07-git.knit

class: title-slide
count: false

.title[
  # 07 - Git
]
.subtitle[
  ## Open Science Tools
]

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

.institute[

]

---
class: center, middle, inverse
# Step VI: Versioning

---
# Versioning

--
.pull-left-50[

- Keep everything in order
- Collaborating
]
.pull-right-50[
.move-up-70[
{{content}}
]
]
--
<img src="images/07-git/final-doc.jpeg" width="85%" style="display: block; margin: auto;" />

---
# Versioning

.pull-left-50[

- Keep everything in order
- Collaborating

.center[
### No problem, there is a solution
]

]
.pull-right-50[
.move-up-70[
<img src="images/07-git/final-doc.jpeg" width="85%" style="display: block; margin: auto;" />
]
]

---
# Git Nice Fact 🐧

.pull-left-50[
<div style = 'margin-top: -10pt;'>
<img src="images/07-git/linus.jpeg" width="60%" style="display: block; margin: auto;" />
</div>
]
.pull-right-50[

]

---
# Git Nice Fact 🐧

.pull-left-50[

]
.pull-right-50[

]
--

---
# Git Concepts

--
.pull-left-30[

- Tracking files
- Managing collaboration
- Branching

]
.pull-right-70[
]

---
# Git Concepts

.pull-left-30[

- Tracking files
- .alpha[Managing collaboration]
- .alpha[Branching]

]
.pull-right-70[

.move-down-80[
.li-small[
- Track all changes to files
- Detailed history and traceability 
- Check earlier versions 
- Restore previous version
]
]
]

---
# Git Concepts

.pull-left-30[

- Tracking files
- .alpha[Managing collaboration]
- .alpha[Branching]

]
.pull-right-70[
<img src="images/07-git/local-work-1.png" width="100%" style="display: block; margin: auto;" />

.width-30[
{{content}}
]
]

---
# Git Concepts

.pull-left-30[

- Tracking files
- .alpha[Managing collaboration]
- .alpha[Branching]

]
.pull-right-70[
<img src="images/07-git/local-work-1.png" width="100%" style="display: block; margin: auto;" />

---
# Git Concepts

.pull-left-30[

- Tracking files
- .alpha[Managing collaboration]
- .alpha[Branching]

]
.pull-right-70[
.move-up-70[
<img src="images/07-git/history.png" width="100%" style="display: block; margin: auto;" />
]

.li-small[
{{content}}
]
]

--
- Commits are identified by unique `SHA-1 hash ID`
- `master` (or `main`) default branch 
  - It is a *pointer* (reference) to a commit
- `HEAD` the current commit we are viewing

---
# Git Concepts

.pull-left-30[

- Tracking files
- .alpha[Managing collaboration]
- .alpha[Branching]

]
.pull-right-70[
.move-up-70[
<img src="images/07-git/history.png" width="100%" style="display: block; margin: auto;" />

.center[`checkout`]

<img src="images/07-git/checkout.png" width="100%" style="display: block; margin: auto;" />
]

.center[
{{content}}
]
]
--

### We have a time machine!

---
# Git Concepts

.pull-left-30[

- Tracking files
- .alpha[Managing collaboration]
- .alpha[Branching]

]
.pull-right-70[
<img src="images/07-git/local-work-2.png" width="100%" style="display: block; margin: auto;" />
]

---
# Git Concepts

.pull-left-30[

- .alpha[Tracking files]
- Managing collaboration
- .alpha[Branching]

]
.pull-right-70[
 
.move-down-80[
.li-small[
{{content}}
]
]
]

- Multiple colleagues
- Work independently 
- Avoiding conflicts

---
# Git Concepts

.pull-left-30[

- .alpha[Tracking files]
- Managing collaboration
- .alpha[Branching]

]
.pull-right-70[
.move-up-70[
<img src="images/07-git/collaborate.png" width="90%" style="display: block; margin: auto;" />
]

.move-up-15[
.li-small[
{{content}}
]
]
]

- Always pull first
- Solve conflicts

---
# Git Concepts

.pull-left-30[

- .alpha[Tracking files]
- Managing collaboration
- .alpha[Branching]

]
.pull-right-70[
<img src="images/07-git/workflow.png" width="100%" style="display: block; margin: auto;" />
]

---
# Git Concepts

.pull-left-30[

- .alpha[Tracking files]
- .alpha[Managing collaboration]
- Branching

]
.pull-right-70[
.move-down-170[
.li-small[
{{content}}
]
]
]
--

- Create different branches 
- Allow us to make changes independently
- Integrate all changes

---
# Git Concepts

.pull-left-30[

- .alpha[Tracking files]
- .alpha[Managing collaboration]
- Branching

]
.pull-right-70[
<img src="images/07-git/branch.png" width="100%" style="display: block; margin: auto;" />
]

---
# Git Concepts

.pull-left-30[

- .alpha[Tracking files]
- .alpha[Managing collaboration]
- Branching

]
.pull-right-70[

.move-down-30[
#### Branching

<img src="images/07-git/merge-extra-1.png" width="100%" style="display: block; margin: auto;" />
]
]

---
# Git Concepts

.pull-left-30[

- .alpha[Tracking files]
- .alpha[Managing collaboration]
- Branching

]
.pull-right-70[

.move-down-30[
#### Merging

.move-down-60[
.li-small[
{{content}}
]
]
]
]

#### Extra: Merging Mechanism

- Obtain a *“merge commit”*
- Branches still exist and are independent

---
# Git Concepts

.pull-left-30[

- .alpha[Tracking files]
- .alpha[Managing collaboration]
- Branching

]
.pull-right-70[
<img src="images/07-git/workflow-adv-2.png" width="100%" style="display: block; margin: auto;" />

]
---
class: inverse, center, middle

# Getting Started

---

# Getting Started: Configure Settings

.pull-left-50[

Add username and email

.code-size-12[
```bash
$ git config --global user.name "<My Name>"
$ git config --global user.email "<user@email.com>"
```
]
]
.pull-right-50[]

---
# Getting Started: Configure Settings

.pull-left-50[

Add username and email

.code-size-12[
```bash
$ git config --global user.name "<My Name>"
$ git config --global user.email "<user@email.com>"
```
]

Configuration file

.code-size-12[
```bash
#----    ~/.gitconfig    ----#
[user]
    name = My Name
    email = user@email.com
```
]
]
.pull-right-50[]

---

# Getting Started: Configure Settings

.pull-left-50[

Add username and email

.code-size-12[
```bash
$ git config --global user.name "<My Name>"
$ git config --global user.email "<user@email.com>"
```
]

Configuration file

.code-size-12[
```bash
#----    ~/.gitconfig    ----#
[user]
    name = My Name
    email = user@email.com
```
]
]
.pull-right-50[
Current settings

.code-size-12[
```bash
$ git config --list
```
]
]

---

# Getting Started: Configure Settings

.pull-left-50[

Add username and email

.code-size-12[
```bash
$ git config --global user.name "<My Name>"
$ git config --global user.email "<user@email.com>"
```
]

Configuration file

.code-size-12[
```bash
#----    ~/.gitconfig    ----#
[user]
    name = My Name
    email = user@email.com
```
]
]
.pull-right-50[
Current settings

.code-size-12[
```bash
$ git config --list
```
]

.move-down-40[
Settings levels
]

.li-small[
- `--system` system level Stored in `/etc/gitconfig`
- `--global` user level Stored in `~/.gitconfig`
- No flag, project level Stored in `.git/config`
]
]
---

# Getting Started: Initialize Repository

.pull-left-50[
- Already existing directory
.code-size-12[
```bash
$ cd <path-to/project-directory>
$ git init
```
]
{{content}}

]

.pull-right-50[]

--
> Create an hidden folder `.git/`
---

# Getting Started: Initialize Repository

.pull-left-50[
- Already existing directory
.code-size-12[
```bash
$ cd <path-to/project-directory>
$ git init
```
]
> Create an hidden folder `.git/`

- Get remote repository
.code-size-12[
```bash
$ git clone <repository-URL>
```
]
]
.pull-right-50[

]

---

# Getting Started: Tracking Files

.pull-left-40[

.move-down-30[
#### Adding Files
]

.li-small[]
]
.pull-right-60[

.move-up-30[
.code-size-12[
{{content}}
]
]
]

# Getting Started: Tracking Files

.pull-left-40[

.move-down-30[
#### Adding Files
]

```bash
$ git status
On branch master

No commits yet

Untracked files:
 (use "git add <file>..." to include in what will be committed)
 code/
 data/
 README

nothing added to commit but untracked files present 
(use "git add" to track)
```
]
]
]

---

# Getting Started: Tracking Files

.pull-left-40[

.move-down-30[
#### Adding Files
]

```bash
$ git status
On branch master

No commits yet

Untracked files:
 (use "git add <file>..." to include in what will be committed)
* code/
* data/
* README

nothing added to commit but untracked files present 
(use "git add" to track)
```
]
]
]

---

# Getting Started: Tracking Files

.pull-left-40[

.move-down-30[
#### Adding Files
]

#### Extra: `.git-track`

Git do not track empty directories Create and hidden empty file to track them

.code-size-12[
```bash
$ touch <path-to-empty-dir>/.git-track
```
]
]
---

# Getting Started: Tracking Files

.pull-left-40[

.move-down-30[
#### Adding Files
]

```bash
$ git add README <other-files>
```
]
]
]

---

# Getting Started: Tracking Files

.pull-left-40[

.move-down-30[
#### Adding Files
]

```bash
$ git add README <other-files>
```

```bash
$ git add --all
$ git status
On branch master

No commits yet

Changes to be committed:
 (use "git rm --cached <file>..." to unstage)
 new file: code/my-functions-1
 new file: code/my-functions-2
 new file: data/raw-data.csv
 new file: README
```
]
]
]
---

# Getting Started: Tracking Files

.pull-left-40[

.move-down-30[
#### Adding Files
]

.li-small[
- `git status` Check the project state
- `git add <file>` Add file to stage area
 - `--all` add files
- `git rm --cached <file>` Remove file from staging area
- `git reset` Remove all files from staging area
]
]
.pull-right-60[
.move-up-30[
.code-size-12[
```
my-project/
 |-- README
 |-- data/
 | |-- raw-data.csv
 |-- documents/
 |-- code/
 | |-- my-functions-1
 | |-- my-functions-2
```

```bash
$ git rm --cached data/raw-data.csv
```

{{content}}
]
]
]

```bash
$ git status
On branch master

No commits yet

Changes to be committed:
 (use "git rm --cached <file>..." to unstage)
 new file: code/my-functions-1
 new file: code/my-functions-2
 new file: README

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

# Getting Started: Tracking Files

.pull-left-40[

.move-down-30[
#### Adding Files
]

# Getting Started: Tracking Files

.pull-left-40[

.move-down-30[
#### Adding Files
]

Matching patterns rules:

.li-small[
- `note.txt` file name (in any directory)
- `folder-A/note.txt` path specification
- `folder-A/` directory name (in any directory)
- `*.log` file extension
- `folder-A/*.log` path specification
- `!important.log` create exceptions
]

]

--
Patterns according to `.gitignore` position

---

# Getting Started: Tracking Files

.pull-left-40[

.move-down-30[
#### Committing Changes
]

.li-small[
- `git commit` Create a commit

]
]
.pull-right-60[
.code-size-12[

.move-down-80[
{{content}}
]
]
]

```bash
$ git commit
```

---

# Getting Started: Tracking Files

.pull-left-40[

.move-down-30[
#### Committing Changes
]

.li-small[
- `git commit` Create a commit

]
]
.pull-right-60[
.move-down-80[
.code-size-12[
```bash
$ git commit
```

```bash
#---- commit messagge -----
Init Repo
    
- add code scripts
- add README
```
]
]

.move-down-30[
.li-small[
{{content}}
]
]
]

Commit Messages:

- Brief title (< 50 characters)
- List of main changes
- Explain **why**

---

# Getting Started: Tracking Files

.pull-left-40[

.move-down-30[
#### Committing Changes
]

.li-small[
- `git commit` Create a commit
 - `-a` all changes to tracked files 
 - `-m <text>` commit message

]
]
.pull-right-60[

.move-down-80[
.code-size-12[
```bash
$ git commit
```

```bash
#---- commit messagge -----
Init Repo
    
- add code scripts
- add README
```

```bash
$ git commit -am "Update README"  
```
]
]
]

---

# Getting Started: Tracking Files

.pull-left-40[

.move-down-30[
#### Committing Changes
]

.li-small[
- `git commit` Create a commit
 - `-a` all changes to tracked files 
 - `-m <text>` commit message
- `git log` See history
 - `--oneline` compact version

]
]
.pull-right-60[
.move-down-80[
.code-size-12[
```bash
$ git log
commit ec15cb085c2e5aa463778bbef3239b06b9ac4010 (HEAD -> master)
Author: username <user@email.com>
Date: Tue Feb 15 10:06:27 2022 +0100

Update README

commit 93398d18e686d4698af3e52a0677585afe467a19
Author: username <user@email.com>
Date: Tue Feb 15 09:26:13 2022 +0100

Init Repo
    
    - add code scripts
    - add README
```
]
]
]

---

# Getting Started: Tracking Files

.pull-left-40[

.move-down-30[
#### Committing Changes
]

]
]
.pull-right-60[
.code-size-12[
.move-down-80[
```bash
$ git diff
diff --git a/README b/README
index 64772c2..e994379 100644
--- a/README
+++ b/README
@@ -1 +1,2 @@
 This is my first project using Git!
+New information
```
]
]
]

---

# Getting Started: Tracking Files

.pull-left-40[

.move-down-30[
#### Committing Changes
]

.li-small[
- `git commit` Create a commit
 - `-a` all changes to tracked files 
 - `-m <text>` commit message
- `git log` See history
 - `--oneline` compact version
- `git diff` See changes since last commit
 - `<commit-ID>` Since specified commit
 - `<commit-A> <commit-B>` From commit-A to commit-B

---
# Getting Started: Tracking Files

.pull-left-40[

.move-down-80[
#### Undoing Commits
]

.li-small[]
]
.pull-right-60[
{{content}}
]

---
# Getting Started: Tracking Files

.pull-left-40[

.move-down-80[
#### Undoing Commits
]

.li-small[
- `git checkout <commit-ID>` Point `HEAD` to commit
]
]
.pull-right-60[
<img src="images/07-git/history.png" width="90%" style="display: block; margin: auto;" />

.code-size-12[
```bash
$ git checkout 60e117d7
```
]

{{content}}
]

---
# Getting Started: Tracking Files

.pull-left-40[

.move-down-80[
#### Undoing Commits
]

.li-small[
- `git checkout <commit-ID>` Point `HEAD` to commit
]
]
.pull-right-60[
<img src="images/07-git/history.png" width="90%" style="display: block; margin: auto;" />

.code-size-12[
```bash
$ git checkout 60e117d7
```
]

.center[*Warning! Detached* `HEAD`]
]

---
# Getting Started: Tracking Files

.pull-left-40[

.move-down-80[
#### Undoing Commits
]

.li-small[
- `git checkout <commit-ID>` Point `HEAD` to commit
]
]
.pull-right-60[
.move-up-30[
In detached `HEAD`, changes will be lost!
]

]

---
# Getting Started: Tracking Files

.pull-left-40[

.move-down-80[
#### Undoing Commits
]

.li-small[
- `git checkout <commit-ID>` Point `HEAD` to commit
]
]
.pull-right-60[
.move-up-30[
In detached `HEAD`, changes will be lost!
]

.code-size-12[
```bash
$ git checkout -b new-branch
```
]

{{content}}
]

--
<img src="images/07-git/checkout-diverge.png" width="90%" style="display: block; margin: auto;" />
---
# Getting Started: Tracking Files

.pull-left-40[

.move-down-80[
#### Undoing Commits
]

.li-small[
- `git checkout <commit-ID>` Point `HEAD` to commit
]
]
.pull-right-60[
<img src="images/07-git/history.png" width="90%" style="display: block; margin: auto;" />
]

---
# Getting Started: Tracking Files

.pull-left-40[

.move-down-80[
#### Undoing Commits
]

.li-small[
- `git checkout <commit-ID>` Point `HEAD` to commit
- `git revert <commit-ID>` Undo commits (keep track)

]
]
.pull-right-60[
<img src="images/07-git/history.png" width="90%" style="display: block; margin: auto;" />

.code-size-12[
```bash
$ git revert 7bf97593
$ git revert 9d109cfe
```
]

{{content}}
]

--
<img src="images/07-git/revert.png" width="95%" style="display: block; margin: auto;" />

---
# Getting Started: Tracking Files

.pull-left-40[

.move-down-80[
#### Undoing Commits
]

.li-small[
- `git checkout <commit-ID>` Point `HEAD` to commit
- `git revert <commit-ID>` Undo commits (keep track)
- `git reset <commit-ID>` Undo commits (delete)

]
]
.pull-right-60[
<img src="images/07-git/history.png" width="90%" style="display: block; margin: auto;" />

.code-size-12[
```bash
$ git revert 7bf97593
$ git revert 9d109cfe
```
]

{{content}}
]

--
<img src="images/07-git/reset.png" width="90%" style="display: block; margin: auto;" />

---
# Getting Started: Tracking Files

.pull-left-40[

.move-down-80[
#### Undoing Commits
]

.li-small[
- `git checkout <commit-ID>` Point `HEAD` to commit
- `git revert <commit-ID>` Undo commits (keep track)
- `git reset <commit-ID>` Undo commits (delete)
 {{content}}

]
]
.pull-right-60[
<img src="images/07-git/history.png" width="90%" style="display: block; margin: auto;" />

.code-size-12[
```bash
$ git revert 7bf97593
$ git revert 9d109cfe
```
]

.center[All changes are maintained in the files]
]

- `--hard` to discard changes (or `git restore <file>`)

---
# Getting Started: Collaboration

.pull-left-40[

.move-down-40[
#### &nbsp;
]

.li-small[
- `git remote add <name> <url>` Add remote repository

]
]
.pull-right-60[

.move-down-90[
.code-size-12[
```bash
$ git remote add origin https://github.com/username/my-project.git
```
]
]

{{content}}
]

> `origin` no special meaning per se!

---
# Getting Started: Collaboration

.pull-left-40[

.move-down-40[
#### &nbsp;
]

.li-small[
- `git remote add <name> <url>` Add remote repository
- `git remote -v` List remote repository
]
]
.pull-right-60[

.move-down-90[
.code-size-12[
```bash
$ git remote add origin https://github.com/username/my-project.git
```
]
]

> `origin` no special meaning per se!

.code-size-12[
```bash
$ git remote -v
origin  https://github.com/username/my-project.git (fetch)
origin  https://github.com/username/my-project.git (push)
```
]

]

---
# Getting Started: Collaboration

.pull-left-40[

.move-down-40[
#### &nbsp;
]

.li-small[
- `git remote add <name> <url>` Add remote repository
- `git remote -v` List remote repository
- `git pull <remote> <branch>` Download commits from remote
]
]
.pull-right-60[

.move-up-30[
.code-size-12[
```bash
$ git pull origin master
```
]
]

{{content}}
]

--
<img src="images/07-git/pull.png" width="75%" style="display: block; margin: auto;" />

> `pull` = `fetch` + `merge`

---
# Getting Started: Collaboration

.pull-left-40[

.move-down-40[
#### &nbsp;
]

.li-small[
- `git remote add <name> <url>` Add remote repository
- `git remote -v` List remote repository
- `git pull <remote> <branch>` Download commits from remote
- `git push <remote> <branch>` Upload commits to remote
]
]
.pull-right-60[

.move-up-30[
.code-size-12[
```bash
$ git push origin master
```
]
]

{{content}}
]

--
<img src="images/07-git/push.png" width="75%" style="display: block; margin: auto;" />

---
# Getting Started: Collaboration

.pull-left-40[

.move-down-40[
#### &nbsp;
]

#### 🌵 Warning: Always `pull` First

.code-small[
```bash
$ git push
To https://github.com/username/my-project.git
 ! [rejected]        master -> master (fetch first)
error: failed to push some refs to 'https://github.com/username/my-project.git'
hint: Updates were rejected because the remote contains work that you do
hint: not have locally. This is usually caused by another repository pushing
hint: to the same ref. You may want to first integrate the remote changes
hint: (e.g., 'git pull ...') before pushing again.
hint: See the 'Note about fast-forwards' in 'git push --help' for details.
```
]
]

---
# Getting Started: Collaboration

.pull-left-40[

.move-down-40[
#### &nbsp;
]

#### 🌵 Warning: Always `pull` First

.move-down-30[
#### Setting Upstream
]

.code-size-12[
```bash
$ git push -u origin master

# or 
$ git branch --set-upstream-to="<remote/branch>"
```
]
]

---
# Getting Started: Branching

--
.pull-left-40[

#### &nbsp;

.li-small[
- `git branch <name>` Create local branch
]
]
.pull-right-60[

.move-down-50[
.code-size-12[
```bash
$ git branch my-branch
```
]
]

.move-down-50[
{{content}}
]
]

--
<img src="images/07-git/branch-extra-1.png" width="100%" style="display: block; margin: auto;" />

---

# Getting Started: Branching

.pull-left-40[

#### &nbsp;

.li-small[
- `git branch <name>` Create local branch
]
]
.pull-right-60[
.move-down-50[
.code-size-12[
```bash
$ git branch my-branch
```
]
]

.move-down-50[
<img src="images/07-git/branch-extra-2.png" width="100%" style="display: block; margin: auto;" />
]

.code-size-12[
{{content}}
]
]

Remote branch created on `push`

```bash
$ git push -u origin my-branch
```

---
# Getting Started: Branching

.pull-left-40[

#### &nbsp;

.li-small[
- `git branch <name>` Create local branch
- `git checkout <name>` Switch to another branch
]
]
.pull-right-60[

.move-down-110[
.code-size-12[
```bash
$ git checkout my-branch
```
]
]
]

---
# Getting Started: Branching

.pull-left-40[

#### &nbsp;

.li-small[
- `git branch <name>` Create local branch
- `git checkout <name>` Switch to another branch
 - `-b` create and move
]
]
.pull-right-60[

.code-size-12[
.move-down-110[
```bash
$ git checkout my-branch
```
]

```bash
$ git checkout -b my-branch
```

]
]

---
# Getting Started: Branching

.pull-left-40[

#### &nbsp;

.li-small[
- `git branch <name>` Create local branch
- `git checkout <name>` Switch to another branch
 - `-b` create and move
- `git branch` list branches
]
]
.pull-right-60[

.code-size-12[
.move-down-210[
```bash
$ git branch 
 * master
   my-branch
```
]

]
]

---
# Getting Started: Branching

.pull-left-40[

#### &nbsp;

.li-small[
- `git branch <name>` Create local branch
- `git checkout <name>` Switch to another branch
 - `-b` create and move
- `git branch` list branches
 - `-vv` verbose
 - `-r` list remote branches
]
]
.pull-right-60[

.move-down-210[
.code-size-12[
```bash
$ git branch 
 * master
   my-branch
```

```bash
$ git branch -vv
 * master    00ab7a8 [origin/master] Update master
   my-branch 702b800 [origin/my-branch] Create my-branch
    
$ git branch -vvr
origin/master    00ab7a8 Update master
origin/my-branch 702b800 Create my-branch
```

]
]
]

---
# Getting Started: Merging

--
.pull-left-40[

#### &nbsp;

]
.pull-right-60[

.code-size-12[
```bash
$ git checkout master
```
]

.move-down-44[
<img src="images/07-git/merge-extra-1.png" width="100%" style="display: block; margin: auto;" />
]
]
---
# Getting Started: Merging

.pull-left-40[

#### &nbsp;

.move-down-50[
.li-small[
- `git merge <name>` Merge branch
]
]
]
.pull-right-60[

.code-size-12[
```bash
$ git checkout master
$ git merge my-branch
```
]

{{content}}
]

>  *“Merge commit”* joining the two branches

---
# Getting Started: Merging

.pull-left-40[

#### &nbsp;

.move-down-50[
.li-small[
- `git merge <name>` Merge branch
- `git branch -d <branch-name>` Remove local branch
- `git push <remote-name> --delete <branch-name>` Remove remote branch
]
]
]
.pull-right-60[

.code-size-12[
```bash
$ git checkout master
$ git merge my-branch
```
]

.move-down-44[
.code-size-12[
```bash
# Remove local branch
$ git branch -d my-branch

# Remove remote branch
$ git push origin --delete my-branch
```
]
]
]

---
# Getting Started: Conflicts

.pull-left-50[

.move-left-130[
.my-code-block[
#### Original
.code-size-12[
```bash
#----    my-file.txt

First text line
Second text line
Third text line
```
]
]
]
]
.pull-right-50[

]

---
# Getting Started: Conflicts

.pull-left-50[

.move-left-130[
.my-code-block[
#### Original
.code-size-12[
```bash
#----    my-file.txt

First text line
Second text line
Third text line
```
]
]
]

.pull-left-50[

#### Branch A
.code-size-12[
```bash
#----    my-file.txt

First text line
Branch-A text line
Third text line
```
]
]
.pull-right-50[

#### Branch B
.code-size-12[
```bash
#----    my-file.txt
  
First text line
Branch-B text line
Third text line
```
]
]
]
.pull-right-50[

]
---
# Getting Started: Conflicts

.pull-left-50[

.move-left-130[
.my-code-block[
#### Original
.code-size-12[
```bash
#----    my-file.txt

First text line
*Second text line
Third text line
```
]
]
]

.pull-left-50[

#### Branch A
.code-size-12[
```bash
#----    my-file.txt

First text line
*Branch-A text line
Third text line
```
]
]
.pull-right-50[

#### Branch B
.code-size-12[
```bash
#----    my-file.txt
  
First text line
*Branch-B text line
Third text line
```
]
]
]
.pull-right-50[

]

---
# Getting Started: Conflicts

.pull-left-50[

.move-left-130[
.my-code-block[
#### Original
.code-size-12[
```bash
#----    my-file.txt

First text line
*Second text line
Third text line
```
]
]
]

.pull-left-50[

#### Branch A
.code-size-12[

```bash
#----    my-file.txt

First text line
*Branch-A text line
Third text line
```

]
]
.pull-right-50[

#### Branch B
.code-size-12[
```bash
#----    my-file.txt
  
First text line
*Branch-B text line
Third text line
```
]
]
]
.pull-right-50[

.code-size-12[
```bash
$ git checkout branch-A
$ git merge branch-B
```
]

]

---
# Getting Started: Conflicts

.pull-left-50[

.move-left-130[
.my-code-block[
#### Original
.code-size-12[
```bash
#----    my-file.txt

First text line
*Second text line
Third text line
```
]
]
]

.pull-left-50[

#### Branch A
.code-size-12[
```bash
#----    my-file.txt

First text line
*Branch-A text line
Third text line
```
]
]
.pull-right-50[

#### Branch B
.code-size-12[
```bash
#----    my-file.txt
  
First text line
*Branch-B text line
Third text line
```
]
]
]
.pull-right-50[

.code-size-12[
```bash
$ git checkout branch-A
$ git merge branch-B
Auto-merging my-file.txt
CONFLICT (content): Merge conflict in my-file.txt
Automatic merge failed; fix conflicts and then 
commit the result.
```
]

.code-size-12[
{{content}}
]
]

```bash
#---- my-file.txt
 
First text line
<<<<<<< HEAD

Branch-A text line

=======

Branch-B text line

>>>>>>> branch-B
Third text line
```

---

# Getting Started: Conflicts

.pull-left-50[

.move-left-130[
.my-code-block[
#### Original
.code-size-12[
```bash
#----    my-file.txt

First text line
*Second text line
Third text line
```
]
]
]

.pull-left-50[

#### Branch A
.code-size-12[
```bash
#----    my-file.txt

First text line
*Branch-A text line
Third text line
```
]
]
.pull-right-50[

#### Branch B
.code-size-12[
```bash
#----    my-file.txt
  
First text line
*Branch-B text line
Third text line
```
]
]
]
.pull-right-50[

.code-size-12[
```bash
#---- my-file.txt
 
First text line
<<<<<<< HEAD

*Branch-A text line

=======

*Branch-B text line

>>>>>>> branch-B
Third text line
```
]
]

---
# Getting Started: Conflicts

.pull-left-50[

.move-left-130[
.my-code-block[
#### Original
.code-size-12[
```bash
#----    my-file.txt

First text line
*Second text line
Third text line
```
]
]
]

.pull-left-50[

#### Branch A
.code-size-12[
```bash
#----    my-file.txt

First text line
*Branch-A text line
Third text line
```
]
]
.pull-right-50[

#### Branch B
.code-size-12[
```bash
#----    my-file.txt
  
First text line
*Branch-B text line
Third text line
```
]
]
]
.pull-right-50[

.code-size-12[
```bash
#----    my-file.txt
  
First text line
Branch-B text line
Third text line
```
]

.code-size-12[
{{content}}
]
]

```bash
$ git commit -m "Solve conflict"
```
{{content}}

--
#### Undo Merge
```bash
$ git merge --abort
```

---

# Getting Started: Conflicts

.pull-left-50[

.move-left-130[
.my-code-block[
#### Original
.code-size-12[
```bash
#----    my-file.txt

First text line
*Second text line
Third text line
```
]
]
]

.pull-left-50[

#### Branch A
.code-size-12[
```bash
#----    my-file.txt

First text line
*Branch-A text line
Third text line
```
]
]
.pull-right-50[

#### Branch B
.code-size-12[
```bash
#----    my-file.txt
  
First text line
*Branch-B text line
Third text line
```
]
]
]
.pull-right-50[

#### Conflict Style Diff3

.code-size-12[
{{content}}
]
]
--

```bash
$ git config --global merge.conflictstyle diff3
```
{{content}}

```bash
#---- my-file.txt
 
First text line
<<<<<<< HEAD

Branch-A text line

||||||| common ancestor commit

Second text line

=======

Branch-B text line

>>>>>>> merging-branch
Third text line
```

---

# Getting Started: Conflicts

.pull-left-50[

.move-left-130[
.my-code-block[
#### Original
.code-size-12[
```bash
#----    my-file.txt

First text line
*Second text line
Third text line
```
]
]
]

.pull-left-50[

#### Branch A
.code-size-12[
```bash
#----    my-file.txt

First text line
*Branch-A text line
Third text line
```
]
]
.pull-right-50[

#### Branch B
.code-size-12[
```bash
#----    my-file.txt
  
First text line
*Branch-B text line
Third text line
```
]
]
]
.pull-right-50[

#### Conflict Style Diff3

.code-size-12[
```bash
$ git config --global merge.conflictstyle diff3
```

```bash
#---- my-file.txt
 
First text line
<<<<<<< HEAD

*Branch-A text line

||||||| common ancestor commit

*Second text line

=======

*Branch-B text line

>>>>>>> merging-branch
Third text line
```
]
]

---

# Git Workflow

--
#### Two Branches approach

---

# Git Workflow

#### Multiple Branches Approach

---
class: inverse, center, middle

# RStudio Git GUI

---
# RStudio: Configure Git

--
*“Tools -> Global Options”*

---
# RStudio: Create Git Repository

.pull-left-50[
#### Create a New Project

<img src="images/07-git/rstudio-new-proj.png" width="85%" style="display: block; margin: auto;" />
]
.pull-right-50[
{{content}}
]

--
#### Clone a Remote Repository

---
# RStudio: Create Git Repository

.pull-left-50[
#### Create a New Project

<img src="images/07-git/rstudio-new-proj.png" width="85%" style="display: block; margin: auto;" />
]
.pull-right-50[
#### Clone a Remote Repository

<img src="images/07-git/rstudio-clone-2.png" width="85%" style="display: block; margin: auto;" />
]

---
# RStudio: Create Git Repository

.pull-left-50[
#### Create a New Project

<img src="images/07-git/rstudio-new-proj.png" width="85%" style="display: block; margin: auto;" />
]
.pull-right-50[
#### Clone a Remote Repository

<img src="images/07-git/rstudio-clone-3.png" width="85%" style="display: block; margin: auto;" />
]

---
# RStudio: Git Panel

.pull-left-50[
#### &nbsp;

<img src="images/07-git/panel-base-1.png" width="85%" style="display: block; margin: auto;" />
]
.pull-right-50[

]

---
# RStudio: Tracking Changes

.pull-left-50[
#### &nbsp;

<img src="images/07-git/panel-files.png" width="85%" style="display: block; margin: auto;" />
]
.pull-right-50[

#### &nbsp;

.li-small[
{{content}}
]
]

- <img src="images/07-git/icon-untraked.png" height="40"> Untracked
- <img src="images/07-git/icon-added.png" height="40"> Added
- <img src="images/07-git/icon-modified.png" height="40"> Modified
- <img src="images/07-git/icon-deleted.png" height="40"> Deleted
- <img src="images/07-git/icon-renamed.png" height="40"> Renamed
- <img src="images/07-git/icon-conflict.png" height="40"> Conflict

---
# RStudio: Tracking Changes

.pull-left-50[
#### &nbsp;

<img src="images/07-git/panel-stage.png" width="85%" style="display: block; margin: auto;" />
]
.pull-right-50[

#### &nbsp;

.li-small[
- <img src="images/07-git/icon-untraked.png" height="40"> Untracked
- <img src="images/07-git/icon-added.png" height="40"> Added
- <img src="images/07-git/icon-modified.png" height="40"> Modified
- <img src="images/07-git/icon-deleted.png" height="40"> Deleted
- <img src="images/07-git/icon-renamed.png" height="40"> Renamed
- <img src="images/07-git/icon-conflict.png" height="40"> Conflict

]
]

---
# RStudio: Tracking Changes

.pull-left-50[
#### Staging and Commiting

<img src="images/07-git/panel-commit.png" width="100%" style="display: block; margin: auto;" />
]
.pull-right-50[
{{content}}
]

--
<img src="images/07-git/rstudio-diff-2.png" width="85%" style="display: block; margin: auto;" />

---
# RStudio: Tracking Changes

.pull-left-50[
#### History

<img src="images/07-git/panel-base-2.png" width="85%" style="display: block; margin: auto;" />
]
.pull-right-50[

#### &nbsp;

{{content}}
]

---
# RStudio: Tracking Changes

.pull-left-50[
#### History

<img src="images/07-git/panel-history-2.png" width="65%" style="display: block; margin: auto;" />
]
.pull-right-50[

#### &nbsp;

]

---

# RStudio: Managing Collaboration

.pull-left-50[
#### &nbsp;

.code-small-12[
```bash
$ git remote add <remote-name> <remote-URL>
```
]

{{content}}
]
.pull-right-50[

]

---
# RStudio: Branching and Merging

.pull-left-50[
#### Change Branch

]
.pull-right-50[

]

#### New branch

<img src="images/07-git/panel-new-branch.png" width="65%" style="display: block; margin: auto;" />
---
class: inverse, center, middle

# Git: your only real friend when programming!

## Moving to the next step...