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class: title-slide
count: false

.title[
  # 05 - Terminal
]
.subtitle[
  ## Open Science Tools
]

.author[
  ### Claudio Zandonella &amp; Davide Massidda
]

.institute[

]

---
class: center, middle, inverse
# Step V: Terminal

---
# Terminal
--

&lt;img src="images/06-terminal/terminal-meme.jpeg" width="45%" style="display: block; margin: auto;" /&gt;

---
# Terminal

&lt;img src="images/06-terminal/terminal.png" width="60%" style="display: block; margin: auto;" /&gt;

--
.center[*“When the going gets tough the terminal gets opening”*]
---

# Terminal


.pull-left-60[
#### Definitions

.li-small[
{{content}}
]
]
.pull-right-40[

]

--

- **Command Line Interface (CLI)**&lt;br&gt;The text-based interface,&lt;br&gt;opposite of Graphical User Interface (GUI)
&lt;br&gt;

{{content}}
--

- **Terminal (or Console)**&lt;br&gt;The graphical window with a command-line interface&lt;br&gt;that allows us to interact with the shell
&lt;br&gt;

{{content}}
--

- **Shell**&lt;br&gt;The interpreter that processes the commands&lt;br&gt;and communicates with the Operating System


---

# Terminal


.pull-left-60[
#### Definitions

.li-small[
- **Command Line Interface (CLI)**&lt;br&gt;The text-based interface,&lt;br&gt;opposite of Graphical User Interface (GUI)

&lt;!-- --&gt;

- **Terminal (or Console)**&lt;br&gt;The graphical window with a command-line interface&lt;br&gt;that allows us to interact with the shell

&lt;!-- --&gt;

- **Shell**&lt;br&gt;The interpreter that processes the commands&lt;br&gt;and communicates with the Operating System

&lt;br&gt;

.center[*Programming Language vs Command Language*]
]
]
.pull-right-40[

{{content}}
]

--
#### Different Shells

---

# Terminal


.pull-left-60[
#### Definitions

.li-small[
- **Command Line Interface (CLI)**&lt;br&gt;The text-based interface,&lt;br&gt;opposite of Graphical User Interface (GUI)

&lt;!-- --&gt;

- **Terminal (or Console)**&lt;br&gt;The graphical window with a command-line interface&lt;br&gt;that allows us to interact with the shell

&lt;!-- --&gt;

- **Shell**&lt;br&gt;The interpreter that processes the commands&lt;br&gt;and communicates with the Operating System

&lt;br&gt;

.center[*Programming Language vs Command Language*]
]
]
.pull-right-40[

#### Different Shells

.move-down-30[
&lt;table class="table" style="width: auto !important; margin-left: auto; margin-right: auto;"&gt;
 &lt;thead&gt;
  &lt;tr&gt;
   &lt;th style="text-align:left;"&gt; Shell Interpreter &lt;/th&gt;
  &lt;/tr&gt;
 &lt;/thead&gt;
&lt;tbody&gt;
  &lt;tr grouplength="3"&gt;&lt;td colspan="1" style="border-bottom: 1px solid;"&gt;&lt;strong&gt;Windows&lt;/strong&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;
   &lt;td style="text-align:left;padding-left: 2em;" indentlevel="1"&gt; Command Prompt (CMD) &lt;/td&gt;
  &lt;/tr&gt;
  &lt;tr&gt;
   &lt;td style="text-align:left;padding-left: 2em;" indentlevel="1"&gt; PowerShell &lt;/td&gt;
  &lt;/tr&gt;
  &lt;tr&gt;
   &lt;td style="text-align:left;padding-left: 2em;" indentlevel="1"&gt; ... &lt;/td&gt;
  &lt;/tr&gt;
  &lt;tr grouplength="4"&gt;&lt;td colspan="1" style="border-bottom: 1px solid;"&gt;&lt;strong&gt;Unix System (macOS and Linux)&lt;/strong&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;
   &lt;td style="text-align:left;padding-left: 2em;" indentlevel="1"&gt; sh (Bourne shell) &lt;/td&gt;
  &lt;/tr&gt;
  &lt;tr&gt;
   &lt;td style="text-align:left;padding-left: 2em;" indentlevel="1"&gt; Bash (Bourne again shell) &lt;/td&gt;
  &lt;/tr&gt;
  &lt;tr&gt;
   &lt;td style="text-align:left;padding-left: 2em;" indentlevel="1"&gt; Zsh (Z shell) &lt;/td&gt;
  &lt;/tr&gt;
  &lt;tr&gt;
   &lt;td style="text-align:left;padding-left: 2em;" indentlevel="1"&gt; ... &lt;/td&gt;
  &lt;/tr&gt;
&lt;/tbody&gt;
&lt;/table&gt;


]
]

---
# Get Started

--

.pull-left-40[

#### Prompt

&lt;img src="images/06-terminal/terminal.png" width="99%" style="display: block; margin: auto;" /&gt;

.code-size-12[
```bash
HOST_NAME:CURRENT_DIRECTORY USER_NAME$
```
]
]
.pull-right-60[

]
---
# Get Started

.pull-left-40[

#### Prompt

&lt;img src="images/06-terminal/terminal.png" width="99%" style="display: block; margin: auto;" /&gt;

.code-size-12[
```bash
HOST_NAME:CURRENT_DIRECTORY USER_NAME$
```
]
]
.pull-right-60[
#### Commands

.code-size-12[
```bash
Command [Options] Argument1 Argument2 ...

# Examples
ls -la ~/Desktop/my-project
cp -r ~/Desktop/my-project/ ~/Document/my-project/
```
]

.li-size-14[
.font-14[
- `Command` function name
- `Options` obtain command specific behaviour
  - square brackets `[...]` indicate optional elements
  - single letters `-&lt;letter/s&gt;` (e.g., `-l`, `-a`, `-la`) 
  - Full word `--&lt;option-name&gt;` (e.g., `--all`)
- `Argument*`, separated by space (need to wrap words!)
]
]
]
---
# Get Started

.pull-left-40[

#### Prompt

&lt;img src="images/06-terminal/terminal.png" width="99%" style="display: block; margin: auto;" /&gt;

.code-size-12[
```bash
HOST_NAME:CURRENT_DIRECTORY USER_NAME$
```
]
]
.pull-right-60[
#### Commands

.code-size-12[
```bash
Command [Options] Argument1 Argument2 ...

# Examples
ls -la ~/Desktop/my-project
cp -r ~/Desktop/my-project/ ~/Document/my-project/
```
]

.li-size-14[
.font-14[
- `Command` function name
- `Options` obtain command specific behaviour
  - square brackets `[...]` indicate optional elements
  - single letters `-&lt;letter/s&gt;` (e.g., `-l`, `-a`, `-la`) 
  - Full word `--&lt;option-name&gt;` (e.g., `--all`)
- `Argument*`, separated by space (need to wrap words!)
]
]

.code-size-12[
```bash
Software Command [Options] Argument1 Argument2 ...

# Example
git push -u origin main
docker build -t my-image:1.0.0 Desktop/my-project
```
]
]

---
# Get Started

.pull-left-40[
#### Navigating Directories
]
.pull-right-60[

]
---
# Get Started

.pull-left-40[
#### Navigating Directories

.li-small[
- `pwd` print working directory
]

]
.pull-right-60[
#### &amp;nbsp;

.code-size-12[
```bash
$ pwd
/Users/myname
```
]
]

---
# Get Started

.pull-left-40[
#### Navigating Directories

.li-small[
- `pwd` print working directory
- `ls` list directory contents
  - `-l` long listing format
  - `-a` list all files (also hidden)
]
]
.pull-right-60[

#### &amp;nbsp;

.move-down-60[
.code-size-12[
```bash
$ ls
Applications               Documents                 Library
Desktop                    Downloads  
```

```bash
$ ls -l Desktop/
drwxr-xr-x@ 17 claudio  staff    23544 Dec 17 17:09 Courses
drwxr-xr-x@ 17 claudio  staff    14590 Dec 17 17:09 Presentations
-rw-r--r--   1 claudio  staff     5928 Feb  3 14:41 Repot.pdf
-rw-r--r--@  1 claudio  staff      160 Jan 18 11:10 TODO-list.txt
```
]
]
]

---
# Get Started

.pull-left-40[
#### Navigating Directories

.li-small[
- `pwd` print working directory
- `ls` list directory contents
  - `-l` long listing format
  - `-a` list all files (also hidden)
- `cd &lt;directory&gt;`&lt;br&gt;change directory
]
]
.pull-right-60[
#### &amp;nbsp;

.move-down-170[
.code-size-12[
```bash
$ cd Desktop/Courses/Open-Science
$ pwd 
/Users/myname/Desktop/Courses/Open-Science
```

```bash
$ cd ../../
$ pwd 
/Users/myname/Desktop
```
]
]
]

---
# Get Started

.pull-left-40[
#### Navigating Directories

.li-small[
- `pwd` print working directory
- `ls` list directory contents
  - `-l` long listing format
  - `-a` list all files (also hidden)
- `cd &lt;directory&gt;`&lt;br&gt;change directory
]

#### Extra

.li-small[
- `Tab` autocomplete / list options
- `up/down keys` navigate history
]
]
.pull-right-60[]

---

# Get Started

.pull-left-40[
#### Modifying Files
]
.pull-right-60[]

---
# Get Started

.pull-left-40[
#### Modifying Files

.li-small[
- `mkdir &lt;dir-name&gt;`&lt;br&gt;Make directory
]
]
.pull-right-60[
#### &amp;nbsp;

.code-size-12[
```bash
$ mkdir my-project
$ cd my-project 
$ pwd
/Users/myname/my-project
```
]
]

---
# Get Started

.pull-left-40[
#### Modifying Files

.li-small[
- `mkdir &lt;dir-name&gt;`&lt;br&gt;Make directory
- `touch &lt;file-name&gt;`&lt;br&gt;Create a blank file
]
]

.pull-right-60[
#### &amp;nbsp;

.move-down-80[
.code-size-12[
```bash
$ touch README
$ ls
README
```
]
]
]
---
# Get Started

.pull-left-40[
#### Modifying Files

.li-small[
- `mkdir &lt;dir-name&gt;`&lt;br&gt;Make directory
- `touch &lt;file-name&gt;`&lt;br&gt;Create a blank file
- `cat &lt;file&gt;`&lt;br&gt;Print content on screen
- `less &lt;file&gt;`&lt;br&gt;Visualize content on screen
]
]

.pull-right-60[
#### &amp;nbsp;

.move-down-140[
.code-size-12[
```bash
$ cat README
$
```
]
]
]
---
# Get Started

.pull-left-40[
#### Modifying Files

.li-small[
- `mkdir &lt;dir-name&gt;`&lt;br&gt;Make directory
- `touch &lt;file-name&gt;`&lt;br&gt;Create a blank file
- `cat &lt;file&gt;`&lt;br&gt;Print content on screen
- `less &lt;file&gt;`&lt;br&gt;Visualize content on screen
- `echo &lt;text&gt;`&lt;br&gt;Print text on screen
]
]

.pull-right-60[
#### &amp;nbsp;

.move-down-270[
.code-size-12[
```bash
$ echo "Hello World!"
Hello World!
```
]
]
]
---
# Get Started

.pull-left-40[
#### Modifying Files

.li-small[
- `mkdir &lt;dir-name&gt;`&lt;br&gt;Make directory
- `touch &lt;file-name&gt;`&lt;br&gt;Create a blank file
- `cat &lt;file&gt;`&lt;br&gt;Print content on screen
- `less &lt;file&gt;`&lt;br&gt;Visualize content on screen
- `echo &lt;text&gt;`&lt;br&gt;Print text on screen
]

#### Extra

.li-small[
- `&gt;` overwrites a file
- `&gt;&gt;` appends to a file 
]
]

.pull-right-60[
#### &amp;nbsp;

.move-down-270[
.code-size-12[
```bash
$ echo "Hello World!"
Hello World!
$ echo "Hello World!" &gt;&gt; README
```

```bash
$ cat README
Hello World!
```
]
]
]

---
# Get Started

.pull-left-40[

#### Modifying Files

.li-small[
- `mkdir &lt;dir-name&gt;`&lt;br&gt;Make directory
- `touch &lt;file-name&gt;`&lt;br&gt;Create a blank file
- `cat &lt;file&gt;`&lt;br&gt;Print content on screen
- `less &lt;file&gt;`&lt;br&gt;Visualize content on screen
- `echo &lt;text&gt;`&lt;br&gt;Print text on screen
]

#### Extra

.li-small[
- `&gt;` overwrites a file
- `&gt;&gt;` appends to a file 
]
]

.pull-right-60[
#### &amp;nbsp;

.li-small[
- `mv &lt;file&gt; &lt;to&gt;`&lt;br&gt;Move file
]

.code-size-12[
```bash
$ mv ../Report.pdf .
$ ls
README                Report.pdf
```
]
]

---
# Get Started

.pull-left-40[

#### Modifying Files

.li-small[
- `mkdir &lt;dir-name&gt;`&lt;br&gt;Make directory
- `touch &lt;file-name&gt;`&lt;br&gt;Create a blank file
- `cat &lt;file&gt;`&lt;br&gt;Print content on screen
- `less &lt;file&gt;`&lt;br&gt;Visualize content on screen
- `echo &lt;text&gt;`&lt;br&gt;Print text on screen
]

#### Extra

.li-small[
- `&gt;` overwrites a file
- `&gt;&gt;` appends to a file 
]
]

.pull-right-60[
#### &amp;nbsp;

.li-small[
- `mv &lt;file&gt; &lt;to&gt;`&lt;br&gt;Move file
- `cp &lt;file&gt; &lt;to&gt;`&lt;br&gt;Copy file
  - `-r` recursive for directories
]

.code-size-12[
```bash
$ cp Report.pdf Report-copy.pdf
$ ls
README                Report-copy.pdf          Report.pdf
```
]
]
---
# Get Started

.pull-left-40[

#### Modifying Files

.li-small[
- `mkdir &lt;dir-name&gt;`&lt;br&gt;Make directory
- `touch &lt;file-name&gt;`&lt;br&gt;Create a blank file
- `cat &lt;file&gt;`&lt;br&gt;Print content on screen
- `less &lt;file&gt;`&lt;br&gt;Visualize content on screen
- `echo &lt;text&gt;`&lt;br&gt;Print text on screen
]

#### Extra

.li-small[
- `&gt;` overwrites a file
- `&gt;&gt;` appends to a file 
]
]

.pull-right-60[
#### &amp;nbsp;

.li-small[
- `mv &lt;file&gt; &lt;to&gt;`&lt;br&gt;Move file
- `cp &lt;file&gt; &lt;to&gt;`&lt;br&gt;Copy file
  - `-r` recursive for directories
- `rm &lt;file&gt;`&lt;br&gt;Remove file
  - `-r` recursive for directories
]

.code-size-12[
```bash
$ rm Report-copy.pdf
$ ls
README                Report.pdf
```
]
]
---
# Get Started

.pull-left-40[

#### Modifying Files

.li-small[
- `mkdir &lt;dir-name&gt;`&lt;br&gt;Make directory
- `touch &lt;file-name&gt;`&lt;br&gt;Create a blank file
- `cat &lt;file&gt;`&lt;br&gt;Print content on screen
- `less &lt;file&gt;`&lt;br&gt;Visualize content on screen
- `echo &lt;text&gt;`&lt;br&gt;Print text on screen
]

#### Extra

.li-small[
- `&gt;` overwrites a file
- `&gt;&gt;` appends to a file 
]
]

.pull-right-60[
#### &amp;nbsp;

.li-small[
- `mv &lt;file&gt; &lt;to&gt;`&lt;br&gt;Move file
- `cp &lt;file&gt; &lt;to&gt;`&lt;br&gt;Copy file
  - `-r` recursive for directories
- `rm &lt;file&gt;`&lt;br&gt;Remove file
  - `-r` recursive for directories
]

.move-down-120[
.li-small[
- `Ctrl + Shift + C` (or `Control + C` on macOS) interrupt the command
]
]
]
---
# Terminal in RStudio
--
 
.pull-left-50[
.move-up-30[
Open a new Terminal window
]

&lt;img src="images/06-terminal/new-terminal.png" width="65%" style="display: block; margin: auto;" /&gt;

&lt;img src="images/06-terminal/terminal-panel.png" width="65%" style="display: block; margin: auto;" /&gt;

]
.pull-right-50[
.move-up-30[
{{content}}
]
]

--
Select the default shell

&lt;img src="images/06-terminal/terminal-settings.png" width="90%" style="display: block; margin: auto;" /&gt;

---
class: inverse, center, middle

# With great power comes great responsibility!!

## Moving to the next step...
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