macOS

MDS software stack install instructions for macOS 2026/27

Table of Contents

Important Nearly every Mac sold since 2020 uses an Apple Silicon (M series) chip, and these instructions assume that is what you have. Wherever a download page offers you a choice, pick the version marked Apple Silicon, Mac M1-M4, arm64, or aarch64. If you have an older Intel Mac, choose the version marked Intel or x86_64 instead. You can check which chip your Mac has under the Apple menu > “About This Mac”.

Installation notes

If you have already installed Git, Latex, 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.

For Python in particular there is a script that reports everything already installed on your machine, so you do not have to hunt for it yourself. You will run it as part of the Python and uv section below.

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.

  • To install Chrome, go to https://www.google.com/chrome/, click on “Download Chrome” and follow the instructions on the website to finish the installation.
  • To install Firefox, go to https://www.firefox.com/, click on “Download Firefox” and follow the instructions on the website to finish the installation.

Password manager

A password manager is an efficient and convenient measure to protect your online accounts from most common threats. While you don’t strictly need to use one for any of the courses in MDS, we highly recommend that you set one up for your own benefit. Examples of reliable password managers include the ones built into Chrome and Firefox, as well as Bitwarden, and KeePassXC (if you prefer to sync your passwords manually).

Slack

For our MDS courses and program announcements, correspondence and course forums we use the communication tool Slack. Slack can be accessed via the web browser, however we strongly recommend installing the Slack App. The Slack app can be installed from the Mac App Store, or from the Slack website. Installation instructions from the Slack website install method are here: https://slack.com/downloads/mac

UBC cloud computing resources

If you at any point during the MDS program are having an issue with your computer, such as not being able to install all the software before the start of the program, it is useful to know UBC offers a free online computing environment that you can use as a backup to follow along in most of the MDS courses. This is called Jupyter Open and you can access it by logging into https://open.jupyter.ubc.ca/ with your UBC CWL. Jupyter Open allow you to work with JupyterLab, R, Python, and Bash, and you can install packages there as well (these are all explained further down in the installation instructions and during the program).

Bash shell

macOS uses Zsh as the default shell in the Terminal, however, we aim to teach with the same shell across all three operating systems we support, which is the Bash shell. Thus, we ask that you change the default shell in your Terminal to Bash by opening the Terminal (how to video) and typing:

chsh -s /bin/bash

You will have to quit all instances of open Terminals and then restart the Terminal for this to take effect.

Xcode command line tools

We will need Xcode command line tools (not full Xcode) to build some of our programs and bring us developer utilities we need.

Open Terminal and type the following command to install Xcode command line tools:

xcode-select --install

After installation, in terminal type the following to ask for the version:

xcode-select -v

Which should return something like xcode-select version 2409.

Positron

Positron is the code editor we will be using throughout the MDS program. It is built specifically for data science and has support for both Python and R built in, including a console, a variables pane, and an editor for Jupyter notebooks.

Installing

Download the macOS version of Positron from https://positron.posit.co/download.html, picking the Apple Silicon build (choose the Intel build only if you have an older Intel Mac). Open the downloaded .dmg file and drag the Positron application into your “Applications” folder.

Note: If macOS tells you that “Positron is damaged and can’t be opened”, the file is fine — this is a known macOS quarantine glitch. Run the following command in the terminal and then open Positron again:

xattr -c /Applications/Positron.app

Launching Positron from the terminal

Throughout these instructions we will open configuration files by typing positron in the terminal, so we need to make that command available first.

Open Positron, then open the Command Palette with Cmd + Shift + P, type Install 'positron' command in PATH, and press enter to run it.

Now restart the terminal and check that it worked:

positron --version

You should see something like this if you were successful (the exact versions and hash will differ):

Positron: 2026.08.0 build 331
Positron SHA: a3a370d4187484ce962794408c76dab702978eaf
Code OSS: 1.124.0
Arch: arm64

Note: If you get an error message such as -bash: positron: command not found, but you can see that the Positron application has been installed, then the command was not added to your path. Quit all open Terminal windows, open a new one, and try again. If it still does not work, see the Positron documentation on adding it to your path.

Note: You do not need to install any extensions for Python, R, or Quarto. Positron already includes support for all three.

Note: The first time you open Positron it may tell you that no interpreters were found. That is expected at this stage — we install Python and R further down these instructions. Once they are installed, Positron finds R automatically, and it finds Python by looking for a .venv folder inside whichever project folder you open.

GitHub

In MDS we will use the publicly available GitHub.com as well as an Enterprise version of GitHub hosted here at UBC, GitHub.ubc.ca. Please follow the set-up instructions for both below.

Important: These are two completely separate GitHub instances. They have separate accounts, separate usernames, and separate repositories, and signing in to one does not sign you in to the other.

  • GitHub.ubc.ca is UBC’s own installation. Your account there is created for you and you sign in with your UBC CWL, so there is no username for you to choose.
  • GitHub.com is the public one. It is your professional profile, and it stays with you after the program ends.

GitHub.com

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

If you do already have a GitHub.com account, use that same account for MDS. We recommend not creating a new one just for the program, since this is the account that builds up your public work over time.

GitHub.ubc.ca

To add you to the MDS organization on Github.ubc.ca we need you to follow the instructions below:

Note: this typically does not work until orientation starts. If you get to orientation and this still does not work, please let us know. It is safe to skip just this until then but please complete all other steps

  1. navigate to https://activate.github.ubc.ca and login with your CWL to setup their access
  2. wait 20 minutes
  3. login to Github.ubc.ca using your CWL credentials

This step is required for

  • being able to store your work
  • all homework submission and grading
  • working collaboratively

Git

We will be using the command line version of Git as well as Git through RStudio and JupyterLab.

If you installed Xcode command line tools above you already should have a recent enough Git

In terminal type the following to ask for the version:

git --version

you should see something like this (does not have to be the exact same version) if you were successful:

git version 2.50.1 (Apple Git-155)

Note: If you run into trouble, please see that Install Git > macOS section from Happy Git and GitHub for the useR for additional help or strategies for Git installation.

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 positron ~/.gitconfig) or by typing git config --list --global.

Setting Positron as the default editor

To make programs run from the terminal (such as git) use Positron by default, we will modify ~/.bash_profile. First, open it using Positron (this will also create the file if it doesn’t already exist):

positron ~/.bash_profile

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

Now append the following lines to ~/.bash_profile:

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

Then save the file and close the Positron window.

Note: 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.

In some cases, Positron is not set as the default text editor for git even after appending the two lines above, so to make sure it is registered properly, also run the following from your terminal:

git config --global core.editor "positron --wait"

On macOS, programs launched from the terminal sometimes read a different configuration file than the one we just edited. To avoid this, open your ~/.bashrc file:

positron ~/.bashrc

And append the following lines:

# Do NOT add anything to this file, use `~/.bash_profile` instead.
# The next line automatically loads your `~/.bash_profile`
# any time a program tries to read your `~/.bashrc` file.
if [ -f ~/.bash_profile ]; then . ~/.bash_profile; fi

The comment is a reminder to your future self who might open up this file a few months from now =)

Quarto CLI

Quarto is an open-source scientific and technical publishing system. In MDS it is how you will turn notebooks and reports into PDF and HTML documents, and you can use it from Positron, JupyterLab, RStudio, or the terminal.

Download the latest version of Quarto CLI for macOS and follow the installer instructions.

Note: RStudio, which we install further down these instructions, comes with its own bundled copy of Quarto. That copy is not necessarily the most recent release, which is why we install the Quarto CLI separately here.

After the installation finishes, quit all open Terminal windows, then open a new one and run:

quarto --version

You should see something like this if you were successful (the exact version will differ):

1.10.3

Pandoc

Pandoc is the program that converts documents from one format into another. JupyterLab and R Markdown both call it when they export to PDF, so it has to be installed and on your PATH.

Note: Quarto ships with its own private copy of pandoc and does not need this one. This install is for the other two export routes.

Go to the pandoc installation page and download the macOS .pkg installer.

Important: Every Mac with an M-series chip (M1 through M4) is ARM64, so choose the file whose name contains arm64, for example pandoc-3.10.2-arm64-macOS.pkg. Only choose the x86_64 file if you have an older Intel Mac.

Open the downloaded file and follow the installer. It places pandoc in /usr/local/bin, which is already on your PATH, so there is nothing to add to your bash configuration file.

Open a new terminal and check that it worked:

pandoc --version

You should see something like this, with a version of 3.10 or newer:

pandoc 3.10.2
Features: +server +lua

Note: RStudio and Positron each bundle a copy of pandoc as well, so you may end up with more than one on your computer. That is expected and harmless. The one you just installed is the one your terminal will use.

Python and uv

Note: Earlier versions of these instructions used Miniforge and conda. If you find MDS material anywhere that tells you to run conda install, it is out of date — ignore it.

Checking for Python installations you already have

Many people arrive with Python already installed a few different ways, from a previous course or from teaching themselves. Those copies can get in each other’s way, so before installing anything new it is worth seeing what is already there.

Run the following in a terminal:

bash <(curl -Ssf https://ubc-mds.github.io/mds-setup-check/check-python-installs.sh)

This only looks and reports — it does not change or remove anything. It prints what it finds in up to three groups: things it recommends removing (conda installations — MDS has moved off conda entirely), things likely to cause confusion later that you can safely leave alone, and things worth fixing regardless. If nothing needs your attention, it says so and prints nothing else. Where it suggests a clean-up, it gives you the exact command to run yourself.

Note: This report is informational. uv will work even if you change nothing at all. If you are not sure about an item, leave it and bring the output to a TA. Never delete anything inside /usr/bin — macOS itself uses those files.

Installing uv

Install uv by running this in a terminal:

curl -LsSf https://astral.sh/uv/install.sh | sh

The installer adds uv to your PATH by editing your ~/.bash_profile, so quit all open Terminal windows and open a new one before continuing. Then check that it worked:

uv --version

You should see something like this if you were successful:

uv 0.12.3

Note: If you get bash: uv: command not found in a brand new terminal, your bash configuration file is not being read. You can get going again in the current terminal by running source $HOME/.local/bin/env, but the underlying problem is worth fixing — revisit the Setting Positron as the default editor section above, which is where ~/.bash_profile gets created.

Installing Python

Now use uv to install the version of Python that MDS starts with:

uv python install 3.14

This does not give you a command called python. That is intentional. Try it and see:

python --version

bash: python: command not found

That is the correct answer. There are still a couple of Python programs on your Mac — python3, which belongs to macOS, and python3.14, which uv just installed — but neither of them has pandas or any other MDS package in it. The packages live inside projects, and uv run is how you reach them.

JupyterLab

JupyterLab is the other coding environment we use in MDS, and there is nothing to install for it here. Like every other Python package it comes with the project you are working in, so you will start it with uv run jupyter lab from inside an assignment folder.

R, XQuartz, and RStudio

R is another programming language that we will be using a lot in the MDS program. We will use R in RStudio and in Positron.

Note: R is not managed by uv. uv looks after Python and Python packages only; R packages are installed with R’s own install.packages() and live in your R library. The two ecosystems stay separate, and that is deliberate — you do not need a project or a uv run prefix to use R.

R

Go to https://cran.r-project.org/bin/macosx/ and download the latest version of R for Mac (4.6.1 at the time of writing). Open the file and follow the installer instructions. Pay attention to which file you download: install the -arm64.pkg file (e.g. R-4.6.1-arm64.pkg) if you are working with a Mac M1 or newer, and the -x86_64.pkg file (e.g. R-4.6.1-x86_64.pkg) if you are working on an Intel Mac.

After installation, open a new terminal window and type the following:

R --version

You should see something like this if you were successful:

R version 4.6.1 (2026-06-24) -- "Happy Hop"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

Note: Install R from CRAN as described above, and not through a package manager such as Homebrew, MacPorts, or conda. Those builds are put together differently and regularly cause problems when installing R packages later on.

XQuartz

Some R packages rely on the dependency XQuartz which no longer ships with the Mac OS, thus we need to install it separately. Download it from here: https://www.xquartz.org/ and follow the installation instructions.

RStudio

Download RStudio Desktop (not Pro) from the Posit downloads page. Under “Direct Downloads (Open Source)”, pick the macOS .dmg file (RStudio requires macOS 13 or newer). You have already installed R, so you only need RStudio itself here. Open the file and follow the installer instructions.

To see if you were successful, try opening RStudio by clicking on its icon (from Finder, Applications or Launchpad). It should open and look something like this picture below:

Now we are going to change RStudio’s Insert Pipe shortcut so that it inserts the native pipe operator |>. Go to Tools > Global Options > Code > Editing and tick the following option:

Once the change is made you can try in the RStudio console Ctrl + Shift + m to check if works.

Next, we will set RStudio to start every session from a clean slate, so that you always know exactly what is loaded in your environment and your analyses run correctly from the code alone. Go to Tools > Global Options > General > Basic and match the settings marked in the screenshot below: untick “Restore most recently opened project at startup”, “Restore previously open source documents at startup”, and “Restore .RData into workspace at startup”, and set “Save workspace to .RData on exit” to “Never”. Click “OK” to save.

Close down RStudio afterwards.

For students that are having computer admin issues, please run this in the terminal sudo chown -R $(whoami) .config

Installing R packages

Next, install the key R packages needed for the start of MDS program, by opening up RStudio and typing the following into the R console inside RStudio.

Note: If you are asked about installing into a personal library, select Yes.

Note: If you are asked to select a mirror, select the first 0-Cloud mirror.

install.packages('pak')
pak::pkg_install(c('tidyverse', 'renv', 'usethis', 'devtools', 'markdown', 'rmarkdown', 'languageserver', 'janitor', 'gapminder', 'readxl', "ucbds-infra/ottr", "ttimbers/canlang"))

Note: If you are asked to update packages during the installation, select the None option.

Stan

Stan is the language we will be using later on in the program for Bayesian statistics. To install it open RStudio and install rstan

install.packages("StanHeaders", repos = c("https://stan-dev.r-universe.dev", getOption("repos")))
install.packages("rstan", repos = c("https://stan-dev.r-universe.dev", getOption("repos")))

Note: If you are asked to update packages during the installation, select the None option.

Test the installation with:

example(stan_model, package = "rstan", run.dontrun = TRUE)

The model should then compile and sample. Here’s a snippet of the output you should see:

SAMPLING FOR MODEL '16a540c6086086816528e4524def24d9' NOW (CHAIN 4).
Chain 4:
Chain 4: Gradient evaluation took 2e-06 seconds
Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.02 seconds.
Chain 4: Adjust your expectations accordingly!
Chain 4:
Chain 4:
Chain 4: Iteration:    1 / 2000 [  0%]  (Warmup)
Chain 4: Iteration:  200 / 2000 [ 10%]  (Warmup)
Chain 4: Iteration:  400 / 2000 [ 20%]  (Warmup)
Chain 4: Iteration:  600 / 2000 [ 30%]  (Warmup)
Chain 4: Iteration:  800 / 2000 [ 40%]  (Warmup)
Chain 4: Iteration: 1000 / 2000 [ 50%]  (Warmup)
Chain 4: Iteration: 1001 / 2000 [ 50%]  (Sampling)
Chain 4: Iteration: 1200 / 2000 [ 60%]  (Sampling)
Chain 4: Iteration: 1400 / 2000 [ 70%]  (Sampling)
Chain 4: Iteration: 1600 / 2000 [ 80%]  (Sampling)
Chain 4: Iteration: 1800 / 2000 [ 90%]  (Sampling)
Chain 4: Iteration: 2000 / 2000 [100%]  (Sampling)
Chain 4:
Chain 4:  Elapsed Time: 0.003828 seconds (Warm-up)
Chain 4:                0.003417 seconds (Sampling)
Chain 4:                0.007245 seconds (Total)
Chain 4:

Note: If this step does not work, that is okay. It will not hold up the start of the program. Stan is not needed until block 5, so let your DSCI 521 instructor know that it failed and we will work on getting it going with you before then.

LaTeX and PDF export

We will install the lightest possible version of LaTeX and it’s necessary packages as possible so that we can render Jupyter notebooks and R Markdown documents to html and PDF. If you have previously installed LaTeX, please uninstall it before proceeding with these instructions.

Open RStudio and run the following commands to install the tinytex package and setup tinytex:

install.packages('tinytex')
tinytex::install_tinytex()

Note: You might be asked to enter your macOS password during the installation, so that TinyTeX can add itself to your PATH.

You can check that the installation is working by opening a terminal and asking for the version of latex:

latex --version

You should see something like this if you were successful:

pdfTeX 3.141592653-2.6-1.40.29 (TeX Live 2026)
kpathsea version 6.4.2
Copyright 2026 Han The Thanh (pdfTeX) et al.
There is NO warranty.  Redistribution of this software is
covered by the terms of both the pdfTeX copyright and
the Lesser GNU General Public License.
For more information about these matters, see the file
named COPYING and the pdfTeX source.
Primary author of pdfTeX: Han The Thanh (pdfTeX) et al.
Compiled with libpng 1.6.55; using libpng 1.6.55
Compiled with zlib 1.3.2; using zlib 1.3.2
Compiled with xpdf version 4.06

The above is all we need to have LaTeX work with R Markdown documents, however for Jupyter we need to add several more packages. Do this by opening a terminal and copying the following there press enter:

tlmgr install eurosym \
  adjustbox \
  caption \
  collectbox \
  enumitem \
  environ \
  fp \
  jknapltx \
  parskip \
  pdfcol \
  pgf \
  rsfs \
  soul \
  tcolorbox \
  titling \
  trimspaces \
  ucs \
  ulem \
  upquote \
  lwarp \
  oberdiek \
  atkinson

Note: atkinson is the Atkinson Hyperlegible typeface, from the Braille Institute. It is designed so that characters which usually look alike do not — I l 1, O 0, rn and m — which is worth having in a program where you read code and output all day. It is installed here so that a document can ask for it; nothing requires you to use it.

If you would also like it in your editor, both families are on Google Fonts (Next for text, Mono for code) and install like any other font. That is entirely optional and separate from the package above.

mds-setup-check carries a short guide with the YAML to copy into a document, for both HTML and PDF.

PostgreSQL

We will be using PostgreSQL as our database management system. Download the latest PostgreSQL 17 installer for macOS from the EnterpriseDB download page. That page also lists newer major versions such as 18, but please install 17. (Ubuntu students install whatever their release carries, which is 16 or 18; the setup check accepts any of the three). Follow the instructions for the installation. In the password page, type whatever password you want, and make sure you save it using a password manager or similar so that you know what it is in November when the SQL course starts (otherwise you will need to reinstall PostgreSQL). For all the other options, use the default. You do not need to run “StackBuilder” at the end of the installation (if you accidentally launch the StackBuilder, click “cancel”, you don’t need to check any boxes).

To test if the installation was successful, open the SQL Shell app from Spotlight search (Cmd + Space) or the Applications folder. You will be asked to setup your configuration:

  • Accept the default value (the one within square brackets) for the first three values by pressing enter three times,
  • Enter postgres as the default username and hit enter,
  • Finally, type in the password that you set during installation and press enter one last time.

It should look like this if it is working correctly:

If you are asked about stackbuilder, you can skip this for now.

Docker

You will use Docker to create reproducible, sharable and shippable computing environments for your analyses. For this you will need a Docker account, which you can sign up for free here.

Then go to the Docker Desktop install instructions for Mac and click the button for “Docker Desktop for Mac with Apple silicon” or “Docker Desktop for Mac with Intel chip”, depending on which kind of Mac you have. Then follow the installation instructions on that page.

To test if Docker is working, after installation open the Docker app by clicking on its icon (from Finder, Applications or Launchpad). Next open Terminal and type the following:

docker run hello-world

you should see something like this if you were successful:

Unable to find image 'hello-world:latest' locally
latest: Pulling from library/hello-world
1b930d010525: Pull complete
Digest: sha256:451ce787d12369c5df2a32c85e5a03d52cbcef6eb3586dd03075f3034f10adcd
Status: Downloaded newer image for hello-world:latest

Hello from Docker!
This message shows that your installation appears to be working correctly.

To generate this message, Docker took the following steps:
 1. The Docker client contacted the Docker daemon.
 2. The Docker daemon pulled the "hello-world" image from the Docker Hub.
    (amd64)
 3. The Docker daemon created a new container from that image which runs the
    executable that produces the output you are currently reading.
 4. The Docker daemon streamed that output to the Docker client, which sent it
    to your terminal.

To try something more ambitious, you can run an Ubuntu container with:
 $ docker run -it ubuntu bash

Share images, automate workflows, and more with a free Docker ID:
 https://hub.docker.com/

For more examples and ideas, visit:
 https://docs.docker.com/get-started/

Improving the bash configuration

To improve your experience using bash, we recommend appending a few lines to the end of your bash configuration file. These make it easier to use the TAB key for autocompletion improves how bash handles the command history, and the appearance of the terminal (we will talk more about these topics during class). It also adds colors to the terminal’s text, which can make it easier to navigate visually. First, run the following command to download a script that always shows information about git in the terminal prompt:

curl -Sso ~/.git-prompt.sh https://raw.githubusercontent.com/git/git/master/contrib/completion/git-prompt.sh

Then open the bash configuration file:

positron ~/.bash_profile

Paste the following at the end of the file (make sure not to overwrite any existing lines) and save it afterwards:

# Silence default shell note when launching bash
export BASH_SILENCE_DEPRECATION_WARNING=1

# Load the git prompt script
source ~/.git-prompt.sh
# Show unstaged (*) and staged (+) changes in the prompt string
export GIT_PS1_SHOWDIRTYSTATE=1

# Color text so it is easier to distinguish elements from each other
export CLICOLOR=1
export LSCOLORS=ExGxFxdxCxDxDxxbaDecac
# Color the prompt string and add git info
export PS1='\[\033[01;32m\]\u@\h\[\033[01;35m\] \w\[\033[34m\]$(__git_ps1 " (%s)")\[\033[00m\]\n\$ '

# TAB completion configuration
# TAB completion ignores case
bind "set completion-ignore-case on"
# Require only one instead of two TAB presses before showing matches
bind "set show-all-if-ambiguous on"
# Unfortunately the tab cycling does not work together with single tab match expansion on macOS
# since bash is too old, so I have commented out the option below,
# but feel free to remove the leading `#` if you want to test it out.
# If there are multiple matches for completion, cycle through them with TAB
# bind 'TAB':menu-complete

# History configuration
# Cycle through history based on characters already typed on the line
bind '"\e[A":history-search-backward'
bind '"\e[B":history-search-forward'
# Append to the history file, don't overwrite it.
shopt -s histappend
# Write commands to history one-by-one right after they are executed
# instead of all together when the terminal is closed.
# Make new terminals see all commands run in currently open terminals and
# prepend a newline to the prompt string to separate it from the last command's output
PROMPT_COMMAND='history -a; echo'
# Increase history size
HISTSIZE=50000
HISTFILESIZE=50000

# Aliases and functions
# Note that aliases only are in effect when you are using the shell interactively
# (e.g. opening the terminal and typing or pasting commands).
# If you run a bash script or makefile,
# the original command is used instead of your alias.
# ---
# MDS help script
alias mds-help='bash ~/.mds-help.sh'
# Some common operations
alias l='ls -lthAF'
alias jl='uv run jupyter lab'
alias gl='git log --date short -10 --pretty=format:"%C(auto,yellow)%h %C(auto,blue)%ad%C(auto)%d %C(auto,reset)%s"'
alias gt='git status'
alias gm='git commit -m'
alias gap='git add -p'
# Move, remove, and copy show what was done and prompt before overwriting files.
alias rm="rm -vi"
alias mv="mv -vi"
alias cp="cp -vi"
alias mkdir="mkdir -vp"
# Case insensitive grep by default
alias grep='grep -i'

Finally, download and save the MDS help script via the following command.

curl -Ssfo ~/.mds-help.sh https://ubc-mds.github.io/mds-setup-check/mds-help.sh

Open a new terminal and type mds-help, your terminal should display the most important terminal commands we will be learning in MDS. You don’t need to memorize these now, just remember that if you ever forget how to do something with bash, git or uv, you can type mds-help in your terminal and use it as a reference.

Post-installation notes

You have completed the installation instructions, well done 🙌! We have created a script to help you check that your installation was successful, and to provide instructions for how you can troubleshoot any potential issues. To run this script, please execute the following command from your terminal.

bash <(curl -Ssf https://ubc-mds.github.io/mds-setup-check/check-setup-mds.sh)

The script checks the Python side of your installation from inside a small project that we ship for the purpose, so it will ask permission to download that project into your home folder as ~/mds-setup-check. Answer y, and give it a few minutes on a good connection — it downloads several hundred megabytes the first time.

Note: The script always makes that folder itself and will not reuse one that is already there, because it can only vouch for a copy it downloaded. So if you run the script again after fixing something, it will ask whether to delete ~/mds-setup-check and download a fresh copy. Answering yes deletes that folder and everything in it, so if you have saved any work of your own in there, answer no and move it somewhere else first. The answer defaults to no — a bare Enter keeps the folder and skips the Python and document export checks. Saying yes costs you very little: the downloads are cached, so setting it up a second time takes seconds.

You can delete the folder for good once you have submitted your setup-check log.

The output from running the script will look something like this:

# MDS setup check v2026.08.18

If a program or package is marked as MISSING,
this means that you are missing the required version of that program or package.
Either it is not installed at all or the wrong version is installed.
The required version is indicated with a number and an asterisk (*),
e.g. 4.* means that all versions starting with 4 are accepted (4.0.1, 4.2.5, etc).

The "Document export" section is the exception. It tries several different ways of
turning a document into a PDF, and you only need one of them to work, so lines
marked FAILED there are fine. What matters is the summary at the end of that
section, which says whether PDF export works at all.

You can run the following commands to find out which version
of a program or package is installed (if any):

```
name_of_program --version  # For system programs
cd ~/mds-setup-check && uv pip list  # For Python packages
R -q -e "as.data.frame(installed.packages()[,3])"  # For R packages
```

Checking program and package versions...

## Operating system
ProductName:	macOS
ProductVersion:	26.5.1
BuildVersion:	25F80

## System programs
OK        psql (PostgreSQL) 17.6
OK        rstudio 2026.08.0+187
OK        R 4.6.1 (2026-06-24) -- "Happy Hop"
OK        uv 0.12.3
OK        bash 3.2.57(1)-release (arm64-apple-darwin25)
OK        git 2.50.1 (Apple Git-155)
OK        make 3.81
OK        latex 3.141592653-2.6-1.40.29 (TeX Live 2026)
OK        tlmgr revision 79491 (2026-06-27 19:40:15 +0200)
OK        docker 29.6.2, build dfc4efb
OK        positron 2026.08.0 build 331
OK        quarto 1.10.3
OK        pandoc 3.10.2

## Python packages
OK        Python 3.14.3
OK        otter-grader=7.0.0
OK        pandas=3.0.5
OK        nbconvert=7.17.1
OK        playwright=1.62.0
OK        jupyterlab=4.6.3
OK        jupyterlab-git=0.54.1
OK        jupyterlab-spellchecker=0.9.0
OK        jupytext=1.19.5
OK        ipykernel=7.3.0

## R packages
OK        tidyverse=2.0.0
OK        markdown=2.0
OK        rmarkdown=2.31
OK        renv=1.2.3
OK        tinytex=0.60
OK        janitor=2.2.1
OK        gapminder=1.0.1
OK        readxl=1.5.0
OK        ottr=1.5.2
OK        canlang=0.0.1

## Document export
You only need ONE of the PDF routes below to work.
A FAILED line here is not a problem by itself -- read the summary at the end.
OK        quarto Typst PDF-generation was successful.
OK        quarto LaTeX PDF-generation was successful.
OK        jupyterlab PDF-generation was successful.
OK        jupyterlab WebPDF-generation was successful.
OK        jupyterlab HTML-generation was successful.
OK        rmarkdown PDF-generation was successful.
OK        rmarkdown HTML-generation was successful.

OK        PDF export works. 5 of 5 routes succeeded,
          and one is all you need. Ignore any FAILED lines above.

## Environment
Not recorded. You were asked, and chose not to include them.

## Content of .bash_profile
...

## Content of .bashrc
...

## Python installations

### Python installations already on this computer (v2026.08.18)

This is a report only. Nothing below has been changed or removed.
uv will work even if you change nothing at all.

## Python and pip commands on your PATH
...

## What to do about it

  Nothing needs your attention. Carry on with the installation instructions.

The above output has been saved to the file /Users/janedoe/check-setup-mds.log
together with system configuration details and any detailed error messages about PDF and HTML generation.
You can open this folder in your file browser by typing `open .` (without the surrounding backticks).
Before sharing the log file, review that there is no SENSITIVE INFORMATION such as passwords or access tokens in it.

As you can see at the end of the output, a log file is saved in your current directory. We might ask you to upload this file if we need to troubleshoot your installation, so that we can help you more effectively. If any of your packages are marked as “MISSING” you will need to figure out what is wrong and possibly reinstall them. A “FAILED” line is different: it appears only in the “Document export” section, where several ways of producing a PDF are tried and you only need one of them. Read the summary at the end of that section rather than the individual lines – if it says “PDF export works”, there is nothing for you to fix. Once all packages are marked as “OK” we will ask you to submit this log file, so that we can confirm that your installation was successful. Details on where to submit will be provided later.

The script asks two questions while it runs.

  1. Whether to set the check project up in your home folder — or, if you have run the script before and ~/mds-setup-check is still there, whether to delete that folder and download a fresh copy. Answer y. Without it, the Python and document export checks are all skipped. (Answering yes to the second form deletes that folder and everything in it, so move out anything of your own first.)
  2. Whether to include your environment variables in the log. Answer no (just press Enter) unless an instructor asks you to include them. Environment variables often hold API keys and access tokens, and you are about to send this log to us.

Copy the command above exactly as written, including the <( and ). If you run it as curl ... | bash instead, the script has no terminal to ask you anything with, both answers stay at their defaults, and it skips every Python and Quarto check.

Note: In general you should be careful running scripts unless they come from a trusted source as in this case (just like how you should be careful when downloading and installing programs on your computer).

Visual Studio Code (optional)

Positron is the editor we use in MDS, and it is all you need for the program. Visual Studio Code (VS Code) is a more general-purpose editor that some students and instructors like to keep around for work outside of data science, so instructions for setting it up are collected here. Nothing in MDS requires it.

You can download and install the macOS version of VS Code from https://code.visualstudio.com/download, choosing the “Apple silicon” build. Once the download is finished, click “Open with Archive utility”, and move the extracted VS Code application from “Downloads” to “Applications”. If you would also like to launch it from the terminal with the code command, follow the “Launch VS Code from the command line” steps.

From within VS Code you can open the Extension Marketplace (read more here) to browse and install extensions by clicking on the Extensions icon in the Activity Bar indicated in the figure below.

To install an extension, go to View -> Extensions or click the icon shown in the image above. Then search for the extension you want and click “Install”. These are the ones that pair well with the rest of the MDS software stack:

  • Python (everything Python: notebooks, debugging, linting, formatting, etc.)
  • markdownlint (markdown linting and style checking extension)
  • GitLens - Git supercharged (powerful extension that extends VS Code’s native git capabilities)
  • Git History (intuitive view of your git history)
  • Container Tools (easily use Docker from VS Code; this replaced the older extension that was called “Docker”)
  • Quarto (integrated render and preview for Quarto documents and more)

Note: The list above is for VS Code only. Do not install Microsoft’s Python or R extensions into Positron: they are not compatible with it, and Positron already has its own Python and R support built in.

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