will ask you to install Anaconda for “Just Me” or “All Users.” You can choose based on your needs.

Step 3: Update the Terminal Profile (optional)

If you want to use conda in the terminal, ensure Anaconda is added to your shell’s startup file.
- For bash users, this is typically in .bash_profile.
- For zsh users, it’s in .zshrc.
You can do this by adding the following line to the respective file:
```
export PATH="/Users/your-username/anaconda3/bin:$PATH"
```

Step 4: Launch Jupyter Notebook

Open the terminal and type:
```
jupyter notebook
```
Jupyter Notebook will open in your default browser.

Linux Installation

Step 1: Download Anaconda

Head over to the Anaconda website and download the Linux installer (64-bit .sh file).

Step 2: Install Anaconda

Open the terminal and navigate to the directory where the installer was downloaded.

Run the following command to start the installation:

bash Anaconda3-2024.XX-Linux-x86_64.sh

Replace `2024.XX` with the version number you downloaded.

Follow the prompts to complete the installation. You’ll be asked to approve the license terms and specify the installation path.

Step 3: Update Shell Profile

After installation, you may need to update your shell’s startup file (e.g., .bashrc or .zshrc) to add Anaconda to your PATH.
```
export PATH="~/anaconda3/bin:$PATH"
```

Step 4: Launch Jupyter Notebook

In your terminal, run:
```
jupyter notebook
```
This will open Jupyter Notebook in your browser.

Verifying Your Installation 2024#

To ensure Anaconda and Jupyter Notebook were installed correctly, you can run the following commands in your terminal or Anaconda Prompt:
```
conda --version
```
This should display the installed version of Conda.
```
jupyter notebook
```

This should launch Jupyter Notebook in your web browser.

Conclusion 2024#

Now that you’ve successfully installed Anaconda, you can easily manage your Python environments and use Jupyter Notebook for interactive coding. Anaconda simplifies package management and deployment, making it a great choice for both beginners and experienced users.

I have significant problems with Anaconda installation or with laptop 2024#

If you’re experiencing issues with installing Anaconda or if your laptop is having performance problems, Google Colab is a great alternative that you can use to run Python code without needing to install anything on your computer. Colab is a free, cloud-based environment that lets you write and run Python code directly in your browser.

Don’t worry your learning experience will be not affected by different IDE enviroment.

Here’s a breakdown of what Colab offers and how it compares to working with Anaconda on your local machine:

What is Google Colab?#

Google Colab (Colaboratory) is an online platform that allows you to write and execute Python code in a notebook environment, similar to Jupyter Notebooks. It’s powered by Google’s cloud infrastructure, so you can access it from anywhere, as long as you have a browser and an internet connection.

Key Benefits of Using Google Colab:#

No Installation Required: You don’t need to install Python, Anaconda, or any libraries locally. Colab comes preloaded with many common Python libraries (like NumPy, pandas, Matplotlib, and even TensorFlow).
Works on Any Device: Whether you’re using a low-spec laptop, a tablet, or a desktop, Colab runs everything in the cloud. This means it’s perfect if your laptop is slow or you can’t install Anaconda due to compatibility issues or lack of storage space.
Free GPU Access: Colab gives you access to free GPU and TPU resources, which can speed up computations if you’re working with machine learning or deep learning models. This is a feature you wouldn’t have with a typical Anaconda setup unless you have a high-performance machine.
Real-Time Collaboration: Just like Google Docs, you can share Colab notebooks with others and collaborate in real-time, making it easier to work with classmates or colleagues on code-based projects.

Anaconda vs Google Colab:#

Feature	Anaconda (Local Setup)	Google Colab (Cloud)
Installation	Requires downloading and installing Anaconda, setting up environments, installing packages	No installation needed, runs in your browser
Libraries	Full control over which libraries and packages you install	Pre-installed libraries (can install additional ones if needed)
Device Requirements	Requires sufficient storage and processing power on your laptop	No device requirements, works on any browser-enabled device
Computation Power	Limited by your machine’s specs (RAM, CPU, GPU)	Uses cloud-based GPUs and TPUs, making it faster for large computations
Offline Use	Can be used offline	Requires an internet connection
Storage	Limited by your local storage space	Saves notebooks to Google Drive with virtually unlimited cloud storage
Collaboration	Can share files manually	Real-time collaboration with easy sharing (like Google Docs)

When Should You Use Google Colab?#

If you’re having trouble with Anaconda installation: Whether it’s due to version conflicts, missing dependencies, or operating system compatibility issues, Colab removes the need to install anything on your local machine.
If your laptop is underpowered: Colab allows you to run even computationally heavy code (such as deep learning models) on Google’s high-performance cloud infrastructure, which may be impossible on a low-spec laptop.
If you’re short on storage space: Running code locally requires ample storage for libraries, data, and environments. Colab eliminates this need by storing everything in the cloud.
For collaboration: If you’re working on a group project, Colab’s real-time sharing features make it a breeze to collaborate.

Required software (Legacy, pre 2024)#

To get the most out of the course, we ask that you arrive with the following software already installed (software/things in () are not entirely necessary but definitely great to have):

A command-line shell: Bash
(A version control system: Git)
A remote-capable text editor: VSCode
Python 3 via Miniconda
(A GitHub account)
Discord (for communication purposes)
A modern web-browser

If you already have all of the above software tools/packages installed (what are you even doing here?), or are confident you’ll be able to install them by the time the course starts, you can jump straight to checking your install. The rest of this page provides more detail on installation procedures for each of the above elements, with separate instructions for each of the three major operating systems (Windows, Mac OS, and Linux).

Some quick general notes on instructions#

There is no difference between Enter and Return in these instructions, so just press whatever the equivalent on your keyboard is whenever one is stated
If you already have some of these things installed on your computer already that should (theoretically) be okay. However, you need to make sure that you are able to complete the steps described in checking your install without issue.
- For example, having multiple different Python installations on your computer can lead to incredibly frustrating issues that are very difficult to debug. As such, if you have already installed Python via some other application (not Miniconda/Anaconda), it’s strongly encouraged to uninstall it before following the instructions below. You must have Python installed via Miniconda for this course.

OS-specific installation instructions#

Select the tab that corresponds to your operating system and follow the instructions therein.

Windows

Windows Subsystem for Linux (WSL)

Search for Windows Powershell in your applications; right click and select Run as administrator. Select Yes on the prompt that appears asking if you want to allow the app to make changes to your device.

Type the following into the Powershell and then press Enter:

 Enable-WindowsOptionalFeature -Online -FeatureName Microsoft-Windows-Subsystem-Linux

Press Enter again when prompted to reboot your computer.
Once your computer has rebooted, open the Microsoft Store and search for “Ubuntu.” Install the program labelled “Ubuntu 18.04” (not “Ubuntu 16.04” or “Ubuntu”) by clicking the tile, pressing Get, and then Install.
Search for and open Ubuntu from your applications. There will be a slight delay (of a few minutes) while it finishes installing.
You will be prompted to Enter new UNIX username. You can use any combination of alphanumeric characters here for your username, but a good choice is <first_initial><last_name> (e.g., jsmith for John Smith). You will then be prompted to enter a new password. (Choose something easy to remember as you will find yourself using it frequently.)
Right click on the top bar of the Ubuntu application and select “Properties”. Under the “Options” tab, under the “Edit Options” heading, make sure the box reading “Use Ctrl+Shift+C/V as Copy/Paste” is checked. Under the “Terminal” tab, under the “Cursor Shape” heading, make sure the box reading “Vertical Bar” is checked. Press “Okay” to save these settings and then exit the application.

(The above step-by-step WSL instructions are distilled from here and here. If you have questions during the installation procedure those resources may have answers!)

From this point on whenever the instructions specify to “open a terminal” please assume you are supposed to open the Ubuntu application.

Bash shell

You already have it, now that you’ve installed the WSL!

Git

You already have it, now that you’ve installed the WSL!

VSCode

Go to https://code.visualstudio.com/ and click the download button, then run the .exe file.
Leave all the defaults during the installation with the following exception:
- Please make sure the box labelled “Register Code as an editor for supported file types” is selected

VSCode extensions

Open the Ubuntu application.
Type code . into the terminal and press Enter. You should see a message reading “Installing VS Code Server” and then a new windows will open up.
Press Ctrl+Shift+P in the new window that opens and type “Extensions: Install extensions” into the search bar that appears at the top of the screen. Select the appropriate entry from the dropdown menu that appears (there should be four entries; simply select the one that reads “Extensions: Install extensions”).
A new panel should appear on the left-hand side of the screen with a search bar. Search for each of the following extensions and press Install for the first entry that appears. (The author listed for all of these extensions should be “Microsoft”.)
- Python (n.b., you will need to reload VSCode after installing this)
- Live Share (n.b., you may need to press “Ctrl/Cmd+Shift+P” and type “install extensions” again after installing this)
- Live Share Extension Pack
- Docker
- Remote - WSL

Python

Open a new terminal and type the following lines (separately) into the terminal, pressing Enter after each one:

 wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
 bash Miniconda3-latest-Linux-x86_64.sh

A license agreement will be displayed and the bottom of the terminal will read --More--. Press Enter or the space bar until you are prompted with “Do you accept the license terms? [yes|no].” Type yes and then press Enter
The installation script will inform you that it is going to install into a default directory (e.g., /home/$USER/miniconda3). Leave this default and press Enter.
When you are asked “Do you wish the installer to initialize Miniconda3 by running conda init? [yes|no],” type yes and press Enter. Exit the terminal once the installation has finished.
Re-open the Ubuntu application. Type which python into the terminal and it should return a path (e.g., /home/$USER/miniconda3/bin/python).
- If you do not see a path like this then please try typing conda init, closing your terminal, and repeating this step. If your issue is still not resolved skip the following step and contact an instructor on the #help-installation channel on the BHS Slack.
Type the following to remove the installation script that was downloaded:
```
 rm ./Miniconda3-latest-Linux-x86_64.sh
```

Python packages

Open a terminal and type the following commands:

    conda config --append channels conda-forge
    conda config --set channel_priority strict
    conda install -y flake8 ipython jupyter jupyterlab matplotlib numpy pandas scipy seaborn pingouin statsmodels plotly

Linux

Bash shell

You already have it! Depending on which version of Linux you’re running you may need to type bash inside the terminal to access it. To check whether this is necessary, follow these steps:

Open a terminal and type echo $SHELL. If it reads /bin/bash then you are all set! If not, whenever the instructions read “open a terminal,” please assume you are to open a terminal, type bash, and the proceed with the instructions as specified.

Git

You may already have it; try typing sudo apt-get install git (Ubuntu, Debian) or sudo yum install git (Fedora) inside the terminal. If you are prompted to install it follow the instructions on-screen to do so.

VSCode

Go to https://code.visualstudio.com/ and click the download button for either the .deb (Ubuntu, Debian) or the .rpm (Fedora, CentOS) file.
Double-click the downloaded file to install VSCode. (You may be prompted to type your administrator password during the install).

VSCode extensions

Open the Visual Studio Code application.
Press Ctrl+Shift+P in the new window that opens and type “Extensions: Install extensions” into the search bar that appears at the top of the screen. Select the appropriate entry from the dropdown menu that appears (there should be four entries; simply select the one that reads “Extensions: Install extensions”).
A new panel should appear on the left-hand side of the screen with a search bar. Search for each of the following extensions and press Install for the first entry that appears. (The author listed for all of these extensions should be “Microsoft”.)
- Python (n.b., you will need to reload VSCode after installing this)
- Live Share (n.b., you may need to press “Ctrl/Cmd+Shift+P” and type “install extensions” again after installing this)
- Live Share Extension Pack
- Docker

Python

Open a new terminal and type the following lines (separately) into the terminal, pressing Enter after each one:

 wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
 bash Miniconda3-latest-Linux-x86_64.sh

A license agreement will be displayed and the bottom of the terminal will read --More--. Press Enter or the space bar until you are prompted with “Do you accept the license terms? [yes|no].” Type yes and then press Enter
The installation script will inform you that it is going to install into a default directory (e.g., /home/$USER/miniconda3). Leave this default and press Enter.
When you are asked “Do you wish the installer to initialize Miniconda3 by running conda init? [yes|no],” type yes and press Enter. Exit the terminal once the installation has finished.
Re-open a new terminal. Type which python into the terminal and it should return a path (e.g., /home/$USER/miniconda3/bin/python).
- If you do not see a path like this then please try typing conda init, closing your terminal, and repeating this step. If your issue is still not resolved skip the following step and contact an instructor on the #help-installation channel of the BHS Slack.
Type the following to remove the installation script that was downloaded:
```
 rm ./Miniconda3-latest-Linux-x86_64.sh
```

Python packages

Open a terminal and type the following commands:

    conda config --append channels conda-forge
    conda config --set channel_priority strict
    conda install -y flake8 ipython jupyter jupyterlab matplotlib numpy pandas scipy seaborn pingouin statsmodels plotly

MacOs

Bash shell

You already have it! Depending on which version of Mac OS you’re running you may need to type bash inside the terminal to access it. To check whether this is necessary, follow these steps:

Open a terminal and type echo $SHELL. If it reads /bin/bash then you are all set!

Note: If you are using Mac Catalina (10.15.X) then it is possible your default shell is NOT CORRECT. To set the default to bash, type chsh -s /bin/bash in the terminal, enter your password when prompted, and then close + re-open the terminal.

Git

You may already have it! Try opening a terminal and typing git --version. If you do not see something like “git version X.XX.X” printed out, then follow these steps:

Follow this link to automatically download an installer.
Double click the downloaded file (git-2.23.0-intel-universal-mavericks.dmg) and then double click the git-2.23.0-intel-universal-mavericks.pkg icon inside the dmg that is opened.
Follow the on-screen instructions to install the package.

VSCode

Go to https://code.visualstudio.com/ and click the download button.
Unzip the downloaded file (e.g., VSCode-darwin-stable.zip) and moving the resulting Visual Studio Code file to your Applications directory.

VSCode extensions

Open the Visual Studio Code application
Type Cmd+Shift+P and then enter “Shell command: Install ‘code’ command in PATH” into the search bar that appears at the top of the screen. Select the highlighted entry. A notification box should appear in the bottom-right corner indicating that the command was installed successfully.
Type Cmd+Shift+P again and then enter “Extensions: Install extensions” into the search bar. Select the appropriate entry from the dropdown menu that appears (there should be four entries; simply select the one that reads “Extensions: Install extensions”).
A new panel should appear on the left-hand side of the screen with a search bar. Search for each of the following extensions and press Install for the first entry that appears. (The author listed for all of these extensions should be “Microsoft”.)
- Python (n.b., you will need to reload VSCode after installing this)
- Live Share (n.b., you may need to press “Ctrl/Cmd+Shift+P” and type “install extensions” again after installing this)
- Live Share Extension Pack
- Docker

Python

Open a new terminal and type the following lines (separately) into the terminal, pressing Enter after each one:

 curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh
 bash Miniconda3-latest-MacOSX-x86_64.sh

A license agreement will be displayed and the bottom of the terminal will read --More--. Press Enter or the space bar until you are prompted with “Do you accept the license terms? [yes|no].” Type yes and then press Enter
The installation script will inform you that it is going to install into a default directory (e.g., /home/$USER/miniconda3). Leave this default and press Enter.
When you are asked “Do you wish the installer to initialize Miniconda3 by running conda init? [yes|no],” type yes and press Enter. Exit the terminal once the installation has finished.
Re-open a terminal. Type which python into the terminal and it should return a path (e.g., /home/$USER/miniconda3/bin/python).
- If you do not see a path like this then please try typing conda init, closing your terminal, and repeating this step. If your issue is still not resolved skip the following step and contact an instructor on the #help-installation channel of the BHS Slack.
Type the following to remove the installation script that was downloaded:
```
 rm ./Miniconda3-latest-MacOSX-x86_64.sh
```

Python packages

Open a terminal and type the following commands:

    conda config --append channels conda-forge
    conda config --set channel_priority strict
    conda install -y flake8 ipython jupyter jupyterlab matplotlib numpy pandas scipy seaborn pingouin statsmodels plotly

Note: If the instructions aren’t working and you have spent more than 15-20 minutes troubleshooting on your own, reach out on the #help-installation channel on the Discord channel with the exact problems you’re having. One of the instructors will try and get back to you quickly to help resolve the situation. If they’re unable to help via Discord, you may be directed to attend one of the installation office hours.

GitHub account#

Go to join/ and follow the on-screen instructions to create an account. It is a good idea to associate this with your university e-mail (if you have one) as this will entitle you to sign up for the GitHub Student Developer Pack which comes with some nice free bonuses.

Checking your install#

Now that you’ve installed everything it’s time to check that everything works as expected! Type the following into your terminal:

bash <( curl -s https://raw.githubusercontent.com/aylinsgl/Python_For_Psychologists_23-24/master/check_install.sh)

If you installed everything correctly you should see a message informing you as such. If any problems were detected you should receive some brief instructions on what is wrong with potential suggestions on how to remedy it. If you followed these instructions step-by-step and cannot resolve the issue please contact one of the course instructors for more help.

Yeah, you did! Great job!

Getting the course content#

Now that you have installed the required software (or not) to follow the course, it’s time to gather the respective materials.

conda logo
_{^{_{^{https://upload.wikimedia.org/wikipedia/commons/e/ea/Conda_logo.svg}}}}

By installing Python on your system (i.e. specifically Conda) and setting up the appropriate environment, you will be able to open all the Jupyter Notebooks and go through the whole content of the course locally.

To get things up and running, please follow these steps:

Download the environment.yml file (e.g. with right mouse click -> Save As). Make sure that the file ends with .yml and not .txt.
Open up a conda terminal (or any other terminal), and create a new conda environment with the following command: conda env create -f /path/to/file/environment.yml - For example ``conda env create -f ~/Downloads/environment.yml`
Download the notebooks in this repository via this link and unzip them to your preferred location, e.g. Desktop/Python_for_Psychologists_Winter2022.
Next, open up a conda terminal (or any other terminal), activate the conda environment with conda activate pfp_2022 (or on older conda environment with source activate pfp_2022 for mac and linux and activate pfp_2022 for windows).
Finally, via the terminal, move to the folder where you’ve put all the unzipped content of this workshop, e.g. with the command cd ~/Desktop/Python_for_Psychologists_Winter2022 and run the command jupyter notebook. If the notebook server isn’t automatically opened in a new browser window, please copy-paste either the http://127.0.0.1:8888/... or the http://localhost:8888/... path into a new browser window and press Enter. You should now see the jupyter notebook server (looking like a file browser and displaying the content of the directory).

Setup for the course

Contents

Setup for the course#

General things 2024#

Required software 2024#

Discord 2024#

Modern web browser 2024#

Anaconda Installation with Jupyter Notebook 2024#

Installation Instructions#

Step 1: Download Anaconda

Step 2: Run the Installer

Step 3: Complete the Installation

Step 4: Launch Jupyter Notebook

Step 1: Download Anaconda

Step 2: Install Anaconda

Step 3: Update the Terminal Profile (optional)

Step 4: Launch Jupyter Notebook

Step 1: Download Anaconda

Step 2: Install Anaconda

Step 3: Update Shell Profile

Step 4: Launch Jupyter Notebook

Verifying Your Installation 2024#

Conclusion 2024#

I have significant problems with Anaconda installation or with laptop 2024#

What is Google Colab?#

Key Benefits of Using Google Colab:#

Anaconda vs Google Colab:#

When Should You Use Google Colab?#

Required software (Legacy, pre 2024)#

Some quick general notes on instructions#

OS-specific installation instructions#

GitHub account#

Checking your install#

Getting the course content#