APC 524 Fall 2022 - Homework 3 Problem 1

This problem will explore the typical use cases of git as a version control for scientific computing. Before proceeding with this problem, make sure you have configured your local git configuration and GitHub account properly. Make sure that the GitHub account that you are using has been added to the class organization. If this is not the case, please contact one of the TA.

This assignment assume that you are using a UNIX shell, you can use the adroit cluster if you wish to. It is a good practice to log the command that you have used as you might need to purge your solution repositories a couple of times while doing this assignment.

Part 1 - Initiating and cloning repository

Most of your work will start by initiating a fresh repository or cloning an already established repository of someone else's codebase. As an eager graduate student you want to do some experiment with the codebase. However, as a nice person, you do not want to accidentally destroy the original codebase or you might not even have write access in the first place. While you can solve this issue by working locally with a cloned repository then pushing it to the remote at the end of your experimentation, this defeats the use of version control for collaboration and additional source of backup.

GitHub has the concept of Fork which creates your own repository based on someone else's repository. Yet, there are several disadvantages of doing this directly especially if you are working with private repositories due to the inherent nature that the forked repositories are always linked to the original repository.

In this part, you are going to learn how to initiate and clone an isolated copy of this repository through these steps:

1. Create a private repository in the class organization with the name format git-exercise-{NETID} such that it is accessible through https://github.com/APC524-F2022/git-exercise-{NETID}.

2. Clone this repository to your local machine and make sure you properly get all of the branches. This can be done by using the command git checkout {branch_name} after cloning.

3. Rename the origin remote pointing to the assignment repository in your local folder to upstream.

4. Add your private repository as the new origin remote and make sure that all local branches are pointing to the new origin as their upstreams.

   After setting this up, you can reset the folder to this point of the assignment whenever you want by using bash reset.sh.

   WARNING: This is an irrecoverable operation!

5. Run this command:

   git checkout main
   git remote -v > remote_data
   git branch -a > branch_data
   git add .
   git commit -m "Remote exercise"
   git push

   Make sure that you can see the same branch structure in your private repository and main is the main branch.

If you make any mistake at this part, you can also delete and recreate your private repository and start from the beginning.

Part 2 - Ignoring files

While doing experimentation with your local copy, you might not want to add some files, like the generated plot or the data file, in your commit. The easiest way to do this is by using .gitignore file, similar to what is included in this repository. As most of you are going to work with python development, the current .gitignore has been populated with a list of typical cache file that can be created during your experimentation.

In this part, you will use .gitignore file to selectively track files in your repositories through these steps:

1. During the compilation process of a C/C++ program you will typically ended up with the object files, with extensions .o and/or .obj, which you want to ignore. Add this new restrictions to your .gitignore and test that it is working as intended by running:

   echo "This file should not be committed" > $(date +%s).o
   echo "This file should not be committed" > $(date +%s).obj
   echo "This file should be committed" > $(date +%s).object
   git add .
   git commit -m "Gitignore exercise part 1"
   git push

2. In your main branch, the file old.o is still currently being tracked, to see that this is the case let's completely change the content of the file before trying to commit using these commands:

   ls -alf > old.o
   git add .
   git commit -m "Gitignore exercise part 2"
   git push

3. Recall that you can remove a file from being tracked by using git rm. Use an option of git rm to stop tracking old.o file without actually removing it from the current directory.

   After doing so run these commands:

   ls -alf > current_files
   git add .
   git commit -m "Gitignore exercise part 3"
   git push

4. Maybe there are some file ending with .obj that you still want to track. Change your .gitignore to make sure this file is tracked. After you finish, run these commands:

   echo "This is an important file" > important.obj
   git add .
   git commit -m "Gitignore exercise part 4"
   git push

Part 3 - Repository conflict

One of the most common issue that you will encounter is that the remote repository is getting updated while you're working on your local branch.

Let's first try to create diverging commit history in the remote repository through these steps:

1. Separately clone your private repository into a different folder in your local machine. Throughout this assignment, this local folder will be referred as friend_copy.

2. Update the file source.py from the current/old version to the new version in friend_copy:

   • Old

     # This is the original source code file
     a = 1 + 1
     print(a)

   • New

     # This is the source code file
     a = 1 + 2.5
     print(a)

3. Commit and push your newly changed source.py from friend_copy to the remote main branch. Use Friend commit as the commit message.

Now go to the original folder that you worked on before where both origin and upstream remotes are defined. Refer this local folder as local_copy and follow these steps:

1. Without pulling, modify the file source.py in local_copy to this new version:

   • Old

     # This is the original source code file
     a = 1 + 1
     print(a)

   • New

     # This is the experimental source code file
     a = 1 + 1
     b = -10
     print(a)
     print(b)

2. Commit your newly changed source.py to your local main branch in local_copy. Use Local commit as the commit message.

3. Attempt to push your commit in local_copy to your origin, make sure to log the error of this to p3_log file using:

   git push 2> p3_log

4. The push should fail as the remote commit history is different than the commit history in the local_copy. The error message suggested that you should try git pull ..., so you should and also log it to your log file using:

   echo "----" >> p3_log
   git pull >> p3_log 2>&1
   git merge --abort

Your goal right now is to incorporate your friend's change to source.py and align the fix history such that the new file has this content:

# This is the source code file
a = 1 + 2.5
b = -10
print(a)
print(b)

There are multiple ways that you can do this with or without overwriting the previous commit. As the conflict is still linear, we can try to put our new commit in local_copy after the last commit in the remote. This can be done using --rebase option of git pull. This option will rebase all of the local commits to the end of remote commit. This means that you might have to resolve merge conflict while doing so.

5. Use git pull --rebase and solve the merge conflict in source.py. After you resolved the merge conflict, execute this command before executing git rebase --continue:

   echo "----" >> p3_log
   cat source.py >> p3_log
   echo "----" >> p3_log
   git status >> p3_log

6. Finish your rebasing process using git rebase --continue, this will put our new commit after the commit from friend_copy.

7. Print out your current commit history using:

   git log --oneline --graph --decorate --all > p3_tree

8. Commit p3_log and p3_tree to a new commit of main branch after the rebased commit and push the two commits to the remote. Use Rebase exercise as the commit message.

Part 4 - Cleaning up

In git, the commit history is not immutable. There might be some cases when you want to change the commit history. For example, you might want to combine the last three commits in the last part as one using git merge --squash option or you might want to remove merge references to other branches.

Using all of the commands that you have seen in class and in this assignment, your goal is to re-organize the commits in your private repository to resemble the following:

                 /----- J -----\
A - B - C ----- G ----- H - I - K - L - M - N - O - P - Q - R - S - T
         \- D - E - F -/

The details of each commits are as follow:

Commit (Branch)	Message	File modified
A	Initial commit	README.md
B	Add miscellaneous files	data.dat, information.txt, PU-standard.png, old.o
C	Add gitignore	.gitignore
D	Add source.py	source.py
E	Fix typo in source.py	source.py
F (python)	Add calculation to source.py	source.py
G	Add reset.sh	reset.sh
H	Merge branch 'python' into main	-
I	Touch up information.txt	information.txt
J (cpp)	Add source.cpp	source.cpp
K	Merge branch 'cpp' into main	-
L	Rewrite README.md; add LICENSE	README.md, LICENSE

Your answers from part 1 will be in the commit M while the answers from part 2 will be in commit N to Q. The last three commits will be coming from your answer to part 3. Your goal is to modify the commit history to be in this form:

 /- J
1 - 3 - 4 - M - 5 - 6
 \- 2 - F

Commit	Message	Commit source or equivalence
1	Initial commit	A, B, C
2	Add source.py	D, E
3	Add source.py and reset.sh	G, H
4	Add source.cpp, edit information.txt README.md	I, K, L
5	Answers from part 2	N, O, P, Q
6	Answers from part 3	R, S, T

While it is possible to use git cherry-pick to simplify some of your task, make sure that each intermediate commits satisfy the prescribed requirements or you will lose some points.

After you finished re-arranging the commit history, please do the following:

1. Print out your current commit history using:

   git log --oneline --graph --decorate --all > p4_tree

2. Commit p4_tree to the current main branch with message Final commit history.

3. As you have now modified your commit history, you will not be able to push your new main branch to the remote. As such create a new private repository within the course organization with a format git-exercise-final-{NETID} and push it to this new remote.