MDS software stack install instructions for macOS - Part 2¶

Important

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

Terminal¶

Apple recently changed the Mac default shell in the Terminal to Zsh - though the reasons for this are complicated, it is a huge improvement over the out-dated Bash version that came pre-installed on macOS.

To make sure your shell is set to Zsh, open up your Terminal and run this command:

chsh -s path

[Optional] Install Ohmyzsh to get Terminal colours, and highlighting¶

Oh My Zsh is installed by running the following command in your Terminal:

sh -c "$(curl -fsSL https://raw.githubusercontent.com/ohmyzsh/ohmyzsh/master/tools/install.sh)"

You may now customize your Terminal with themes by [following the directions here](“https://github.com/ohmyzsh/ohmyzsh#selecting-a-theme”].

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 ~/.z_profile. First, open it using VS Code:

code ~/.z_profile

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

Paste the following lines to the new file that opens up:

# 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), 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 \
 "jupyterlab=2.*" \
 "numpy=1.*" \
 "pandas=1.*" \
 "flake8=3.*" \
 "black=19.*"

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 JupyterLab¶

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!

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