Frequenty Asked Questions

I am stuck inside something weird on the command line!

If you ever get 'stuck' inside a command line session and you want to get unstuck the most reliable trick is to type Ctrl+c (hold the control key and push 'c'). This is like an instant quit command for 99% of command line tools.

What do I do when I get stuck in this window and why did it happen?

This is the nano command-line text editor. On the first day we set nano as the default editor for git. You will see this in your terminal if you forget to add the -m argument when you commit files (e.g. git commit vs git commit -m "my commit message"). All commits require a commit message, so if you leave off the -m then it drops you into the default editor so you can type in the commit message manually (which is also totally fine).

How do I get out of this?: nano accepts keyboard shortcut commands, most of which it shows at the bottom of the screen. The '^' symbol means 'Ctrl', so ^X hold the Ctrl key and push "X", which will exit the program.

How do I properly reference files inside my class github repository?

The absolute path to your class github repository is: /home/jovyan/BIO597-SpatialBiodiversity.

If you are working on an assignment, the relative path to the EasternSnakes directory is: ../labs/EasternSnakes.

File paths are always tricky because they rely on having a 'sense' of where you are in the filesystem and how to navigate around it. Absolute paths fully specify the location of a file from the 'root' of the filesystem (which is indicated by the first "/"). Relative paths will usually start with a '.' (meaning "this directory") or a '..' (meaning one directory up).

How do I see information about all the variables that are active in a jupyter notebook?

There are two ways to do this. The first way is to use the %whos magic command. Inside a new cell you can type %whos and it will give information about all the variables you have created.

This is fine but you can't browse it like the variables pane in RStudio. To get a more interactive view of the variables you can enable the debugger by clicking the little bug shaped button (it might be hidden inside a 'three-dots' menu on the right side of the command bar).

After you do this (it might open immediately) you will see the 'bug' menu on the right side and if you open this you will see a 'variables' panel much like in RStudio, where you can click on variable names to see their current contents.