05-git.qmd

---
title: "Version Control with `Git`"
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
---

## Version What?


::::: {.callout-note}
# Question

* What is Version Control and Why Should I Care?
:::::

::::: {.callout-tip}
# Objectives
- Understand the benefits of an automated version control system.
- Understand the basics of how automated version control systems work.
::::::

---

## Final.doc  

!["Piled Higher and Deeper" by Jorge Cham, http://www.phdcomics.com](/images/phd101212s.png)



---

## Undo

* The *latest version* is often best for text documents. 
* However, sometimes our view of *best* evolves. Then, we want to *undo*.
* *Undo* means going back in history.

. . .

* MS Word etc have *track changes* features.
* Once you accepted the proposed changes of a collaborator, can you go back?
* What about Dropbox-like solutions? (What *is* dropbox actually?)

---

## Which Version: 20210611_draft.tex

:::: {.columns}

::: {.column width="50%"}

* Hey, fixed that thing last week.
* In `20220629-paper.tex`?
* Erm. Yes. No. I think `20211203-paper.tex` - messed up the file name.
* Ok, can you copy it into the latest version?
* Sure. Damn, can't find it anymore. I'll just write it again. All in my head.  🤯
:::

::: {.column width="40%"}
!["True Story" by Florian Oswald](/images/which-version.png)
:::

::::


---

## Which Version 2: **Why is the sample size so small suddenly**?


::::: {.columns}

:::: {.column width="40%"}

* We had 800 observations, now 733. Why?
* Erm...😱 No clue!
* Well you must have changed the code.
* Yes, I *improved* the code in several parts.
* Well you have to find out what happened.
* But that was weeks ago - I don't remember! 😢
::::
:::: {.column width="50%"}


### Hard Bugs

* The hard bugs 🐛 are the ones you see only after a while.
* See result today, error was introduced long ago.
* You can rewind dropbox 30 days. What if... ?
* Also, throw away 30 days of work?
* 😱 😱 😱 😱 

::::
:::::


---

## {background-image="./images/removed-that.png" background-size=100%}



---


## Setting Up Git

* We all installed `git`. 
* Let's setup our name

```bash
$ git config --global user.name "Your Name"
$ git config --global user.email "your@mail.com"
```

* Line Endings on Windows:

```bash
git config --global core.autocrlf false
```

---


## Creating a Git **Repository**


::::: {.callout-note}
# Question

* Where does Git store information?

:::::

::::: {.callout-tip}
# Objectives
- Create a local repository
- Describe purpose of `.git` directory
::::::


---

## Gas Prices Project

* Let's create a project folder in our home to look at the gas prices from last week.

```bash
$ cd    # going to home dir 
$ mkdir gasprices  # create directory
$ cd gasprices 
$ git init
```

* Now the directory `~/gasprices` is endowed with `git` version control. 
* What does that look like?


---

## Where is Git?

* Remember *hidden files* and folders?

```bash
$ ls -a 
./    ../   .git/
```

* Git for this repository resides in `.git`

::: {.callout-warning}

# Danger Zone

* If you _delete_ that folder, the entire version control is GONE. 
* Be very careful that you really want to do that.

:::


---


## Tracking Changes with Git



::::: {.callout-note}
# Question

* How do I record changes in Git?
* How do I check the status of my version control repository?
* How do I record notes about what changes I made and why?
:::::

::::: {.callout-tip}
# Objectives
- Understand the benefits of an automated version control system.
- Understand the basics of how automated version control systems work.
::::::




---

## Adding Code and Text

::: {.callout-note}

* Notice: The code we produce **is** text.
* Remember what we learned about **file endings**.

:::

* Let's add a shell script where we add our pipeline from last week.

1. run to get the raw data again:
```bash
wget https://www.data.gouv.fr/fr/datasets/r/64e02cff-9e53-4cb2-adfd-5fcc88b2dc09 -O ~/gasprices/carburants.csv
```

---

## Adding Code and Text


2. create a script

```bash
nano maketable.sh  # open nano
# type this:
cd ~/gasprices   # make sure we are in the right place
cut -d ';' -f 5 carburants.csv | tr [:lower:] [:upper:] | sort | uniq -c | sort
# save and exit 
```

3. (Does it work?)
```bash
ls .  # check the new file is there
./maketable.sh   # run it!
```

. . .

4. No, it doesn't. 😖
```bash
chmod +x ./maketable.sh  # add executable mode
ls -a
./maketable.sh
```



---

## Viewing Changes

* Ok, now let's see what `git` makes of our additions to this directory.

```tcl
floswald@PTL11077 ~/gasprices (main)> git status
On branch main

No commits yet

Untracked files:
  (use "git add <file>..." to include in what will be committed)
        carburants.csv
        maketable.sh
```

* It is actually helpful **not** to use `bash` as a shell...
* Customizing your shell is an extremely effective procrastination device.
* You must know what [*shaving a Yak*](https://projects.csail.mit.edu/gsb/old-archive/gsb-archive/gsb2000-02-11.html) means before you walk out of my class.


---

## Seeing the Difference

* the command `git diff` shows you what changed between versions.
* lets see what it shows now:

```bash
$ git diff
```

* It shows nothing, i.e. an _empty_ diff, because _there are no commits yet_ to compare with.
* Ok, let's change that.


---

## Modify-Add-Commit 1

* git reports about _untracked files_. We need to decide *what to track*.

1. Move files to *staging area*:
```bash
git add maketable.sh 
git status
```

* Notice that I did *not* want to track the `csv` file.

```bash
On branch main

No commits yet

Changes to be committed:
  (use "git rm --cached <file>..." to unstage)
        new file:   maketable.sh

Untracked files:
  (use "git add <file>..." to include in what will be committed)
        carburants.csv
```


---

## Modify-Add-Commit 2

* Now, let's *record* what is in the staging area. 

```bash
$ git commit -m 'added the maketable script'

[main (root-commit) 9956506] added the maketable script
 1 file changed, 2 insertions(+)
 create mode 100644 maketable.sh
```

* check status:

```bash
$ git status

On branch main
Untracked files:
  (use "git add <file>..." to include in what will be committed)
        carburants.csv

nothing added to commit but untracked files present (use "git add" to track)
➜  gasprices git:(main) ✗ 
```

---

## Modify-Add-Commit 3

* Let's check what's in the log.

```bash
$ git log 

commit 9956506dc3159403b87aea3b04654c293e82c680 (HEAD -> main)
Author: Florian Oswald <florian.oswald@gmail.com>
Date:   Tue Feb 7 10:50:51 2023 +0100

    added the maketable script
```

---

## Modify-Add-Commit 4

* Now let's _modify_ the script finally.

```bash
$ nano maketable.sh

# add this line on top 
echo hello user, will make a contigency table now.
# save and exit
```

* now - what's the difference in the repo?

---

## Diffing

* there are still the same files here:

```bash
$ ls 
carburants.csv  maketable.sh
```

* But we can now _compare_ versions:

```bash
$ git diff 

diff --git a/maketable.sh b/maketable.sh
index 7e01058..3b7007e 100644
--- a/maketable.sh
+++ b/maketable.sh
@@ -1,2 +1,3 @@
+echo hello user, will make a contigency table now.
 cd ~/gasprices   # make sure we are in the right place
 cut -d ';' -f 5 carburants.csv | tr [:lower:] [:upper:] | sort | uniq -c | sort
```


---

## Commiting Changes Again

* let's first check everything runs

```bash
$ ./maketable.sh
```

* good. commit!
```bash
$ git add maketable.sh 
$ git commit -m 'added message to user'
```


---

## Adding a README

* Good. Now let's add a `README` file.
* It's customary to write this in [markdown](https://carpentries-incubator.github.io/markdown-intro/)

```bash
$ nano README.md 
```
write this in nano and save when done.

```md
# Gas Prices

This repo contains code to analyse gas prices at French gas stations.
```

* add to staging area, so we can take a snapshot

```bash
$ git add README.md 
$ git commit -m 'added readme'
```

---

## What is this Staging Area

* git is like a foto camera.
* before you take a picture of your friends, you need to arrange them somehow, so that all fit, and all 😁.
* You put them _on stage_. Same for files in your repo.

![figure from [software carpentry]()](/images/git-staging-area.svg)


---

## Looking at History




::::: {.callout-note}
# Question
* How can I identify old versions of files?
* How do I review my changes?
* How can I recover old versions of files?

:::::

::::: {.callout-tip}
# Objectives


* Explain what the HEAD of a repository is and how to use it.
* Identify and use Git commit numbers.
* Compare various versions of tracked files.
* Restore old versions of files.
::::::


---

## The most recent version: HEAD

* Let's change the `maketable.sh` script again:
```bash
$ nano maketable.sh
echo program run successfully
# save exit

$ git add maketable.sh 
```

* The most recent version of our repo is called `HEAD`.
```bash
$ git diff # compares entire repo to HEAD 
$ git diff HEAD maketable.sh  
```

---

## Whoops, typo

* Oh no, we wrote _program run successfully_. That should be _ran_ not _run_. 
* What now?

 . . .

* we have not committed this yet! 
* we can just get back the version in HEAD, and edit again:

```bash
$ git restore maketable.sh
$ git checkout maketable.sh # also works
```

* edit the script, add and commit.

---

## How to get a *specific* version

* What if you want something else than `HEAD`?
* like, the first version of `maketable.sh`?
* look at history:

```bash
$ git log --oneline --graph

* a6f023b (HEAD -> main) added readme
* 9956506 added the maketable script
```

* The `9956506` is the unique identifier of that version.
* We can go back to that version:

```bash
$ git checkout 9956506 maketable.sh 
```


---


::: {.callout-tip}

# Key Points

* `git diff` displays differences between commits.
* `git checkout` recovers old versions of files.
:::

---

## So, how does this thing work?

![software carpentry image.](/images/git_staging.svg)


---

## Version Control with VScode

* Download [Visual Studio Code](https://code.visualstudio.com/)
* Start
* Open folder `~/gasprices`
* check version control tab on the left.



---

## Version Control with RStudio

* top right click on *new project*
* Select *existing directory*
* Select `~/gasprices`
* checkout out the `git` tab in Rstudio!


---

## Collaborating with Git on GitHub

* Create repo
* copy ssh remote URL
* connect local to remote repo

---

## SSH connections

* Secure Shell Protocol
* Private-Public key pair. It's like a lock, and you have the only key.
* Let's check if you have one already!

```bash
ls -la ~/.ssh 
```
 
if error, create one:

```bash
ssh-keygen -t ed25519 -C "your@email.com"
```
press enter (no passphrase)

check
```bash
ls -la ~/.ssh 
```

---

## Communicate with GitHub Remote

* Let's ping the remote server at GitHub now.

```bash
ssh -T git@github.com
```

* right, of course Github doesn't have our public key yet (the _lock_ for our key!)

* copy from your terminal
```bash
cat ~/.ssh/id_ed25519.pub  # or your *.pub 
```

* Go to github.com, click top right corner, settings, SSH keys.


---

## Adding a Remote to your local Repo

* Now that we can talk to Github.com, let's add the remote to our local repo.
* We `add` a remote by getting the `SSH` url from the repository (green button) online.

```bash
$ git remote add origin git@github.com:YOUR_USER/YOUR_REPO.git
```
* `origin` is the _name_ of the remote server. your choice, but _origin_ is common.
* this should set that remote both for sending and retrieving stuff from the repo. _pull_ and _push_, in git language:

```bash
$ git remote --v
```



---

## Pushing It

* Now we can _push_ our local repository to the remote repo.
* There will be a full copy of what is in `.git` (i.e., the entire history of the repo) on that remote machine.
* You will be able to use it like a central backup location for your work.


```bash
$ git push -u origin main
```

* the `-u` flag sets the _main_ branch as default _upstream_ branch to track.


---

## Branching It

* Next to different _versions_ of a file/directory _over time_, we can have versions evolving in parallel.
* Imagine development history _branching_ off into 2 separate directions at one point.
* They may converge at some point again, but maybe one of them will turn out a failure and we drop it.
* Branches are hugely useful to organize team work.

```bash
$ git checkout -b testing # checkout repo on new branch `testing`
Switched to a new branch 'testing'
```

* Now can develop stuff on the `testing` branch.
* Later on, we can `merge` it back into `main` if we like it.


---

## The Full Picture(s)

![picture from [@MarkLodato](https://marklodato.github.io/visual-git-guide/index-en.html) - click for more!](/images/git-images/full.png)


---

## Pushing Branches to GitHub

* Once you created a local branch you can of course copy (_push_) it to your remote to share with others.
* you would amend the push command:

```bash
# make sure you are on the desired branch 
$ git branch 
  main
* testing

$ git push origin testing
```