intro-to-reticulate

These instructions were created using computers that satisfied these requirements (i.e., no promises they will work on other systems):

• 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 for on campus work
• has access to an internet connection that is fast and stable enough for video calling and conducting online quizzes
• 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
• uses English as the default language

Table of Contents:

• Bash shell
• Python and Conda
• R, XQuartz and RStudio

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:

chsh -s /bin/bash

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

Python and Conda

We will be using Python for this demo, 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 3.8 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:

conda --version

which should return something like this:

conda 4.8.2

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:

python --version

which should return something like this:

Python 3.8.3

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 3.8.

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 our program:

conda install \
 numpy=1.* \
 pandas=1.* 

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.

R, XQuartz 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 (Should look something like this: R-3.6.1.pkg). Open the file and follow the installer instructions.

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

R --version

You should see something like this if you were successful:

R version 4.0.0 (2020-04-24) -- "Arbor Day"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under the terms of the
GNU General Public License versions 2 or 3.
For more information about these matters see
https://www.gnu.org/licenses/.

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 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:

{tidyverse} 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:

install.packages('tidyverse', 'rmarkdown', 'usethis')

Note: we will install reticulate together during the demo.

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