sciware

Sciware

Command line and Shell interaction

https://sciware.flatironinstitute.org/27_SummerIntro

Sciware goal

Activities where participants all actively work to foster an environment which encourages participation across experience levels, coding language fluency, technology choices*, and scientific disciplines.

*though sometimes we try to expand your options

Summer Intros

today 2-4: command line & cluster
Jun 7 2-4 in 162-2 IDA: git & Github, Part I
Jun 14 2-4 in 162-2 IDA: git & Github, Part II
Jun 21 1-3 in 162-2 IDA: VS Code

Today’s Agenda

Pre-session: setup a terminal (15 min)
Command-line intro (45 min, with terminal)
Cluster intro (30 min)
VS code intro, terminal (10 min)
Homework for next time: create a github account

Preparation Instructions

Instructions to get your laptop set up before the session

Windows
- See next slide
Mac
- Install xcode: open a terminal and run
  - xcode-select --install
- Install VS Code: https://code.visualstudio.com/docs/setup/mac
Linux
- Install VS Code: https://code.visualstudio.com/docs/setup/linux

Windows Instructions

Follow the three steps at this link to install WSL, VS Code, and the WSL extension for VS Code: https://code.visualstudio.com/docs/remote/wsl#_installation
Check if your installation worked: follow these instructions to open VS Code and connect to WSL: https://code.visualstudio.com/docs/remote/wsl#_open-a-remote-folder-or-workspace
If you see “WSL” in the bottom left of your VS Code window, your installation is working

Getting started

Let’s start a terminal!

“Terminal” (or “wsl” on Windows)

Shell Command Example

Here’s a typical shell command, separated by spaces:

A prompt displayed by the shell
A command, the program to run
options or flags control behavior, starting with -
arguments, additional words that will be passed to the command

Command Line

“CLI” = command line interface
- Compare to GUI = graphical user interface
In a terminal, you run a shell
With the shell, you run programs
Shell may be on another (remote) computer (e.g., ssh)

Working directory

A shell always has a “current working directory”: the directory (or folder) that’s used by default

pwd shows you the current directory (“print working directory”)
cd changes the current directory, by default to your “home” directory (~)

> pwd
/home/you/somewhere
> cd
> pwd
/home/you
> cd ~
> cd /home/you # same thing, for your home directory path

Clone a git repo

ls lists the files and directories (…in a specific directory, or your current by default)

> ls
Desktop
> git clone https://github.com/flatironinstitute/sciware-command-intro
Cloning into 'sciware-command-intro'...
> ls
Desktop  sciware-command-intro
> cd sciware-command-intro
> pwd
/home/you/sciware-command-intro

Advanced exercises

See advanced/README

https://wiki.flatironinstitute.org/SCC/Software/UnixIntroduction

Paths

combine directories with / to make longer paths
paths starting with / start at the “top” or root of the system, full absolute path
others are relative paths, starting with current directory
. means current directory
.. means parent directory (up one)
if pwd is /home/you, then these are all the same:
- /home/you/dir/file
- dir/file
- ./dir/file
- ../you/dir/../dir/file
- ../..///../.././home//you/dir/./file

Tab completion

No one wants to type all these file names: use tab!

> cd ~
> cd sciware-<tab>
> cd ~/sciware-<tab>

If there are multiple things, press tab twice:

> cd di<tab><tab>

Looking at files

To see inside a file, the contents, you need something else

cat just prints an entire file to the terminal
less lets you scroll around (q to quit)
You can also use an editor

> cat README
> less README

Listing files

ls lists files in a directory, and has many options to show more/different information

> ls -l # long
> ls -l -t -r # long, sort by modification time, reversed
> ls -ltr # same
> ls --help # may not work on Mac
> man ls # MANual page

Creating directories

Create a new directory with mkdir, remove with rmdir

> mkdir mydir
> cd mydir
> ls
> cd ..
> cd -
> pwd
> cd -
> rmdir mydir

cd - can be used to “go back” or “undo” the last cd

Quoting, spaces, arguments

What if we want to make a directory work stuff?

> mkdir work stuff
> ls
> rmdir work stuff
> mkdir "work stuff"
> cd work<tab>

The shell always splits arguments into words before the command gets it.
To avoid this, use quotes, or \ , which “escapes” any character
We usually avoid putting spaces in filenames because it’s annoying (often use _ underscores)

More file manipulation

mv renames or moves files or directories
rm removes files, or rm -r removes directories and contents (careful!)

> cd ~/sciware-command-intro
> mv filea fileb
> mv fileb dir1
> ls dir1
> rmdir dir1
rmdir: failed to remove 'dir1': Directory not empty
> rm dir1/fileb dir1/deleteme
> rmdir dir1
> ls dir2
> rm -r dir2

Hidden “dot” files

Files and directories that start with . don’t show up by default, but you can access them as usual.

> cd notempty
> ls
> ls -a # all
> ls -la
> mv .hiddenfile nothidden
> ls
> cd ..

Copying files

cp makes an identical copy of a file.

> cp README readnot
> cat readnot

To copy entire directories, use cp -a.

Interactive programs

Some programs are interactive, don’t immediately return you to the shell.
You can often use Control keys to stop them, written <Ctrl-X> (or sometimes ^X or C-X)
- <Ctrl-D> tells a program you’re done
- <Ctrl-C> tells a program to exit (“cancel”)

> python3
Python 3
>>> 1+1
2
>>> ^D

Globbing

You can use * to mean “anything”, any file that matches:

> ls *.txt
> echo *.txt

echo just prints its arguments

> echo "*.txt"
> echo \*.txt

Run something again

> <Up><Down>
> history
> <Ctrl-R>

Navigation

> <Left><Right><Home><End>

Shell interaction

<Ctrl-A> = Home (beginning of line), <Ctrl-E> = End (end of line)
<Ctrl-Left>, <Ctrl-Right> = move by word
<Ctrl-L> = clear

https://vhernando.github.io/keyboard-shorcuts-bash-readline-default

> exit

Shells and configuration

There are multiple different shells with different features.

bash (usually default on Linux): .bashrc
zsh (usually default on Mac): .zshrc

Shells are extremely customizable, including prompts, keybindings, aliases, plugins

Questions and exercise

Organize the files in animals directory:

create directories to categorize the animals
move files into these directories
hint: use ls, cat, mkdir, mv

VS code

Interactive demo

look at a couple files
correspond to command line
terminal