This introduction to the shell is designed to run on EarthscapeHub.
Information on a computer is stored in files and directories. The part of an operating system that handles this information is called the file system. Think of the file system as a tree with branches (directories) and leaves (files).
Let's find out where we are in the file system when we start a terminal:
$ pwd
/home/jupyter-mpiper
The pwd command prints the current directory to the terminal.
You can see that I'm in the directory jupyter-mpiper under the directory home.
The forward slash / is used as a delimiter between directory names.
The string "/home/jupyter-mpiper" is called a path. Think of a path as directions used to get to a location on the file system. This path is an example of an absolute path because it starts at "/", the root of the file system.
The directory /home/jupyter-mpiper is special--it's the home directory
of the user jupyter-mpiper.
Every user has a home directory.
It's the default location for you to create and store information.
Note that I executed this command on a JupyterHub running Linux; the home directory on a macOS or Windows machine will be slightly different.
Next, let's look at the contents of user jupyter-mpiper's home directory:
$ ls
CoCoLessons bin bmi-topography ivy scratch
README.md bmi-geotiff data projects tmp
The ls command provides a directory listing.
This home directory holds a set of files and directories.
We can drill down through directories by providing arguments to ls.
For example, to see the contents of the ivy directory, type:
$ ls ivy
AUTHORS.rst LICENSE.md lessons
CHANGES.md README.ipynb media
CITATION.cff README.md noxfile.py
CODE-OF-CONDUCT.md environment.unix.yaml pyproject.toml
CONTRIBUTING.md environment.yaml pytest.ini
You can see that the CSDMS Ivy lesson files have been added to the JupyterHub. We can drill further; for example, to see into the directory containing lessons, type:
$ ls ivy/lessons
best-practices git permamodel shell
bmi hpc pymt
conda jupyter python
editors landlab requirements.in
Although we've peered into the directory of Ivy files,
we remain in the home directory.
To change directories, use the cd command:
$ cd ivy
$ pwd
/home/jupyter-mpiper/ivy
The pwd command shows that we've switched to the ivy directory.
The cd command can take a directory name as an argument.
It can also take no arguments:
$ cd
$ pwd
/home/jupyter-mpiper
With no arguments, cd always returns to your home directory.
The cd command can also take a set of special characters as arguments.
To switch to the previous directory, use a dash -:
$ cd -
/home/jupyter-mpiper/ivy
When working with directories, a dot . is a shortcut for the current directory,
while two dots .. are a shortcut for the parent directory,
one directory closer to the root of the file system:
$ cd .
$ pwd
/home/jupyter-mpiper/ivy
$ cd ..
$ pwd
/home/jupyter-mpiper
Likewise, the tilde ~ is a shortcut for the user's home directory:
$ cd ~
$ pwd
/home/jupyter-mpiper
From your home directory, use the mkdir command to make a new directory:
$ mkdir new
$ ls
CoCoLessons bin bmi-topography ivy projects tmp
README.md bmi-geotiff data new scratch
Change to the new directory and get a listing:
$ cd new
$ ls
The new directory is empty.
Let's copy a file from the ivy directory to our new directory:
$ cp ../ivy/README.md .
$ ls
README.md
Here, we instructed the cp command to go up a directory and over to the
ivy directory to get a file and copy it to the current directory.
In this example,
the arguments to cp are both relative paths
because their starting points are relative
to the current directory on the file system.
Note that the copy and the original both exist, and are the same:
$ $ diff -s README.md ../ivy/README.md
Files README.md and ../ivy/README.md are identical
The diff command compares files and reports how they differ.
The mv command can be used to rename a file.
$ mv README.md readme.md
$ ls
readme.md
The mv command can also be used to move a file from one location to another.
Let's move readme.md up to the home directory:
$ mv readme.md ~
$ ls
$ ls ~
CoCoLessons bin bmi-topography ivy projects scratch
README.md bmi-geotiff data new readme.md tmp
Note that the new directory is now empty because readme.md has been moved to the home directory. Also note that README.md and readme.md in the home directory are different files! The file systems in Linux and macOS are case-sensitive.
We've seen how to manipulate the names and locations of files. How can we see what's in a file?
There are several shell tools available to do this.
The simplest is cat,
which prints the contents of the file to the screen.
For example, try:
$ cat readme.md
(The output is long, so we've chosen to omit it here.)
Similar to cat are head and tail, which by default show the first and last 10 lines of a file:
$ head readme.md
<!-- Links -->
[jhub]: https://csdms.colorado.edu/wiki/JupyterHub
[jupyter]: ./lessons/jupyter/index.md
[shell]: ./lessons/shell/index.md
[editors]: ./lessons/editors/index.md
[conda]: ./lessons/conda/index.md
$ tail readme.md
Portions of the CSDMS Ivy shell and Python lessons are derived
from material that is copyright
[Software Carpentry][swc]
and remixed under their [license][swc-license].
The Project Jupyter lesson
is taken from the [Code to Communicate][coco] project
and modified under their [license][coco-license].
CSDMS Ivy is supported with funding from the National Science Foundation.
Slightly more advanced are tools called "pagers"; more and less are examples.
A pager fills the screen with lines of text.
If there's more text than screen,
tap the Space key on your keyboard to advance to the next screen of text.
Use the b key to go back.
Use the q key to quit the pager.
Try this with:
$ more readme.md
Pagers are handy for stepping through large files one screen at a time.
How would we change the contents of a file? That's a topic unto itself. We'll visit it in a separate lesson on text editors.
Files can be deleted with the rm command.
Remove our readme.md file with:
$ cd
$ rm readme.md
There is no concept of a "trash" or "recycle" bin in the shell. Once a file is removed, it's gone, irrevocably.
Directories are deleted with the rmdir command.
As a last step, let's delete the new directory:
$ rmdir new
$ ls
CoCoLessons bin bmi-topography ivy scratch
README.md bmi-geotiff data projects tmp
As rm removes files, the rmdir command removes directories.
However, the directory must be empty before it can be removed.
The table below summarizes the concepts described in this lesson.
| Concept | Description |
|---|---|
| file system | the part of operating system that organizes how information is stored and accessed |
| path | a string that gives the location of a file or directory on the file system |
| absolute path | a path that starts at the root of the file system |
| relative path | a path that starts at the current directory |
| current directory | the path where the shell process is currently working |
| home directory | the default path location for a user to store files and directories |
| parent directory | the path one directory closer to the root |
The table below summarizes the commands and special characters described in this lesson.
| Command | Description |
|---|---|
| pwd | print working directory |
| ls | directory listing |
| cd | change directory |
| / | path delimiter |
| ~ | home directory |
| . | current directory |
| .. | parent directory |
| - | previous directory |
| cp | copies a file |
| mv | moves or renames a file |
| diff | compares contents of files |
| cat | display contents of file |
| head | display first lines of file |
| tail | display last lines of file |
| more | page through contents of file |
| rm | deletes a file (permanently) |
| mkdir | creates a directory |
| rmdir | deletes a directory (permanently) |