Unix Tricks

Unix tricks

In the background, Jupyter Hub runs on Unix, and you can access the Unix bash shell to do all your Unix magic from the command line. Just open a new “terminal” from the front page of your Jupyter server.

However, I am not a big Unix fan. I prefer to point and click. So here are a few tricks I’ve learned to avoid the terminal commands.

Unix and Magic in a Notebook.

While running a Jupyter Notebook, you can access many Unix commands directly, without opening a terminal window using so called “magic” commands. These commands always start with the percent sign %.

Here are a few familiar Unix commands you might find useful:

  • %ls – to list all files in the current directory
  • %cd – to see the name of your current directory
  • %cd dirname - to change directory (enter the name of the directory you want)
  • %cp oldfile newfile – to copy the oldfile onto a newfile
  • %rm filename – to remove (delete) the file named “filename”

Thankfully, you can move all around the directory tree using these magic commands. So for instance, you might want to copy a file from Directory1 into Directory2. You would use a command like this: - %cp /home/myusername/Directory1/filename /home/myusername/Directory2/filename

Where “myusername” is whatever the Jupyter server has called your account. Use the %cd (with no arguments) followed by %pwd to see the path to your home directory (including your user name.)

Advanced use

In a python 3 kernel you can also run arbitrary unix commands by putting an exclamation mark “!” at the beginning of a line, e.g.

!cp /home/myusername/Directory1/filename /home/myusername/Directory2/filename

Whenever possible, prefer the ‘%’ for, but ! is also available.

More Magic in a Notebook

The magic system is much richer than just the unix commands listed above. A good reference to what is possible is available in the ipython documentation

With a double percentage sign %% you signal to Jupyter that the whole cell is to be interpreted accordingly. For instance a cell like this:

%%latex
\[ \int_0^1 f(x) \,dx = F(1) - F(0) \]

tells the notebook to read the whole cell as latex code, and render it accordingly. $$ [ \int_0^1 f(x) \,dx = F(1) - F(0) ] $$

To see all defined magic commands available in a Jupyter notebook, type the (magic) command - %lsmagic

Magics can help with debugging, working with files, defining macros and much much more.