Contents

MDS software stack install instructions for Windows¶

Important

This guide has been (lightly) adapted from the UBC-Vancouver MDS Install stack under a CC-BY-SA 4.0 license.

These instructions will walk you through installing the required Data Science software stack for the UBC Master of Data Science program. Before starting, ensure that your laptop meets our program requirements:

Attention

Those computer requirements are not necessary for COSC/DATA 301 students. However, at a minimum you will need a good Internet connection to complete your assignments on the cloud.

  • runs one of the following operating systems: macOS 10.15.X (Catalina), Ubuntu 20.04, Windows 10 Professional, Enterprise or Education; version 2004.

    • Windows 10 Home is not sufficient as not all the software required for the program can be installed on that OS. Click here to download Windows 10 Education for free from UBC.

    • When installing Ubuntu, checking the box “Install third party
” will (among other things) install proprietary drivers, which can be helpful for wifi and graphics cards.

  • can connect to networks via a wireless connection

  • has at least 50 GB disk space available

  • has at least 8 GB of RAM

  • uses a 64-bit CPU

  • is at most 6 years old at the start of the program (4 years old or newer is recommended)

  • uses English as the default language

Students’ whose laptops do not meet the requirements specified above will not be able to receive technical assistance from the MDS team in troubleshooting installation issues.

Installation notes¶

If you have already installed Git, Latex, Make, or any of the R or Python related packages please uninstall these and follow the instructions below to reinstall them (make sure to also remove any user configuration files and backup them if desired). In order to be able to support you effectively and minimize setup issues and software conflicts, we require all students to install the software stack the same way.

In all the sections below, if you are presented with the choice to download either a 64-bit (also called x64) or a 32-bit (also called x86) version of the application always choose the 64-bit version.

Once you have completed these installation instructions, make sure to follow the post-installation notes at the end to check that all software is setup correctly.

UBC Student Email¶

Please sign up for a UBC Student Email. This account will also grant you access to a range of UBC services, including Microsoft Teams and OneDrive. To do so navigate to https://it.ubc.ca/services/email-voice-internet/ubc-student-email-service and follow the instructions under “Get Started”.

Web browser¶

In MDS we will be using many tools that work most reliably on Google Chrome and Firefox (including our online quiz software), so we recommend that you use one of these browsers.

Install Microsoft Office¶

UBC students have free access to a Microsoft Office 365 annual subscription, which is renewed for students enrolled in at least one course. Office 365 includes Word, Excel, PowerPoint, Outlook, and OneNote, and is available on a variety of platforms, including Windows, Mac, and Linux/Android.

To get your free Office 365 license and download the installer files, visit [UBC IT] (https://it.ubc.ca/services/desktop-print-services/software-licensing/office-365-students) and click Download Office 365. Note that you will need your CWL login credentials in order to download the software and activate your license.

Visual Studio Code¶

The open-source text editor Visual Studio Code (VS Code) is both a powerful text editor and a full-blown Python IDE, which we will use for more complex analysis. Go to https://code.visualstudio.com/download and download the windows version of VS Code. After the download has finished, run the installer and accept the default configuration for all pages except for the following:

  • Optional On the Select Additional Tasks page, check “Create a desktop icon” under “Additional icons”.

  • Also on the Select Additional Tasks page check all four boxes under “Other”

    • “Add ‘Open with Code’ action to Windows file context menu”

    • “Add ‘Open with Code’ action to Windows directory context menu”

    • “Register Code as an editor for supported file types”

    • “Add to PATH” (this should be selected by default).

VS Code extensions¶

The real magic of VS Code is in the extensions that let you add languages, debuggers, and tools to your installation to support your specific workflow. From within VS Code you can open up the Extension Marketplace to browse and install extensions by clicking on the Extensions icon in the Activity Bar indicated in the figure below.

To install an extension, you simply search for it in the search bar, click the extension you want, and then click “Install”. There are extensions available to make almost any workflow or task you are interested in more efficient! Here we are interested in setting up VS Code as a Python IDE. To do this, search for and install the following extensions:

  • Python (everything Python: notebooks, debugging, linting, formatting, etc.)

  • markdownlint (markdown linting and style checking extension)

  • GitLens (powerful extension that extends VS Code’s native git capabilities)

  • (Optional) Bracket Pair Colorizer 2 (add colour to help distinguish your brackets: (), [], {})

This video tutorial is an excellent introduction to using VS Code in Python.

GitHub.com¶

In MDS we will use the publicly available GitHub.com. Please follow the set-up instructions for both below.

Sign up for a free account at GitHub.com if you don’t have one already.

Configure Git on your computer¶

Although Git and Bash are two separate programs, we are including them in the same section here since they are packaged together in the same installer on Windows. Briefly, we will be using the Bash shell to interact with our computers via a command line interface, and Git to keep a version history of our files and upload to/download from to GitHub. We will be using the command line version of Git as well as Git through RStudio and JupyterLab. Some of the Git commands we will use are only available since Git 2.23, so if you’re Git is older than this version, we ask you to update it.

Go to https://git-scm.com/download/win and download the windows version of git. After the download has finished, run the installer and accept the default configuration for all pages except for the following:

  • Optional On the Select Components page, check “On the Desktop” under “Additional icons”.

  • On the Choosing the default editor used by Git page, select “Use Visual Studio Code as Git’s default editor” from the drop-down menu’

Note if you wish to pin Git Bash to the taskbar, you need to search for the program in the start menu, right click the entry and select “Pin to taskbar”. If you instead first launch the program and pin it by right clicking on the taskbar icon, Git Bash will open with the wrong home directory (/ instead of /c/users/$USERNAME.

After installation, test if you were successful by opening the Git Bash program. Below is a picture of the Git Bash icon on the Desktop and an opened instance of the Git Bash terminal (we will often refer to this as just “the terminal”):

In the terminal, type the following to check which version of Bash you just installed:

bash --version

The output should look similar to this:

GNU bash, version 4.4.23(1)-release (x86_64-pc-sys)
Copyright (C) 2019 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>

This is free software; you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.

If you tried to paste the above into the Git Bash terminal, you will have noticed that Ctrl+V does not work in Git Bash. Instead you need to right click and select “Paste” or use the Shift+Insert shortcut. To copy from the Git Bash terminal you simply select the text you want and it is copied automatically.

Via right click you can also reach the settings menu where you can configure Git Bash to your preferences, a couple of tips would be to check “Mouse -> Clicks place command line cursor” and change the font to something more legible, e.g. Consolas (“Text -> Select”).

Let’s also check which version of git was installed:

git --version

git version 2.28.0.windows.1

You can launch many windows programs from the Bash terminal, e.g. to launch VS Code that we installed previously, you would type in code, let’s use this to check the version of vscode that we installed:

code --version

1.47.3
91899dcef7b8110878ea59626991a18c8a6a1b3e
x64

Configuring Git user info¶

Next, we need to configure Git by telling it your name and email. To do this type the following into the terminal (replacing Jane Doe and janedoe@example.com, with your name and email (the same used to sign up for GitHub), respectively):

git config --global user.name "Jane Doe"
git config --global user.email janedoe@example.com

Note: to ensure that you haven’t made a typo in any of the above, you can view your global Git configurations by either opening the configuration file in a text editor (e.g. via the command code ~/.gitconfig) or by typing git config --list --global.

Setting VS Code as the default editor¶

To make programs run from the terminal (such as git) use VS Code by default, we will modify ~/.bash_profile. First, open it using VS Code:

code ~/.bash_profile

Note: If you see any existing lines in your ~/.bash_profile related to a previous Python or R installation, please remove these.

Append the following lines:

# Set the default editor for programs launch from terminal
EDITOR="code --wait"
VISUAL=$EDITOR  # Use the same value as for "EDITOR" in the line above

Then save the file and exit VS Code.

Most terminal programs will read the EDITOR environmental variable when determining which editor to use, but some read VISUAL, so we’re setting both to the same value.

Python, Conda, and JupyterLab¶

Python and Conda¶

We will be using Python for a large part of the program, and conda as our Python package manager. To install Python and the conda package manager, we will use the Miniconda platform (read more here), for which the Python 3.8 64-bit version can be downloaded here. After the download has finished, run the installer and accept the default configuration for all pages.

Do not add miniconda to PATH. We will set this up later.

After installation, open the Start Menu and search for the program called “Anaconda Prompt (miniconda3)”. When this opens you will see a prompt similar to (base) C:\Users\your_name. Type the following to check that your Python installation is working:

python --version

which should return something like this:

Python 3.8.3

If instead you see Python 2.7.X you installed the wrong version. Follow these instructions to delete this installation and try the installation again, selecting Python 3.8.

Integrating Python with the Git Bash terminal¶

To avoid having to open the separate Anaconda Prompt every time we want to use Python, we can make it available from the (Git Bash) terminal, which is what we will be using most of the time. To set this up, open the “Anaconda Prompt (miniconda3)” again and type:

conda init bash

You will see that this modified a few configuration files, which makes conda visible to the terminal. Close all open terminal windows and launch a new one, you should now see that the prompt string has changed to include the word (base) as in the screenshot below:

If you type

python --version

you should now see the same output as above:

Python 3.8.3

Note that if you want to run Python interactively from the Git Bash terminal, you need to prepend the winpty command, so the full command would be winpty python (if you run this, note that you can exit the Python prompt by typing exit()). Running just python works on other setups, but will freeze the Git Bash terminal.

Let’s also check the version of the conda package manager. If you type

conda --version

you should see something like this

conda 4.8.3

Optional One annoyance with our current terminal setup is that the word (base) is not on the same row as the rest of the prompt string (the part with your_name@your_computer. To fix this we can edit the .bash_profile configuration file to indicate that we do not want a newline at the beginning of the prompt string. Open up the configuration file using VS Code by typing the following command into a terminal:

code "/c/Program Files/Git/etc/profile.d/git-prompt.sh"

Delete the line that reads the following (it should be line 13):

PS1="$PS1"'\n'       # new line

Click to save the file, when VS Code prompts you that the saving failed, click “Retry as Admin” and then “Yes”. That’s it! Now if you launch a new terminal instance, you will see (base) on the same line as the rest of the prompt string as in the screenshot below.

Essential Python packages¶

conda installs Python packages from different online repositories which are called “channels”. A package needs to go through thorough testing before it is included in the default channel, which is good for stability, but also means that new versions will be delayed and fewer packages are available overall. There is a community-driven effort called the conda-forge (read more here), which provides more up to date packages To enable us to access the most up to date version of the Python packages we are going to use, we will add the more up to date channel, To add the conda-forge channel by typing the following in the terminal:

conda config --add channels conda-forge

To install packages individually, we can now use the following command: conda install <package-name>. Let’s install the key packages needed for the start of the MDS program:

conda install \
 "jupyterlab=2.*" \
 "numpy=1.*" \
 "pandas=1.*" \
 "flake8=3.*" \
 "black=19.*"
 "nbconvert=6.*"

conda will show you the packages that will be downloaded, and you can press enter to proceed with the installation. If you want to answer yes by default and skip this confirmation step, you can replace conda install with conda install -y.

Test Jupyter Lab setup¶

To test that your JupyterLab installation is functional, you can type jupyter lab into a terminal, which should open a new tab in your default browser with the JupyterLab interface. To exit out of JupyterLab you can click File -> Shutdown, or go to the terminal from which you launched JupyterLab and hold Ctrl while pressing c twice.

You’re all done!!

MDS software stack install instructions for macOS Jupyter Lab in the cloud