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Table of Contents

Installation notes

If you have already installed Git, Latex, or any of the R or Python related packagesplease 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 effectivelyand minimize setup issues and software conflicts,we require all students to install the software stack the same way.

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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 endto 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.mozilla.org/en-US/firefox/new/, 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, 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/intl/en-ca/help/articles/207677868-Download-Slack-for-Mac

Bash shell

Apple recently changed the Mac default shell in the Terminal to Zsh, 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:

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

Visual Studio Code

Installing

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. You can download and install the macOS version of VS Code from the VS code website https://code.visualstudio.com/download. Once the download is finished, click “Open with Archive utility”, and move the extracted VS Code application from “Downloads” to “Applications”.In addition to reading the getting started instructions, be sure to follow the “Launching from the command line” steps as well.

You can test that VS code is installed and can be opened from Terminal by restarting terminal and typing the following command:

you should see something like this if you were successful:

Note: If you get an error message such as -bash: code: command not found, but you can see the VS Code application has been installed, then something went wrong with setting up the launch from the command line. Try following these instructions again, in particular you might want to try the described manual method of adding VS Code to your path.

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.

GitHub.com

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

GitHub.ubc.ca

To add you to the MDS organization on Github.ubc.ca we need you to 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. Some of the Git commands we will use are only available since Git 2.23, so if your Git is older than this version, we ask you to update it using the Xcode command line tools (not all of Xcode), which includes Git.

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

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

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

Note: If you run into trouble, please see that Install Git > Mac OS 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 [email protected], with your name and email (the same used to sign up for GitHub), respectively):

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 vscode by default, we will modify ~/.bash_profile. First, open it using VS Code (this will also create the file if it doesn’t already exist):

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

Now append the following lines to ~/.bash_profile:

Then save the file and exit VS Code.

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,VScode is not set as the default text editor for giteven after appending the two lines above,so to make sure it is registered properly,also run the following from your terminal:

On MacOS,VScode sometimes reads a different configuration file than your other programs.To avoid this,open your ~/.bashrc file:

And append the following line:

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), which Miniconda MacOSX 64-bit pkg install for Python 3.x can be downloaded here..

After installation, restart the terminal. If the installation was successful, you will see (base) prepending to your prompt string. To confirm that conda is working, you can ask it which version was installed:

which should return something like this:

Note: If you see zsh: command not found: conda, see the section on Bash above to set your default Terminal shell to Bash as opposed to Zsh.

Next, type the following to ask for the version of Python:

which should return Python 3.9.0 or greater:

Note: If instead you see Python 2.7.X you installed the wrong version. Uninstall the Miniconda you just installed (which usually lives in the /opt directory), and try the installation again, selecting Python 3.9.

Installing 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:

To install packages individually,we can now use the following command:conda install <package-name>.After running that commandconda 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.Also note that we may occasionally need to install packages using pip, the standard Python package manager. The installation command is very similar to that of conda: pip install <package-name>.Let’s try this out in the next section,by installing some of the key packages we will use in MDS.

JupyterLab setup

We will be using JupyterLab as our main coding environmentand pandas is one of the key data analyses packages in MDS.The Jupytext Python package and the JupyterLab git extension facilitatesusing notebooks in JupyterLab together with Git & GitHub.The spellchecker helps us correcting typos in our writingand the LSP packages fill the same function for our code.Install them via the following commands:

We will grade part of your assignments in MDS using the Otter-Grader package. For your Jupyter-based assignments, you need to install Otter-Grader using the following command:

Note: You will also install Otter-Grader for R in the later sections of this guide.

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.

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Note: we will use many more packages than those listed above across the MDS program, however we will manage these using virtual environments (which you will learn about in DSCI 521: Platforms for Data Science).

R, XQuartz, IRkernel, and RStudio

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

R

Go to https://cran.r-project.org/bin/macosx/ and download the latest version of R for Mac. Open the file and follow the installer instructions.

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

You should see something like this if you were successful:

Note: Although it is possible to install R through conda, we highly recommend not doing so. In case you have already installed R using conda you can remove it by executing conda uninstall r-base.

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 the macOS Desktop version (not Pro) of RStudio Preview from https://rstudio.com/products/rstudio/download/preview/. 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 new 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.

Installing R packages

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

Note: If you are asked to update packages during the installation via devtools::install_github, select 3: None.

IRkernel

The IRkernel package is needed to make R work in Jupyter notebooks. To enable this kernel in the notebooks, install by pasting the following command into the RStudio Console:

Next, open a terminal and type the following(you can’t use RStudio for this stepsince it doesn’t honor $PATH changes in ~/.bash_profile)

To see if you were successful, try running JupyterLab and check if you have a working R kernel. To launch the JupyterLab type the following in Terminal:

A browser should have launched and you should see a page that looks like the screenshot below. Now click on “R” notebook (circled in red on the screenshot below) to launch an JupyterLab with an R kernel.

Sometimes a kernel loads, but doesn’t work as expected. To test whether your installation was done correctly now type library(tidyverse) in the code cell and click on the run button to run the cell. If your R kernel works you should see something like the image below:

To improve the experience of using R in JupyterLab,we will add keyboard shortcuts for inserting the common R operators <- and >.Go to Settings -> Advanced Settings Editor -> Keyboard Shortcutsand paste the following in the rightmost panel that says User Preferences(replacing the {}):

After you have pasted this text,hit the small floppy disk in the top right (or Ctrl + s)to save the settings.Here is a screenshot of what it looks like with the settings saved:

To check that the extension is working,open JupyterLab,launch an R notebook,and try inserting the operators by pressing Alt + - or Shift + Cmd + m, respectively.You could add any arbitrary text insertion command the same way,but this is all that is required for MDS.

LaTeX

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.

First, run the following command to make sure that /usr/local/bin is writable:

Note: You might be asked to enter your password during installation.

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

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

You should see something like this if you were successful:

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:

To test that your latex installation is working with jupyter notebooks,launch jupyter lab from a terminal and open either a new notebookor the same one you used to test IRkernel above.Go to File -> Export notebook as... -> Export Notebook to PDF.If the PDF file is created,your LaTeX environment is set up correctly.

WebPDF export

Jupyter recently added another way to export notebooks to PDFwhich does not require Latexand makes the exported PDF look similar to notebooks exported to HTML.This requires the pyppeteer package,which we can install as follows.

Try this by going to File -> Export notebook as... -> Export Notebook to WebPDF.

PostgreSQL

We will be using PostgreSQL as our database management system. You can [download PostgreSQL 13.x from here. 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 the LaunchPad or applications directory. 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:

Docker

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

After signing-up and signing into the Docker Store, go here: https://store.docker.com/editions/community/docker-ce-desktop-mac and click on the “Get Docker” button on the right hand side of the screen. Then follow the installation instructions on that screen to install the stable version.

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:

you should see something like this if you were successful:

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. Now that we have installed all our other Data Science tools, we can install the VS Code extensions that work really well with them. From within VS Code you can open up 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, 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:

File Explorer Search For Extension

  • 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 (intutive view of your git history)
  • Docker (easily use Docker from VS Code)
  • (Optional) Material Theme and/or Predawn Theme Kit (additional colour themes to choose from)
  • (Optional) Material Icon Theme (great-looking custom file icons!)
  • (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.

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See Full List On Pypi.org

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 autocompletionimproves 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 scriptthat always shows information about git in the terminal prompt:

Then open the bash configuration file:

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

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

Open a new terminal and type mds-help,your terminal should displaythe 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 conda,you can type mds-help in your terminaland 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.

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

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 fileif 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.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.

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).

Attributions

  • UBC STAT 545 licensed under the CC BY-NC 3.0.
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