An entry-level resource for Data Science in Radiology
These are optional steps for those interested in taking advantage of some advanced tools for the CLI. I find these tools very useful, but it takes a fair amount of time to get everything installed and running. There’s also the possibility that you’ll spend a considerable amount of time tweaking things to your liking…
Also, if you haven’t yet installed the Xcode Developer Command Line Tools, return to the Basic Setup Guide and do this first.
Zsh is an alternative shell that offers some really nice features like improved tab-completion (probably the most routinely useful one), syntax highlighting, and extended “globbing” - I’ll explain the last one in a separate post under the Command Line page.
Let’s start by installing iTerm2, Homebrew, the Z shell (Zsh), Oh My Zsh and Powerline fonts to make sure everything runs smoothly once we actually start to use Zsh.
bash
line-by-line and don’t include the $ - it’s just there to tell you that
each command goes on it’s own line.$ /usr/bin/ruby -e "$(curl -fsSL https://raw.zshhubusercontent.com/Homebrew/install/master/install)"
$ brew doctor
$ brew install zsh
$ sudo -s 'echo /usr/local/bin/zsh >> /etc/shells' && chsh -s /usr/local/bin/zsh
Welcome to Zsh! Now on to installing Oh My Zsh, which is a collection of themes
for taking full advantage of Zsh and “beautifying your shell”. Start by
installing git, a version management command line tool that you’ll be using a
lot, if you continue to use this site.
$ brew install git
Next, we’ll install Oh-My-Zsh from Robby Russell’s GitHub repository (or ‘repo’).
$ sh -c "$(curl -fsSL https://raw.githubusercontent.com/robbyrussell/oh-my-zsh/master/tools/install.sh)"
Once this is is done, you’ll be running your fancy new Zsh with Oh My Zsh. The
default theme is robbyrussell. We’ll change that shortly, though you can
certainly keep it if you like it.
Many Oh My Zsh themes require a Powerline
font to be rendered properly in the terminal. So, naturally, we’ll install
those here to keep things running smoothly as we proceed. (Note: In the code
block below, the # indicates a comment, not a command.) Back to our new
friend git…
# clone the Powerline fonts repo to your machine
$ git clone https://github.com/powerline/fonts.git --depth=1
# run the install script
$ cd fonts
$ ./install.sh
# clean up the files you no longer need
$ cd ..
$ rm -rf fonts
Now, head to “Preferences” in iTerm2 by pressing {CMD + ,}. Then go to
“Profiles > Text” to set the “Regular” and non-ASCII fonts to one of your newly
installed Powerline fonts (I recommend SourceCodePro for starters). I also
recommend switching your color palette to “Solarized”, as it plays nicely with
Oh My Zsh.
Most commonly, people configure Zsh in their .zshrc file. The first time you
install and run Zsh, you probably won’t have one of these files in your home
directory ~. However, installing OMZ will create one for you and prepopulate
it with some useful stuff. Running ls in ~ won’t show you “Dotfiles” (e.g.
.zshrc) by default. For that, you should run ls -a (or la - an “alias” or
shortcut for the preceding command). You should see something similar to what
I’ve shown below, though everyone will probably have many other files and
folders that get printed to the standard output (or “stdout”) when they run
this command.
$ ls -a
-rw------- 1 walter walter 496 Oct 6 22:36 .bash_history
-rw-r--r-- 1 walter walter 220 Oct 6 22:50 .bashrc
drwxr-xr-x 11 walter walter 4.0K Oct 6 22:46 .oh-my-zsh
-rw------- 1 walter walter 56K Nov 15 11:35 .zsh_history
-rw-r--r-- 1 walter walter 3.8K Nov 15 11:25 .zshrc
# ... with other files mixed in
Now, on to configuring Zsh in .zshrc. The first thing you should do is decide
which text editor you want to use. Your options are a graphical text editor or
one of the built-in text editors that run in the shell itself. For simplicity,
we’ll go with nano - one of the built-in options. It’s far easier to use than
vi or vim and simpler than opening a separate window every time you want to
make a minor change to your config. Entering nano ~/.zshrc will launch nano
with your config file in the editor. At the bottom of the window, you should
see the commands available to you (FYI: ^G is shorthand for {CTRL + G}).
After you make changes, you will need to press ^O (letter O, not number) to
“write out” (i.e. save) your changes before you ^X (exit). Also, you’ll be
navigating with the keyboard as your mouse won’t work.
Everything you see in your .zshrc has been added by OMZ. The first thing we’ll
do is change the theme. Navigate to the line that says ZSH_THEME="robbyrussell".
We’re going to change the theme to “agnoster”, so delete “robbyrussell” and
replace it with “agnoster” such that the line now looks like this
ZSH_THEME="agnoster". Then ^O and ^X. Now you’ve saved your changes,
exited nano and are back in Zsh…but everything looks the same.
To see the effects of your changes to the config, you’ll have to reload your
shell. The command for this is source ~/.zshrc. Over time, you may find
yourself tweaking your shell config regularly, adding or changing different
aliases, etc. Thus, I recommend you go ahead and add the following lines to your
.zshrc under # Aliases. You may wish to delete the existing ones.
alias zshconfig="nano ~/.zshrc"
alias reload="source ~/.zshrc"
You will have to reload your shell profile with the full command before you can
use your new aliases. But after you do that, you’ll be able to edit your config
in nano simply by entering zshconfig, then reload when you’re done.