1.2. Terminal, Shell, & Bash#

https://raw.githubusercontent.com/van-richard/CodingNotes/main/static/gif/terminal-header.gif — Fig. 1.1 Example of command line in the `terminal` application of MacOS. The line you are working on is noted with the `$`. The format of this line is: computer name, `;` , username, and then `$`. `Bash` commands are typed by line, and ran by hitting the `[enter]` key.where, (1) :term:`echo` will return `"[`some text`]"` as an output, (2) :term:`echo` to output “2 + 2”, the `|` (pipe) takes this as input for the next command, `bc -l` (calculator), (3) `echo` prints the variable, `$SHELL`, which points to the program `/bin/bash`, and (4) cowboy.#

In this section, we’ll delve into the basics of the terminal, its role, and why it’s crucial in computational research.
Approaches to “using” computer programs:
- A common way makes use of a Graphical User Interface (GUI)
  - Programs that use a mouse and keyboard with on-screen menus, buttons, sliders, etc.
  - Relies on the user to click on-screen options for specific instructions
- Alternatively, computer programs can be operated via the Command Line Interface (CLI)
  - Uses text-based instructions, only requiring input from the keyboard
  - Often used for computing many files or automating repetitive tasks.

1.2.1. wtf is terminal?#

Terminal is a graphical-based application, providing access to the CLI
- This is preinstalled on MacOS as the terminal app
- Windows has variations called Command Prompt and PowerShell
Using command line is a fundamental tool in computational research, offering advantages like:
- More control in running applications
- Faster management across operating systems (OS)
- Ability to automate repetitive tasks (scripting)

1.2.1.1. Example: Opening the Terminal App#

You can find the terminal by:

MacOS

Manually looking through your files for it

Open launchpad -> Look for terminal.
Open Finder -> Applications/ -> terminal
Search
Press cmd+[space]. Then type terminal.

Windows

To use a Linux terminal on a Windows machine, you will need to install the Ubuntu application. This will differ if you’re using Windows 10 or Windows 11.

I will write this up, but here is my reference.

Install Ubuntu on WSL

Several data analysis tools and computing servers require proficiency with the command line. It may have a steep learning curve and be a bit confusing initially, but once you get the hang of it. Automation will be E Z!

Notation and pre-defined commands will depend on your shell!

Users can send instructions to the computer by running commands

Like GUIs, these instructions can be for manipulating files or running software
Often, a command is an abbreviation of common words (copy = cp, move = mv)

1.2.2. $SHELL#

When you open terminal, a shell session starts immediately, containing the current state or environment

Only one session per shell exists

Shells are programs that understand and execute user commands:

interpreting human language (text input) into computer language (output)
Various shells are available, such as csh, zsh

I use bash shell, so my notes will only cover bash!

An interactive prompt is when users run each “command” line by line.

Note

Later, we will see that combining multiple command lines into one file is called a “shell script.”

Example: Bash Shell Commands

In a shell, predefined commands are computer processes.

Commands are typed and interpreted by the computer to run processes
Users provide input in the form of commands, and the computer outputs the result
To update the output, run the command again.

Some commands can be modified by options following the command with a hyphen -. Others take arguments as input. Look at the following examples:

1.2.3. Navigating#

Understand the general layout of the terminal
Compare differences from GUIs like Finder or File Explorer
Find your start, current position, and navigate in terminal.
View files/folders.
Differentiate between absolute and relative paths.

The default location when you first login is called your “home” directory

1.2.3.1. Where Are We?#

# `pwd` - print working directory

- Use `pwd` (Print Working Directory) to find your current working directory (folder).

```bash
pwd
```

- Navigate in the terminal, relying on being in the right location. As you move around directories, use `pwd` often to remind yourself where you are.

1.2.3.2. What Files/Folders are Here?#

# `ls` - list information about files/folders 

- Use `ls` (List) to see what files/folders are in the current location.

- The default is to list the files in the current directory. Adding options can change how the list is organized.

```bash
ls [option] [directory]
```

List directories

```bash
ls -d
```

Long list format 

```bash
ls -l
```

Sort by time (newest first)

```bash
ls -t
```

List files with file size in kilobytes/megabytes/gigabytes

```bash
ls -h
```

Sort alphabetically

```bash
ls -X
```

1.2.3.3. How to Make a New Folder/Directory?#

# `mkdir` - make new directories.

- Use `mkdir` (Make Directory) to create a new folder.

```bash
mkdir [new folder name]
```

- For example, create a folder called `test`.

```bash
mkdir test
```

```bash
mkdir myNewDir
```

The `-p` flag causes new intermediate directories to be created as necessary.

```bash
mkdir -p myNewDir/with/intermediate/directories
```

If the intermediate directories didn't already exist, running the above command without the `-p` flag would return an error

1.2.3.4. Enter/Exit Folders#

# `cd` - change directories

- Use `cd` (Change Directory) to enter a folder.

```bash
cd [folder name]
```

- Check your current location with `pwd`.

```bash
pwd
```

- To go back one directory, use `cd ../`. To return to your "home" directory:

```bash
cd    # Option 1
cd ~  # Option 2
```

- Check your current location again to ensure you're back home.

```bash
pwd
```

Since bash works in the context of a current directory, you might want to run your command in some other directory. We have cd for changing location:

Change to home directory

```bash
cd ~ 
```

or

```bash
cd     
```

Go back one directory

```bash
cd ../
```

Go to specific directory

```bash
cd /home/username/Documents  
```

Go the the previous directory you were in

```bash
cd -   
```

1.2.4. What are Paths?#

Two types of paths:

Absolute - relative to the root directory (e.g., /home, /Users).
Relative - relative to your current working directory.

File or directory references use one of these paths.

1.2.5. File Management#

How to copy, move, rename, and/or delete files?
Tasks like copying, moving, renaming, and deleting files/folders (cp, mv, rm) need to be typed!

1.2.5.1. Copy using `cp`#

# `cp` - copy files or folders

- Use `cp` to copy files or folders 
  - The `[source]` is the original file/folder or `/path/to/OriginalFile` or `/path/to/OriginalFolder`
  - The `[destination]` is where you want the *new copy* to go, this can be in the same folder, or to another path (`/different/path/to/NewFile`)

```bash
cp [source] [destination]
```

- Again, both `[source]` and `[destination]` can use absolute or relative paths


```bash
# Copy file in current working directory, OriginalFile.txt, to another directory in /path/to/destination and name it NewFile.txt
cp OriginalFile.txt /path/to/destination/NewFile.txt 

# Copy file from another directory here (.)
cp /path/to/OriginalFile.txt . 
```

- The `.` means `./` or the current directory you're in
  - Remember to go back a folder, we run `cd ../` ? 
  - `../` points back on directory while `./` means the current one

### Copy Folders with `cp -r`

- Copying a directory requires the option `-r`.

```bash
# Option, -r, tells cp to copy the entire folder to a new path
cp -r directory /path/to/destination

# Can also copy things "here" (.)
cp /path/to/directory .

# Copy directory in the current working directory using the name, directory2
cp -r directory directory2
```

To copy file1 to file2 (new name):

```bash
cp [FILE_1] [FILE_2]
```

Copy folders:

```bash
cp -r [FOLDER_1] [FOLDER_2]
```

Use `cp` to copy files or directories from one place to another.

- `cp` creates NEW versions of the sources, so editing the copy won't affect the original (and vice versa).

**Note that it will overwrite the destination if it already exists.**

```bash
cp srcFile.txt clone.txt
```

or

```bash
cp -r srcDirectory/ dst/ # recursively copy
```

Copying can be down with paths

```bash
cp -r /path/to/dir_1 /path/to/dir_2
```

1.2.6. Moving & Renaming with `mv`#

# `mv` - move files/folders from one place to another.

- Both are performed with `mv`
- Follows the same notation as `cp`
- **Does not require the option, `-r` !!**

```bash
mv [source] [destination]
```
- `[source]` can be a file, folder, `/path/to/file`, or `/path/to/folder`
- `[destination]` can be `/path/to/file`, or `/path/to/folder` with `NewFileName` or `NewFolderName`

### Move/Rename Files and Folders

- Moving a file is straightforward; you can even rename it at the destination

```bash
# Move file.txt to the folder, destination, in /path/to, and rename it to newname.txt
mv file.txt /path/to/destination/newname.txt
```

- Same for folders

```bash
mv directory path/to/destination/newname
```

`mv` is similar to `cp`, but it deletes the source.
`mv` is also useful for renaming files!

```bash
mv source.txt new.txt
```

1.2.7. Deleting Files and/or Folders with `rm`#

# `rm` - delete files


```{caution}
This command is permanently delete your files / folders
No trash can to recover "accidental" events
```

- Use `rm` (Remove) to delete files/folders.

```bash
# Delete file1.txt
rm file1.txt
```

### Deleting Multiple Files

```bash
# Deleting 2 files named, file1.txt and file2.txt
rm file1.txt file2.txt
```

### Deleting Folders

- Like `cp`, you need the option `-r` to delete a folder
- `-f` can force delete

```bash
# Delete entire folder called directory/
rm -r directory/

# Force delete all contents with `-f`
rm -rf directory/
```

:::{code} bash
rm file.txt
:::

:::{code} bash
rm -r directory/
:::