---
tags: BMMB554-23
---

[](https://xkcd.com/1597/)

# Lecture 13: Git and GitHub

:::warning
Today we will talk about *local* use of `git` because GitHub requires authentication that you will need to set up before Thursday
:::

## Lecture setup

1. Start [JupyterLab](https://mybinder.org/v2/gh/jupyterlab/jupyterlab-demo/try.jupyter.org?urlpath=lab)
2. Start terminal within JupyterLab instance

## Git resources

- [The Git Book](https://git-scm.com/book/en/v2)
- Troubleshooting [PG13](https://dangitgit.com/en) [R](https://ohshitgit.com/)

## Version control

- Manages changes over time
- Enables collaboration
- Provides complete history

## Git versus GitHub

- Git - version control system
- GitHub - hosting service

### Logic:
> From tutorials by [Kyle Bradbury](https://www.kylebradbury.org/index.html)

### Main commands:
> From tutorials by [Kyle Bradbury](https://www.kylebradbury.org/index.html)

### Branch flow

> From [GitBetter](https://gitbetter.substack.com/p/how-to-work-in-multiple-git-branches)

## Clone a [sample repo](https://github.com/nekrut/bmmb554_foo_bar) from GitHub

git clone https://github.com/nekrut/bmmb554_foo_bar.git

## Check history of this repo using `git log`

$git log
commit de89f51d8e124665713f6fd94cd46447d172033b (HEAD -> main, origin/main, origin/HEAD)
Author: Anton Nekrutenko <[e-mail]>
Date:   Tue Feb 21 08:02:50 2023 -0500

    Create file2.txt

commit bc3e5c4a9d54203739bb90f29d92e20082b9e5d4
Author: Anton Nekrutenko <[e-mail]>
Date:   Tue Feb 21 08:02:25 2023 -0500

    Create file1.txt

commit 99dd43783be37b08c1ca80cdc881eae537526396
Author: Anton Nekrutenko <[e-mail]>
Date:   Tue Feb 21 08:00:34 2023 -0500

    Updated readme

commit 18ebdabfe6f92f33ea626994ce6c9998cbe63522
Author: Anton Nekrutenko <[e-mail]>
Date:   Tue Feb 21 07:59:46 2023 -0500

    Initial commit

## Check status of the repo

$git status
On branch main
Your branch is up to date with 'origin/main'.

nothing to commit, working tree clean

## Let's change and stage a file

Use editor to modify `file1.txt`. Once it is saved, we can see what is happening by using `git status` again:

$git status
On branch main
Your branch is up to date with 'origin/main'.

Changes not staged for commit:
  (use "git add <file>..." to update what will be committed)
  (use "git checkout -- <file>..." to discard changes in working directory)

        modified:   file1.txt

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

        .ipynb_checkpoints/

no changes added to commit (use "git add" and/or "git commit -a")

You can see, that the file is modified, but it is *not staged*. Tio stage it for commit you need to explicitly add it to staging:

git add file1.txt 

If you run `git status` now you will get:

$git status
On branch main
Your branch is up to date with 'origin/main'.

Changes to be committed:
  (use "git reset HEAD <file>..." to unstage)

        modified:   file1.txt

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

        .ipynb_checkpoints/

## Oh :shit:: `get reset`

Running `git reset` will restore the *status quo* as it was prior to `git add`:

$git reset
Unstaged changes after reset:
M       file1.txt

and `git status` will look as it did prior to `git add`:

git status
On branch main
Your branch is up to date with 'origin/main'.

Changes not staged for commit:
  (use "git add <file>..." to update what will be committed)
  (use "git checkout -- <file>..." to discard changes in working directory)

        modified:   file1.txt

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

        .ipynb_checkpoints/

no changes added to commit (use "git add" and/or "git commit -a")

## Let's stage and commit

If you are indeed ready to go ahead let's `add`:

git add file1.txt

and `commit`

$git commit -m 'modified file1'
[main 476adb7] modified file1
 1 file changed, 1 insertion(+), 1 deletion(-)

If run `git log` you will this addition commit:

$git log
commit 476adb7b64a9330199fea13ca2e7523f7fe90189 (HEAD -> main)
Author: nekrut <[e-mail]>
Date:   Tue Feb 21 13:23:24 2023 +0000

    modified file1

or alternatively you can use `--oneline` flag:

$git log --oneline
476adb7 (HEAD -> main) modified file1
de89f51 (origin/main, origin/HEAD) Create file2.txt
bc3e5c4 Create file1.txt
99dd437 Updated readme
18ebdab Initial commit

## Oh :shit:: `get revert`

To roll everything back you can do this:

[main 1f13d5f] Revert "modified file1"
 1 file changed, 1 insertion(+), 1 deletion(-)

This will bring `vim` editor with a pre-filled rollback message:


To save this and get out:

- press <kbd>ESC</kbd>
- type `:wq`
- hit <kbd>Enter</kbd>

Now, let's look at the log (showing just two lat commits):

 git log
commit 1f13d5fcf38057db9a90066b99aa475a6eeb1bae (HEAD -> main)
Author: nekrut <[e-mail]>
Date:   Tue Feb 21 13:31:24 2023 +0000

    Revert "modified file1"
    
    This reverts commit 476adb7b64a9330199fea13ca2e7523f7fe90189.

commit 476adb7b64a9330199fea13ca2e7523f7fe90189
Author: nekrut <[e-mail]>
Date:   Tue Feb 21 13:23:24 2023 +0000

    modified file1

## Let's actually do make changes and highlight them with diff

First, let's modify, say, `file2.txt` by adding a line. In this example I modified it from:

This
is
another
file
I've
made

to

This
is
file2
I've
made

Now `add` and `commit`:

$ git status
On branch main
Your branch is ahead of 'origin/main' by 2 commits.
  (use "git push" to publish your local commits)

Changes not staged for commit:
  (use "git add <file>..." to update what will be committed)
  (use "git checkout -- <file>..." to discard changes in working directory)

        modified:   file2.txt

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

        .ipynb_checkpoints/

no changes added to commit (use "git add" and/or "git commit -a")

$ git add file2.txt 

$ git commit -m 'changed file2'
[main a947686] changed file2
 1 file changed, 1 insertion(+), 2 deletions(-)

Let's now compare the changes between two commits:

$ git diff a947686 1f13d5f
diff --git a/file2.txt b/file2.txt
index 1f383ac..e13e461 100644
--- a/file2.txt
+++ b/file2.txt
@@ -1,5 +1,6 @@
 This
 is
-file2
+another
+file
 I've
 made

here:

- `a` and `b` = tags of files being compared
- `---` and `+++` marked to indiciate differences between `a` and `b`
- `@@ -1,5 +1,6 @@` file chunk header which has the following format:
- `@@ [file a range][file b range] @@`
- File ranges are: `<start line><number of lines>`

## Branches


> From [GitBetter](https://gitbetter.substack.com/p/how-to-work-in-multiple-git-branches)

To enable collaborations and to give the ability to develop major features without disrupting production (`master` or `main`) branch Git allows creation of multiple branches.

### Create a new branch and switch to it

Let's create branch dev:

git branch dev

to see existing branches:

$ git branch
  dev
* main

The `main` branch is active (tagged with `*`). To actually switch branches:

$ git checkout dev
Switched to branch 'dev'

### Make changes

Let's make some changes, say, to `file1.txt` from this:

This
is
a 
file

to this:

This
is
a 
file1

and then get `status`, `add`, and `commit`:

$ git status
On branch dev
Changes not staged for commit:
  (use "git add <file>..." to update what will be committed)
  (use "git checkout -- <file>..." to discard changes in working directory)

        modified:   file1.txt

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

        .ipynb_checkpoints/

no changes added to commit (use "git add" and/or "git commit -a")

$ git add file1.txt 

$ git commit -m 'changes to file1.txt'
[dev 05ce64d] changes to file1.txt
 1 file changed, 1 insertion(+), 1 deletion(-)

### Switch to another branch and look at the modified file

If we switch back to `main` and look at the content of `file1.txt` we will see the "old" content:

This
is
a 
file

### Merge branches

To incorporate changes from `dev` to `master` we need to do a merge:

$ git merge dev main
Updating a947686..05ce64d
Fast-forward
 file1.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

and if we look at `file1.txt` again we will see the change:

$ more file1.txt
This
is
a
file1

We can now delete the branch:

$ git branch -d dev
Deleted branch dev (was 05ce64d).

### Merging with conflicts

To simulate a merging conflict we need to make different changes to the same line of a file in different branches.

#### Modify `file1.txt` in `main`

First, let's checkout `main` and make the following change to `file1.txt`, say, from

This
is
a 
file1

to

This
is
a 
file1 - the first file we created

now we add and commit:

$ git add file1.txt 

$ git commit -m 'main changes to file1'
[main dfd0598] main changes to file1
 1 file changed, 1 insertion(+), 1 deletion(-)

:::info

You can use `git diff` to see the differences between branches such as, for example:

$ git diff main dev
diff --git a/file1.txt b/file1.txt
index f8e8191..e82ee85 100644
--- a/file1.txt
+++ b/file1.txt
@@ -1,4 +1,4 @@
 This
 is
 a 
-file1 - the first file we created
+file1

:::

#### Modify `file1.txt` in `dev`

Checkout `dev`:

$ git checkout dev
Switched to branch 'dev'

Change `file1.txt`, say, from:

This
is
a 
file1

to

This
is
a 
file1 - the first file

now we add and commit:

$ git add file1.txt 

$ git commit -m 'dev changes to file1'
[dev b2b8b9e] dev changes to file1
 1 file changed, 1 insertion(+), 1 deletion(-)

#### Checkout `main` and try to `merge`

$ git merge main dev
Auto-merging file1.txt
CONFLICT (content): Merge conflict in file1.txt
Automatic merge failed; fix conflicts and then commit the result.

If then actually look at the content of the file, you will see this:


so here you need to decide which version you will keep and edit the file correspondingly. For example, I edited it to this form and saved:


Now I need to `add` and `commit`:

$ git add file1.txt
jovyan@jupyter-jupyterlab-2djupyterlab-2ddemo-2dryet2dsd:~/bmmb554_foo_bar$ git commit -m 'merged dev into main'