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title: Reproducible Research 3 - Git
tags: RR2024 - DS/QF
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theme: night

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## Reproducible Research 3 - Git: 2 devs and a central repository

Wojciech Hardy
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link: https://hackmd.io/@WHardy/RR24-git2


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### How does it work? (quick recap)


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## Cheatsheet: Basic commands

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## Cheatsheet: Advanced commands


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### Useful links

[Read more on `git reset`](https://git-scm.com/book/en/v2/Git-Tools-Reset-Demystified)

[Other cheat sheet 1 (Atlassian)](https://www.atlassian.com/git/tutorials/atlassian-git-cheatsheet)

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## Git commands: working with a central repository

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**`git init --bare`** to create barebones for a central repository (with no initial commits)

**`git clone [repo_name] [clone_name]`** to create a linked copy of the **`repo_name`** repository.

**`git fetch`** grab information about new commits/branches from the central repository.

**`git pull`** to grab the (new) commits from the central repository to our repository.

**`git push`** to put our (newly created) commits in the central repository.

We're going to pretend we have two developers and a central repository.

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## Quick recap

1. In our workspace, let's create a new folder RR_git2 and go inside

`mkdir RR_git2`
`cd RR_git2`

2. Let's create a repository named RecapRepo and go inside

`git init RecapRepo`
`cd RecapRepo`
`git status`

3. Change local user.name to "RecapRepoUser"

`git config --local user.name "RecapRepoUser"`

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3. Create three files: commit the first; only stage the second; do nothing to the third

`echo "this file will be commited" > file1.txt`
`echo "this file will be staged" > file2.txt`
`echo "this fille will be in the working directory" > file3.txt`

`git add file1.txt`
`git commit -m "Added file1.txt"`
`git add file2.txt`

`git status`

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4. In RR_git2 create a clone of the first repository; go inside

`cd ..`
`git clone RecapRepo RecapCloned`
`cd RecapCloned`

5. View the contents; check the status

`ls`
`git status`

6. View the `config` file in the `.git` folder.

(e.g. in notepad)

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## Exercise 5: simulating central repo with two locals

We're now going to pretend we have two people collaborating, using a central repository to manage the workflow.

1. In your RR_git2 directory create a new, **bare** repository called "CentralRepo"

(Remember to use the appropriate option when initiating the repository!)

`cd RR_git2`
`git init --bare CentralRepo`

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2. In your RR_git2 directory create a clone of the CentralRepo, named Dev1

`git clone CentralRepo Dev1`

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3. In your RR_git2 directory create a clone of the CentralRepo, named Dev2

`git clone CentralRepo Dev2`

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4. Set the local **`user.name`** for Dev1 repository to "Developer_1"

`cd Dev1`
`git config --local user.name "Developer_1"`

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5. Set the local **`user.name`** for Dev2 repository to "Developer_2"

`cd ../Dev2`
`git config --local user.name "Developer_2"`

We'll be imitating this:

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## So far all repositories are empty. Let's imagine:

1. Dev1 kick-starts the project by creating the branch with one commit and sending it `upstream`

`echo "This will be the file with code" > code.R`
`git add .`
`git commit -m "Added the file with code"`
`git status`
`git push`
`git status`

2. Dev2 wants to get up-to-speed so grabs the changes

`git pull`

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## Exercise 6: fetching and updating before pushing

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As you go, try to remember what are the states of the Dev1, the Dev2 and the Central Repositories at each step. (You can even draw them)

1. Create a readme.txt file in your Dev1 repository.

`cd ../Dev1`
`touch readme.txt`

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2. Stage, commit and push the file.

`git add .`
`git commit -m "Added readme.txt"`
`git push`

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3. Go to the Dev2 repository.

`cd ../Dev2`

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4. Run `git status`

`git status`

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5. Fetch information about changes from the central repository. Run **`git status`**.

`git fetch`
`git status`

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6. Pull the information. Check folder contents.

`git pull`
`ls`

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7. Add a new line to readme.txt and create a readme.md file.

`echo "second line of text" >> readme.txt`
`touch readme.md`

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8. Stage, commit and push the file to the central repository.

`git add .`
`git commit -m "Added readme.md and changed readme.txt"`
`git push`

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9. In Dev1, create a text3.txt file with the line "A line added by Dev1". Stage, commit and push - what happens? Resolve the issue following the hints.

`cd ../Dev1`
`echo "A line added by Dev1" > text3.txt`
`git add .`
`git commit -m "Added text3"`
`git push`

Follow the instructions from Git to resolve merge conflicts.

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## Exercise 7: a merge conflict

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In Exercise 6 we had a divergence, but without a conflict (commits differed, but there were no conflicting changes to files).

What if two devs make two different versions of a file?

1. In Dev2, create a new file called text3.txt with the line "A line added by Dev2". Stage, commit and try to push. Read the hints, follow and go to step 2.

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2. There's a conflict because Dev1 committed a different text3.txt file earlier.

We're in a merging mode. We can edit the file (e.g. in Notepad) to figure out what should remain. Then stage it and commit it.

The merge becomes a new commit (try **`git log`**)

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## Assignment

While still in your Dev2 repository, run these three commands:
`git status` > git2_a.txt
`git log` >> git2_a.txt
`git ls-files` >> git2_a.txt

Send me the notepad file git2_a.txt ([e-mail]).

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## Stuck in VIM?

If you forgot about adding a message to your commit, you might have ended up in VIM. It's a free, text-editting software that sometimes feels like a trap.

*Tl;dr:* hit [ESC], then type **`:q`* * and press **`Enter`** .
Repeat your commit with a helpful description.

You can also try adding the comment in VIM instead, and then exit with **`:wq`** instead, which should do the commit with the comment.

See more in this [helpful Stackoverflow answer](https://stackoverflow.com/a/11828573).

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## Useful links

[Read more on the three trees with the **`git reset`** guideline](https://git-scm.com/book/en/v2/Git-Tools-Reset-Demystified)

[Cheat sheet 1 (Atlassian)](https://www.atlassian.com/git/tutorials/atlassian-git-cheatsheet)

[Git-scm in general](https://git-scm.com)

[Atlassian in general](https://www.atlassian.com/git)

If you need more, just Google tutorials/blog posts/YouTube videos until you find one that makes it clear :) Lots to choose from!

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