Intermediate Git and GitHub

Assumed knowledge

In this course, we assume familiarity with the following Git commands and GitHub concepts:

• add, commit, push, pull, log
• Issues
• Pull requests (PRs)

If these are new to you then please join the Introduction to Git and GitHub for Beginners course, which is running in parallel.

Contents

1. Branching and conflicts.
2. Intermediate Git commands.
3. Software engineering with GitHub.
4. Tips, tricks, and fun stuff!

GitHub

Navigate to the GitHub repo: https://github.com/Cambridge-ICCS/intermediate-git-iccs-summer-school-2024

Exercises

1. Check you are happy with the contents of the README.
2. Create a fork of the repo under your username.
3. Clone your fork to your local machine.

1. Branching and conflicts

Branching basics

The main branch is protected in our repo, meaning contributors cannot push directly to it. (More on this later.)

To contribute to main, create a branch for your developments and open a PR when it's ready.

Branching basics

The main branch is protected in our repo, meaning contributors cannot push directly to it. (More on this later.)

To contribute to main, create a branch for your developments and open a PR when it's ready.

Branch-of-branch

Suppose mybranch adds a significant new feature. What if you spot a bug and have a fix for it?

develop branch

Large codes often have a develop branch in addition to the main branch.

Merge conflicts

What if two branches modify the same part of a file?

Merge conflict example

Consider the following enhancements to equation_of_line:

#12: Implement Lagrange polynomial approach.
#13: Check that the points provided differ.
#14: Implement SymPy approach.

2. Intermediate Git commands

Checking state: git status

Snapshot of changes staged and not staged for commit.

On branch mybranch
Your branch is up-to-date with 'origin/mybranch'.

Changes to be committed:
  (use "git restore --staged <file>..." to unstage)
	deleted:    README.md
	renamed:    maths.py -> mathematics.py
	new file:   physics.py

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

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

Checking state: git diff

Useful but not meant for human consumption

Checking state: git difftool

• Syntax highlighting AND context
• Much easier to read
  Image Not Showing Possible Reasons

  • The image file may be corrupted
  • The server hosting the image is unavailable
  • The image path is incorrect
  • The image format is not supported

  Learn More →

Checking state: git difftool

Configure by adding the following to your ~/.gitconfig:

[diff]
	tool = vimdiff
[difftool]
	prompt = false

Or run these commands:

git config --global diff.tool vimdiff
git config --global difftool.prompt false

Temporary work: git patch

I need to put aside temporary work and do some branch manipulations. How?

git diff > my_patch.patch  # Stash your current changes
git restore .              # Restore latest commit

# <Do the required branch manipulations>

git apply my_patch.patch   # Reapply changes from the patch

Temporary work: git patch

I need to put aside temporary work and do some branch manipulations. How?

git diff > my_patch.patch  # Stash your current changes
git restore .              # Restore latest commit

# <Do the required branch manipulations>

git apply my_patch.patch   # Reapply changes from the patch

Temporary work: git patch

I need to put aside temporary work and do some branch manipulations. How?

git diff > my_patch.patch  # Stash your current changes
git restore .              # Restore latest commit

# <Do the required branch manipulations>

git apply my_patch.patch   # Reapply changes from the patch

Temporary work: git stash

Why do I keep finding tmp.patch files everywhere?
Stashing changes puts them on the stack.

git stash
    
# <Do the required branch manipulations>
    
git stash pop

git stash list

stash@{0}: WIP on impl3: 8895c93 Add SymPy as a dependency
stash@{1}: WIP on check_points_differ: a92866d Raise error if points are identical
stash@{2}: WIP on main: a58ff9a Merge pull request #9 from Cambridge-ICCS/impl1

Editing history: git rebase

Image Not Showing Possible Reasons

• The image file may be corrupted
• The server hosting the image is unavailable
• The image path is incorrect
• The image format is not supported

Learn More →

Some common problems:

1. I want to drop some commits from my branch.
2. I want to reword a commit message.
3. I want to squash some commits in my branch.
4. I want to change the 'base' of my branch to start at the head of another branch.

All these things (and more) can be done with git rebase - one of the most powerful Git tools.

Editing history: git rebase

Image Not Showing Possible Reasons

• The image file may be corrupted
• The server hosting the image is unavailable
• The image path is incorrect
• The image format is not supported

Learn More →

I want to change the 'base' of my branch to start at the head of another branch.

Consider the simple case of upgrading to a later version.

Editing history: git rebase

Image Not Showing Possible Reasons

• The image file may be corrupted
• The server hosting the image is unavailable
• The image path is incorrect
• The image format is not supported

Learn More →

Some common problems:

1. I want to drop some commits from my branch.
2. I want to reword a commit message.
3. I want to squash some commits in my branch.
4. I want to change the 'base' of my branch to start at the head of another branch.

Editing history: git reflog

Ahh, my rebase broke things! How can I reverse it?

92d0571 (HEAD -> rebase-exercise, origin/rebase-exercise) HEAD@{0}: commit: Instructions for task 4
e6509be HEAD@{1}: commit: Drop this commit
3131c09 HEAD@{2}: commit: Reword this commit message
007117a HEAD@{3}: commit: Squash this commit into the previous one
09a6337 HEAD@{4}: commit: Squash the following commit into this one
93212e5 (origin/main, origin/HEAD, main) HEAD@{5}: checkout: moving from main to rebase-exercise

Go back to an earlier state with (for example)
git reset --hard 3131c09.

Note that the reset goes in the reflog, too!

3. Software engineering with GitHub

GitHub: Project boards

The example repository has a Project Board for planning and tracking progress.

Note: project boards are associated with users or organisations, rather than repositories.

GitHub Actions: cloud testing

From Wikipedia:

Continuous integration (CI) is the practice of integrating source code changes frequently and ensuring that the integrated codebase is in a workable state.

CI testing is the part that ensures the codebase is in a 'workable state'.

This was added to the example repo in #9.

GitHub: Files to always include

• LICENSE: Sets out how the code may be interacted with (e.g., can it be redistributed?)
• README.md: Tells users what the repository is for and important details about its usage (e.g., installation instructions).

GitHub: Settings to always use

• Protect main branch.
• Ensure tests pass before merging PRs.
• Require PR approvals.
• Do not allow bypassing rules.

Debugging on GitHub Actions

Debug GitHub Actions using tmate

name: CI
on: [push]
jobs:
  build:
    runs-on: ubuntu-latest
    steps:
    - uses: actions/checkout@v4
    - name: Setup tmate session
      uses: mxschmitt/action-tmate@v3

4. Tips, tricks, and fun stuff!

The following slides are for information. We might not get to them in the live course.

git bisect: a debugging life-saver

A bug was introduced somewhere in the development process, but it's unclear when. What do I do?

GitHub Container Registry

• Like DockerHub but easier to integrate with GitHub
• Store container images on your account
• Inherit project permissions or set granular permissions

runs-on: ubuntu-latest
container:
    image: ghcr.io/<YOUR_USERNAME>/<IMAGE_NAME>:<IMAGE_TAG>
    credentials:
       username: <YOUR_USERNAME>
       password: ${{  secrets.DOCKER_CONTAINER_REGISTRY_TOKEN }} 

.gitignore

Does this git status look familiar to anyone?

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

Untracked files:
  (use "git add <file>..." to include in what will be committed)
	FIXME
	Notes.txt
	TODO
	__pycache__/
	a.out
	job.err
	job.out
	maths.py.swp
	output.nc
	test_maths.py.swp
	tmp.patch
	tmp2.patch

.gitignore

Ignore certain subdirectories, filename patterns, and/or extensions with a .gitignore file. For example:

# Directories
__pycache__/

# Other common files
FIXME
NOTES
Notes.txt
TODO

# File extensions
*.*.swp
*.err
*.nc
*.out
*.patch
*.pyc

git config

Recall how we configured git difftool with a .gitconfig file. We can do the same for other Git commands:

[user]
    name = Joe Bloggs            # User credentials to be used in
    email = j.bloggs@blogco.com  #   commits
[init]
    defaultBranch = trunk        # Default branch other than 'main'
[core]
    commentChar = &              # Comment character other than '#'
    excludesFile = ~/.gitignore  # Global .gitignore file
[column]
    ui = auto                    # Allow multi-column output
[alias]
    ci = commit                  # Aliases/shortcuts for Git commands
    co = checkout                #   (Any subversion users in the
    st = status                  #   room?)

Fun stuff

Image Not Showing Possible Reasons

• The image file may be corrupted
• The server hosting the image is unavailable
• The image path is incorrect
• The image format is not supported

Learn More →

Thank you for attending!