03-filework.qmd

---
title: "Working with Files and Directories"
format: 
  revealjs:
    theme: _extensions/metropolis-theme/metropolis.scss
    chalkboard: true
    logo: /images/ScPo-logo.png
    footer: ScPo Intro To Programming 2023
    incremental: false
    code-line-numbers: false
    highlight-style: github
author: Florian Oswald and The Software Carpentry
---


## Intro

::: {.callout-note}

# Questions

- How can I create, copy, and delete files and directories?
- How can I edit files?

:::

::: {.callout-tip}

# Objectives

- Create a directory hierarchy that matches a given diagram.
- Create files in that hierarchy using an editor or by copying and renaming existing files.
- Delete, copy and move specified files and/or directories.

:::

---

## Creating Directories

* Let's create a directory `thesis` here:
```bash
$ cd ~/shell-lesson-data/exercise-data/writing
$ ls -F
```
this outputs:

```
haiku.txt  LittleWomen.txt
```

* Use `mkdir` to create:
```bash
$ mkdir thesis
```

used like this, `thesis` is created in the current directory. While with the `-p` flag we created nested subdirectories:

```bash
$ mkdir -p ../project/data ../project/results
```

---

## Good File Names


::: {.callout-warning}

# Bad File Names

1. Don't use spaces. `north pacific gyre` is not a good one. Use `north-pacific-gyre` instead.
2. Don't begin with `-`.
3. Stick with letters, numbers, `.`, `-`, and `_`

:::

---

## Creating a Text File

* Let's go into the `thesis` directory and create a text file called `draft.txt`.

```bash
$ cd thesis
$ nano draft.txt
```

::: {.callout-note}

# TEXT Editor

`nano` is a super simple editor, and you can use it *only* to edit text files (That's normal for *text editors* 😉). You will probably switch to a more powerful editor later on (I recommend `VSCode`), but `nano` is a good starting point.
Notice that `^` key is the `Ctrl` key, so `^X` means `Ctrl + X`.
:::


---

## Filename Extensions


### Task

1. Go to your home directory: `cd`
2. create an *empty* file with the `touch` command:

```bash
$ # this is a comment, by the way 
$ cd  # so, going home.
$ touch new_doc.pdf  # creating an empty file.
```

3. Open your file browser and double click on `new_doc.pdf`. What is going to happen?


---

* Ok, let's get rid of that file now.
* use the `rm` command (more later)
```bash
$ rm new_doc.pdf
```
* Caution: `rm` is forever gone.
* You can add `-i` *interactive* to be safe(r).


---

## Moving Files and Directories

* Let's go back to the `writing` directory
```bash
$ cd ~/shell-lesson-data/exercise-data/writing
```
* Let's *rename* `draft.txt` to `quotes.txt` with `mv`.
```bash
$ mv thesis/draft.txt thesis/quotes.txt
```
* Now let's actually *move* it into the current dir:
```bash
$ mv thesis/quotes.txt .
```
* Notice: `mv x y` means `x` is gone afterwards!

---

::: {.callout-caution}

# Challenge

Jamie placed `maltose.dat` and `sucrose.datfiles` in the `analyzed` folder by mistake. He wants to move those back to the `raw` folder now:

```bash
$ ls -F  
 analyzed/ raw/
$ ls -F analyzed
fructose.dat glucose.dat maltose.dat sucrose.dat
$ cd analyzed
```
What has to go in the blanks to achieve this?

```bash
$ mv sucrose.dat maltose.dat ____/____
```
:::

<details>
<summary>Show Solution</summary>

::: {.callout-note}
# Solution

```bash
$ mv sucrose.dat maltose.dat ../raw
```

:::
</details>


--- 

## Copying Files and Directories

* `cp x y` is similar to `mv x y`, but you keep `x`.
```bash
$ cp quotes.txt thesis/quotations.txt
$ ls quotes.txt thesis/quotations.txt
```

* the `-r` option means *recursively* and copies entire folders:
```bash
$ cp -r thesis thesis_backup
$ ls thesis thesis_backup
```

* Notice that `rm -r mydir` will delete everything inside the `mydir` folder!


---

## Using *Wildcards*

* the `*` character is a *wildcard*, i.e it matches all characters:
```bash
$ cd shell-lesson-data/exercise-data/
$ ls proteins/p*
proteins/pentane.pdb	proteins/propane.pdb
```


---

## Reproducing a Folder Structure

Suppose we want to create the following structure on our computer:

```bash
2016-05-20/
└── data
   ├── processed
   └── raw
```

::: {.callout-caution}
# Challenge

Which sequence will achieve this result?

```
1.
$ mkdir 2016-05-20
$ mkdir 2016-05-20/data
$ mkdir 2016-05-20/data/processed
$ mkdir 2016-05-20/data/raw
```

```
2.
$ mkdir 2016-05-20/data/raw
$ mkdir 2016-05-20/data/processed
```

```
3.
$ mkdir -p 2016-05-20/data/raw
$ mkdir -p 2016-05-20/data/processed
```

:::


---

## Nice Trick

* Oh by the way.
* If you are on MacOS, try to this on the command line

```bash
$ open .
```

* Pretty handy!

---

::: {.callout-tip}

- `cp [old] [new]` copies a file.
- `mkdir [path]` creates a new directory.
- `mv [old] [new]` moves (renames) a file or directory.
- `rm [path]` removes (deletes) a file.
- `*` matches zero or more characters in a filename, so `*.txt` matches all files ending in `.txt`.
- `?` matches any single character in a filename, so `?.txt` matches `a.txt` but not `any.txt`.
- Use of the Control key may be described in many ways, including `Ctrl-X`, `Control-X`, and `^X`.
- The shell does not have a trash bin: once something is deleted, it's really gone.
- Most files' names are `something.extension`. The extension isn't required, and doesn't guarantee anything, but is normally used to indicate the type of data in the file.
- Depending on the type of work you do, you may need a more powerful text editor than Nano.

:::