Programming Tools in Data Science

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.title[
# Programming Tools in Data Science
]
.subtitle[
## Lecture #3: GitHub
]
.author[
### Samuel Orso
]
.date[
### 26 September 2024
]

---

# GitHub
<img src="images/github.png" width="950" height="450" style="display: block; margin: auto;" />

---
# Motivation

* When working on a project, there are usually different people working on the same file/folder
* You want to avoid sending each modification by email
* You could use dropbox/google drive and the likes but it is good practice to keep track of modifications and have a platform to plan and discuss changes

---
# Motivation

GitHub allows you:
- record the entire history of a file;
- revert to a specific version of the file;
- collaborate on the same platform with other people;
- make changes without modifying the main file and add them once you feel comfortable with them.

---
# Motivation

GitHub will be used for:
- work in group on projects and homeworks;
- submit projects/homeworks;
- develop R packages and website;
- ...

---
# Ready ?
<center>
<iframe src="https://giphy.com/embed/h4TdHo3RExSbHd9bOe" width="480" height="425" frameBorder="0" class="giphy-embed" allowFullScreen></iframe><p><a href="https://giphy.com/gifs/cbc-schitts-creek-h4TdHo3RExSbHd9bOe">via GIPHY</a></p>
</center>

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# In fact, what is Git?
<img src="images/git.png" style="width:150px; position:absolute; top:9%; left:40%" />

Git is a **distributed version control system**.

* **distributed**: whenever you instruct Git to share files, Git does not only share the latest file version, but instead, it distributes **every version** it has recorded for that project.

* **version control system**: many people are used to have *their own version control system* e.g. by having different versions of the same file (`file_v1.R`, `file_v2.R`, ...). This approach is error-prone and ineffective when working in team project. Thus, a version control system keeps track of changes to modification in your project.

---
# Types of VCS
There are three types of version control system (VCS):
* local
* centralized
* distributed

---
# Types of VCS
## Local

.pull-left[
<img src="images/local_vcs.jpg" width="451" height="300" style="display: block; margin: auto;" />
]

.pull-right[
* One of the simplest and most commonly used VCS
* It keeps patch sets (modification of a file) locally (on your computer)
* It can recreate the file at any point in time by adding up the patches
]

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# Types of VCS
## Centralized

.pull-left[
<img src="images/centralized_vcs.png" width="490" height="317" style="display: block; margin: auto;" />
]

.pull-right[
* A single server contains all the versioned files
* Risk of failure
* Risk of database corruption
]

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# Types of VCS
## Distributed
.pull-left[
<img src="images/dst_vcs.jpg" width="460" height="416" style="display: block; margin: auto;" />
]

.pull-right[
* Store the entire history of files locally
* Sync local changes back to server
* Allow multiple users and minimize risks of centralized VCS
]

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# Benefits of VCS
* Allow multiple users to collaborate and communicate while working on a project.
* Keep tracks of the change history of the files (risk mitigation) with possibility to roll back to previous version.
* Different workflows such as branching and merging (not discussed)

---
# So Git and GitHub are the same things?
<center>
<iframe src="https://giphy.com/embed/3o6YglDndxKdCNw7q8" width="480" height="478" frameBorder="0" class="giphy-embed" allowFullScreen></iframe><p><a href="https://giphy.com/gifs/nba-basketball-chicago-bulls-3o6YglDndxKdCNw7q8">via GIPHY</a></p>
</center>

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# Git vs GitHub
Git is a distributed VCS, so what is GitHub exactly?

* Git is a software...
* ...and GitHub is web-based plateform for software development and version control that uses Git.
* GitHub hosts and shares Git repository.
* GitHub is not the only service provider

---
#BitBucket
<img src="images/bitbucket.png" width="2525" style="display: block; margin: auto;" />

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#GitLab
<img src="images/gitlab.png" width="2476" style="display: block; margin: auto;" />

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#SourceForge
<img src="images/sourceforge.png" width="2511" style="display: block; margin: auto;" />

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# Okay to continue ?

.center[
<iframe src="https://giphy.com/embed/sG4PBWRjI4GSVCDXEq" width="480" height="480" frameBorder="0" class="giphy-embed" allowFullScreen></iframe><p><a href="https://giphy.com/gifs/nickelodeon-drama-club-sG4PBWRjI4GSVCDXEq">via GIPHY</a></p>
]

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# Files states in Git
A file can have different states: **untracked**, **modified**, **staged** or **committed**

* **untracked**: a new file that is not tracked by Git (yet);
* **modified**: a tracked file which is modified but not recorded (not committed yet);
* **staged**: a tracked file which is modified and that has been selected to be saved (committed) into the repository during the next commit snapshot;
* **committed**: a file that is successfully recorded into the (local) repository.

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# Files states in Git
<img src="images/git-basic-workflow-codesweetly.png" width="2560" style="display: block; margin: auto;" />

---
# you can also `.gitignore`
* Some files or folders of your project can be excluded from version control by specifying `.gitignore`
* These files or folders will not be shared to other users

---
# GitHub
## Basic workflow

The basic workflow is as follows...

1. Open the RStudio Project connected to your Git(Hub) Repo
2. Work on your computer just like always
3. **Save** your work often just like always
4. When you want to preserve a **snapshot** of your project, you make a "commit"
5. When you have a few commits and want to archive them, you "push" them to the GitHub remote server
6. If you decide to work from a different computer, or want to pick up where a collaborator left off, you can "pull" the most up-to-date version of the files from the GitHub remote to your local computer and go back to step 2.

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# Demo on RStudio

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# GitHub
## New habits
* When you want to preserve a **snapshot** of your project, you make a "commit."
* When you have a few commits and want to archive them, you "push" them to the GitHub remote server.
* If you decide to work from a different computer, or want to pick up where a collaborator left off, you can "pull" the most up-to-date version of the files from the GitHub remote to your local computer.

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# GitHub
## Commits
Make your commit message as informative and concise as possible.

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# GitHub
## "pull" before you "push"
Make sure you have the up-to-date version of your project before working on it.

Try to avoid the headaches of "merge conflict".

.center[
<iframe src="https://giphy.com/embed/cFkiFMDg3iFoI" width="480" height="269" frameBorder="0" class="giphy-embed" allowFullScreen></iframe><p><a href="https://giphy.com/gifs/git-merge-cFkiFMDg3iFoI">via GIPHY</a></p>
]

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# GitHub
## Common mistakes (and how to solve them)

* **Commits in the wrong Repo**. Nothing seems to work? It's a common mistake. Solution: make sure you work on the correct RStudio project that is correctly linked to GitHub.

* **Large files error**. GitHub blocks pushes that exceed 100 MB. Solution: find another solution for large files (Dropbox, ...)

* **Conflict (not merge)**. Conflicts may happen when two collaborators make different changes to part of a program at the same time but on different lines of code. One of them push the modification to the remote. The second one to push will have a conflict as his/her version of the project is "outdated". Solution: `git pull --rebase`

* **Merge conflict**. It happens when two collaborators work on the same lines of code at the same time. It is often a problem of miscommunication within groups and lack of organization. Solution: To resolve these conflicts, we must directly edit the documents making sure potential conflicts are discussed before pushing.

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# GitHub

> git gets easier once you get the basic idea that branches are homeomorphic endofunctors mapping submanifolds of a Hilbert space.
> <cite> Isaac Wolkerstorfer </cite>

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# Question ?

.pull-down[
<a href="https://ptds.samorso.ch/">
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</a>
]