Git and GitHub

CS 4411
Spring 2020
If that doesn’t fix it, git.txt contains the phone number of a friend of mine who understands git. Just wait through a few minutes
of “It’s really pretty simple, just think of branches as...” and eventually you’ll learn the commands that will fix everything.
Outline for Today
• Git overview
• Git vs. GitHub
• Basic Git commands
• Conflicts and merges
• Branches
• Recovering from errors
 Git Model
Remote repo
Head Commit C:
/src/grass/process.c
/src/grass/process.h
Commits A B C /src/apps/mt.c

Origin Repo contents

Local repo Makefile
src
Head |---apps
|---earth “Working tree”
|---grass
A B C | |---process.c
| |---process.h
|---lib
Making a Commit
Remote repo
Head

A B C D

Origin push
Local repo
Head Commit D:
/src/apps/mt.c
/src/apps/myprogram.c
A B C D
/src/make/Makefile.apps
Git with GitHub
GitHub repo: etremel/egos GitHub repo: jsmith/egos
Head Head
Fork
A B C D A B C E

Origin Origin
Local repo Local repo
Head Head

A B C D A B C E
Outline
• Git overview
• Git vs. GitHub
• Basic Git commands
• Conflicts and merges
• Branches
• Recovering from errors
Getting Started with Clone
• git clone: Create a new local repository by copying a remote repo
$ git clone https://github.coecis.cornell.edu/cs4411-2020sp/ejt64-egos.git

Protocol Server Path to repository on server

• Result: New folder named “ejt64-egos” in current directory,
containing new git repo
• Contents identical to repo on server
• Origin set to https://github.coecis.cornell.edu/cs4411-
2020sp/ejt64-egos.git
HTTPS or SSH?
$ git clone https://github.coecis.cornell.edu/cs4411-2020sp/ejt64-egos.git

• Easy to start, no setup required

• Must enter username and password every time you pull or push
$ git clone git@github.coecis.cornell.edu:cs4411-2020sp/ejt64-egos.git

• Once set up, no username or password required

• Need to create an SSH key on your
computer and add it to your Cornell
GitHub account
Add and Commit
1. Make changes to files
2. Choose some changed files that you’re ready to “publish”
3. git add the changed files
4. git commit and write a message

~/egos$ vim src/apps/mt.c

~/egos$ vim src/grass/process.c
~/egos$ git add src/apps/mt.c
~/egos$ git commit Commit E:
/src/apps/mt.c
Pull and Push
• At first, a commit is only on your local repo
• git push copies commits to the “origin” remote repo
• git pull downloads commits from origin and applies them
Origin repo Head

A B C D
Local repo Partner’s repo
Head pull Head
push

A B C D A B C D
Understanding Git Status
~/egos$ git status Current branch
On branch master
Your branch is up to date with 'origin/master' Whether you have
unpushed commits
Changes to be committed:
(use "git reset HEAD <file>…" to unstage)
Changes you have
modified: src/grass/process.c added with git add

Changes not staged for commit:

(use "git add <file>…" to update what will be committed)
git knows a file has
changed, but you
modified: src/grass/disksvr.c
haven’t added it yet
Untracked files:
(use "git add <file>…" to include in what will be committed)
New files you have not
src/apps/myprogram.c yet added in any commit
Git Status After a Commit
~/egos$ git status
On branch master
Your branch is 1 commit behind 'origin/master' You made a commit,
but haven’t pushed
Changes not staged for commit:
(use "git add <file>…" to update what will be committed)
After your last commit,
modified: src/grass/process.c you continued editing
this file
Untracked files:
(use "git add <file>…" to include in what will be committed)

src/apps/tags
src/grass/tags These files still haven’t
been added to any commit
Ignoring Files You’ll Never Add
• Some files you never want ~/egos$ cat .gitignore
to commit: ctags files, # ctags files
compiled output, LaTeX aux tags
files… # LaTeX junk
*.aux
• Git will keep bothering you *.log
about them in git status *.bbl
• Add a file named # The debug log directory
logs/
.gitignore to the root # Object files in the build dir
of your repo, and then add build/**/*.o
it to a commit ~/egos$

https://www.atlassian.com/git/tutorials/saving-changes/gitignore
Diff: What Am I Committing?
~/egos$ git diff First file with
diff --git a/src/lib/queue.c b/src/lib/queue.c changes
index c638853..19106c3 100644
Line number
--- a/src/lib/queue.c
skipped to
+++ b/src/lib/queue.c
@@ -19,7 +19,7 @@ struct element {
void queue_init(struct queue *q){ Deleted from original
q->first = 0; (last commit)
q->last = &q->first;
- q->nelts = 0; Added in current
+ q->num_elements = 0; state of file
}

/* Put it on the wrong side of the queue. I.e., make it the next
@@ -34,7 +34,7 @@ void queue_insert(struct queue *q, void *item){
}
e->next = q->first; Skip ahead again
q->first = e; to line 34
Diff Details
~/egos$ git diff src/grass/process.c

• Shows differences only for that file

~/egos$ git diff
~/egos$

• Why does it give no results? I know I made changes!

• Answer: you have already git added your changes
~/egos$ git diff --staged
diff --git a/src/lib/queue.c b/src/lib/queue.c
index c638853..19106c3 100644
--- a/src/lib/queue.c
+++ b/src/lib/queue.c
@@ -19,7 +19,7 @@ struct element {
Un-Adding and Deleting
• Oops, I didn’t mean to add that file!
~/egos$ git add src/lib/queue.c
~/egos$ git reset HEAD src/lib/queue.c

• Telling git you want to delete myprogram.c:

~/egos$ git rm src/apps/myprogram.c
~/egos$ git status
On branch master
Your branch is up to date with 'origin/master'

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

deleted: src/apps/myprogram.c
Renaming
• Telling git you want to rename myprogram.c:
~/egos$ git mv src/apps/myprogram.c src/apps/newname.c
~/egos$ git status
On branch master
Your branch is up to date with 'origin/master'

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

renamed: src/apps/myprogram.c -> src/apps/newname.c

• Otherwise, git will think you deleted myprogram.c, and both

myprogram.c and newname.c will end up in the repo
Outline
• Git overview
• Git vs. GitHub
• Basic Git commands
• Conflicts and merges
• Branches
• Recovering from errors
Concurrent Changes
GitHub repo
Head

A B C D

push
My local repo Partner’s local repo
Head Head

A B C D A B C E
Possible Outcomes
• No conflicts, just merge
~/egos$ git pull
# Editor pops up
Merge made by the 'recursive' strategy
src/lib/queue.c | 14 branch
Merge +++++++-------
'master' of https://github.coecis.cornell.edu/etremel/egos.git
1 file changed, 7 insertions (+), 7 deletions (-)
# Please enter the commit message for your changes. Lines starting
# with '#' will be ignored, and an empty message aborts the commit

Partner’s local repo

D Head

A B C E M
Possible Outcomes
• Conflicting changes to the same file(s)
~/egos$ git pull
Auto-merging src/lib/queue.c
CONFLICT (content): Merge conflict in src/lib/queue.c
Automatic merge failed; fix conflicts and then commit the result
~/egos$ git status
On branch master
Your branch and 'origin/master' have diverged,
and have 1 and 1 different commits each, respectively.
…
Unmerged paths:
(use "git add <file>..." to mark resolution)

both modified: src/lib/queue.c

Conflict File Syntax
Inside queue.c: Merged lines
with no conflicts
void queue_add(struct queue *queue, void *item){
struct element *e = calloc(1, sizeof(*e));
HEAD means these
e->item = item; changes are in your
e->next = 0; local HEAD commit
<<<<<<< HEAD
*queue->last = e; Your local version of
queue->last = &e->next; conflicting lines
queue->nelts++;
=======
*q->last = e; Origin repo’s version
q->last = &e->next;
of conflicting lines
q->num_elements++;
>>>>>>> 354a72479204de581ffa83551843b92e585506b8
} Hash of commit from
origin that contains these
conflicting changes
Finishing the Merge
• Edit the file to choose a single version of the conflicting lines
• Make sure to delete the <<<<<<< and ======= lines!
• When you have resolved the conflict:

~/egos$ git add src/lib/queue.c

~/egos$ git commit
# Write a message for the merge commit
~/egos$ git push
Outline
• Git overview
• Git vs. GitHub
• Basic Git commands
• Conflicts and merges
• Branches
• Recovering from errors
Git Branches
• Track different
sequences of commits new-
feature
diverging from common
starting point D E
• Make explicit what A B C J K
happened already when
you & your partner made master
conflicting commits
• Let you choose when to
merge
Branch Basics
thread-
~/egos$ git checkout -b thread-develop develop
Switched to a new branch 'thread-develop'

• Creates a new branch, pointing to same A B C

commit as master
master

~/egos$ git add src/apps/mt.c thread-

~/egos$ git commit develop

• New commit goes on thread-develop,

D
master still points to last commit
A B C

master
Branch Basics
~/egos$ git checkout master
Switched to branch 'master'
Your branch is up to date with 'origin/master'

• Changes your repo’s active branch to thread-

develop
master – you’ll notice the changes you
made to mt.c are gone D

~/egos$ git add src/grass/process.c A B C J

~/egos$ git commit
master
• This commit goes on master, and the
HEAD pointer for master moves up
Pushing and Pulling
• You want to push the commit on your new branch to GitHub:
~/egos$ git checkout thread-develop
Switched to branch 'thread-develop'
~/egos$ git push
fatal: The current branch thread-develop has no upstream branch.
To push the current branch and set the remote as upstream, use

git push --set-upstream origin thread-develop

• OK, do what it says

• After this point, git push will just work
Why Was That Necessary?
• checkout -b only creates a branch on
GitHub repo
your local repo
• GitHub repo won’t add a commit to a ?
branch that doesn’t exist Push

“add this commit to A B C

thread-
thread-develop”
Local repo develop

master
D
Origin
A B C J

master
 Pushing and Pulling
• You want to switch to a new branch your partner created
~/egos$ git checkout thread-develop
error: pathspec 'thread-develop' did not match any file(s) known to git

• Why didn’t that work?

~/egos$ git pull Now the local repo
Remote: Enumerating objects knows about the branch
…
From github.coecis.cornell.edu:etremel/egos
* [new branch] thread-develop -> origin/thread-develop
Already up to date.
~/egos$ git checkout thread-develop
Branch 'thread-develop' set up to track remote branch 'thread-develop' from 'origin'
Switched to a new branch 'thread-develop'
Merging Branches
• Eventually, you’ll want to new-
merge your branch back feature
D E
into master
• First, switch your current A B C J K M
branch to master
master
~/egos$ git pull
~/egos$ git checkout master

• Then, merge the feature Resolve any merge conflicts, same

as when you pull and see conflicts
branch into master
~/egos$ git merge new-feature
~/egos$ git push Publish the merge commit, so
everyone else can see the merge
Repository Design with Branches
• In many software teams, master is the “stable” branch
• Each new feature or bug fix is developed on its own branch
• When tested and safe, branch is merged into master
• While developing on a branch, merge from master into your
branch to get updates and bugfixes

D E F

A B C J K M

L
Outline
• Git overview
• Git vs. GitHub
• Basic Git commands
• Conflicts and merges
• Branches
• Recovering from errors
Some Useful Incantations
• Oops! I made a commit but then made one small change
# Do this BEFORE you push
$ git add changed-file.c
$ git commit --amend --no-edit
• Oops! I want to edit the message on the commit I just made
$ git commit --amend
# Edit the message in your editor

• Oops! I deleted a file and didn’t mean to

$ git checkout path/to/file.c
Branch-Related Problems
• I just made a commit to master, but I should have put it on a new
branch instead
# Create a new branch with the same state as master
$ git branch new-branch-name
# Remove the latest commit from master
$ git reset HEAD~ --hard
# Switch to the new branch, which still has the commit
$ git checkout new-branch-name
Branch-Related Problems
• I just committed to the wrong branch – I thought I was on the
queue-develop branch but I’m on the experiments branch
# Undo the last commit, but leave files changed
$ git reset HEAD~ --soft
# Stash the changed files, then move to the right branch
$ git stash
$ git checkout queue-develop
$ git stash pop
# Commit the changes on the correct branch
$ git add queue.c queue.h
$ git commit
The Unnecessary Merge
• Make changes, commit, push…then realize your repo is stale
$ git push
! [rejected] master -> master (fetch first)
error: failed to push some refs to 'https://github.com/etremel/egos.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.

• Upon pull, you’re prompted to create a merge commit

$ git pull

Merge branch 'master' of https://github.com/etremel/egos.git

# Please enter the commit message for your changes. Lines starting
# with '#' will be ignored, and an empty message aborts the commit
The Unnecessary Merge
• If I had known to pull first, I wouldn’t have to merge!
• First, ensure the merge aborts without making a merge commit
• Either due to genuine conflict, or by deleting the merge commit
message and saving (empty commit message aborts the commit)
• Then:
$ git reset --hard Discard changes made by merge
$ git reset HEAD^ Undo your last commit, leaving files changed
$ git stash
$ git pull # no merge this time Stash your changes, then pull again
$ git stash pop
$ git add foo.c bar.c # etc Re-do your commit on the new head
$ git commit
Further Reading
• Atlassian Git Tutorials:
https://www.atlassian.com/git/tutorials
• Detailed documentation on every command:
https://git-scm.com/docs
• Happy Git with R’s “Useful Git Patterns:”
https://happygitwithr.com/workflows-intro.html
• Oh Shit, Git!?! (source of my error-recovery examples):
https://ohshitgit.com/