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Gameplan for moving a GitHub repository subdirectory to its own new repository

Relevant discussion with GPT4

Relevant discussion with GPT4

Me
I want to move a GitHub repository subdirectory to its own new repository. Any advice regarding this?

GPT4
Moving a subdirectory from one GitHub repository to its own new repository while preserving its commit history involves a few steps. Here's a step-by-step guide to help you through the process:

Step 1: Clone the Original Repository
First, you'll need a local copy of the original repository. Replace original-repo-url with the URL of your GitHub repository.

git clone original-repo-url
cd name-of-original-repo

Step 2: Filter the Subdirectory
Use the git filter-branch command or the newer git-filter-repo command (which you might need to install separately) to rewrite the repository's history, keeping only the commits that affect the specified subdirectory.

Using git filter-branch (pre-installed with Git but considered somewhat legacy):

git filter-branch --prune-empty --subdirectory-filter path/to/subdirectory HEAD

Using git-filter-repo (faster and more flexible, but requires separate installation): First, install git-filter-repo if you haven't already (see the official documentation for installation instructions).

Then, run:

git-filter-repo --subdirectory-filter path/to/subdirectory

This command rewrites the repository's history to make the root of the subdirectory the new root of the repository.

Step 3: Create a New Repository on GitHub
Go to GitHub and create a new repository for the subdirectory. Note the URL of the new repository.

Step 4: Change the Remote Repository URL
Now, you'll want to push the filtered local repository to the new GitHub repository you just created. First, change the remote URL to the new repository's URL:

git remote set-url origin new-repo-url

Replace new-repo-url with the URL of the new repository you created on GitHub.

Step 5: Push to the New Repository
Finally, push the local repository's content to the new GitHub repository:

git push -u origin master

If you're using a branch name other than master (such as main or something else), adjust the command accordingly.

Additional Considerations

  • Large Repositories: For very large repositories, the filter-branch command can be slow. In such cases, git filter-repo is recommended due to its better performance.
  • Dependencies and References: If the subdirectory has dependencies on other parts of the original repository or if there are references you need to update (such as CI configurations), make sure to adjust those after moving the subdirectory.
  • Archiving: If the original subdirectory will no longer be used in the original repository, consider removing it from there and committing that change to avoid confusion.

By following these steps, you can effectively move a subdirectory from one GitHub repository to its own new repository while retaining its commit history.



On installing git-filter-repo

Relevant conversation with GPT4

Relevant discussion with GPT4

Me
To install git-filter-repo, I just need to put the script somewhere in my system (e.g., maybe my ${HOME}) and then add it to my ${PATH}. How should I go about this?

GPT4
To install git-filter-repo and make it accessible from anywhere on your system, you indeed need to place the script in a directory that's included in your system's ${PATH} variable. Here's a step-by-step guide on how to do this on a Unix-like system (Linux/macOS):

Step 1: Download git-filter-repo
First, download git-filter-repo from its official repository. You can do this by visiting the git-filter-repo GitHub page and downloading the script manually or by using wget or curl in the terminal. For example:

curl -O https://raw.githubusercontent.com/newren/git-filter-repo/main/git-filter-repo

Step 2: Move the Script to a Suitable Location
It's a good practice to keep custom scripts in a dedicated directory within your home directory, such as ${HOME}/bin. If this directory doesn't exist, create it:

mkdir -p ${HOME}/bin

Then move git-filter-repo to this directory:

mv git-filter-repo ${HOME}/bin/

Step 3: Make the Script Executable
Change the permissions of the script to make it executable:

chmod +x ${HOME}/bin/git-filter-repo

Step 4: Add the Directory to Your ${PATH}
To make sure your system can find git-filter-repo when you run it from any location, add ${HOME}/bin to your ${PATH}. Edit your shell's configuration file (.bashrc for Bash, .zshrc for Zsh, etc.):

For Bash, edit .bashrc:

nano ${HOME}/.bashrc

For Zsh, edit .zshrc:

nano ${HOME}/.zshrc

Add the following line to the end of the file:

export PATH="${HOME}/bin:${PATH}"

Save and close the file. Then, apply the changes:

source ${HOME}/.bashrc

Or, if you're using Zsh:

source ${HOME}/.zshrc

Step 5: Verify the Installation
Verify that git-filter-repo is correctly installed and accessible from anywhere by running:

git-filter-repo --version

You should see the version number of git-filter-repo printed to the console.

This completes the installation. You now have git-filter-repo installed and added to your ${PATH}, making it accessible from any location in your terminal.


On using usr/local/bin as the location to store git-filter-rep

Breakdown of what's in my ${PATH}

Here's a breakdown of what's in my ${PATH} as of 2024-0311:

Breakdown of what's in my `${PATH}` 
/opt/homebrew/opt/grep/libexec/gnubin
/opt/homebrew/opt/gnu-which/libexec/gnubin
/opt/homebrew/opt/gnu-tar/libexec/gnubin
/opt/homebrew/opt/gnu-sed/libexec/gnubin
/opt/homebrew/opt/gnu-indent/libexec/gnubin
/opt/homebrew/opt/findutils/libexec/gnubin
/opt/homebrew/opt/ed/libexec/gnubin
/opt/homebrew/opt/libressl/bin
/opt/homebrew/opt/bison/bin
/opt/homebrew/opt/flex/bin
/opt/homebrew/opt/python/libexec/bin
/opt/homebrew/opt/unzip/bin
/opt/homebrew/opt/file-formula/bin
/opt/homebrew/opt/m4/bin
/opt/homebrew/opt/make/libexec/gnubin
/opt/homebrew/opt/coreutils/libexec/gnubin
/opt/homebrew/bin
/Users/kalavattam/miniconda3/bin
/Users/kalavattam/miniconda3/condabin
/opt/homebrew/bin
/opt/homebrew/sbin
/usr/local/bin
/System/Cryptexes/App/usr/bin
/usr/bin
/bin
/usr/sbin
/sbin
/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/local/bin
/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/bin
/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/appleinternal/bin
/opt/X11/bin
/opt/homebrew/opt/fzf/bin
/Users/kalavattam/GTFtools_0.8.0
/Users/kalavattam/bbmap

Relevant discussion with GPT4

Relevant discussion with GPT4

Me
Here are the bin options I have in my $PATH:
/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin

Which one do you think I should work with for git-filter-repo?

GPT4
Given the options in your $PATH, /usr/local/bin is generally the best choice for installing user-level software and scripts like git-filter-repo. This directory is intended for software and scripts that are not managed by the system's package manager and are intended to be accessible to all users on the system. Installing custom or third-party software in /usr/local/bin helps keep them separate from the system's default binaries located in /usr/bin and /bin, and it's a common practice on Unix-like systems.

Here's why /usr/local/bin is a suitable choice:

  • User-installed Software: It's a conventional location for software and scripts installed by the user, rather than software provided by the system's package manager.
  • System-wide Accessibility: Placing the script in /usr/local/bin makes it accessible to all users on the system (assuming they all have /usr/local/bin in their $PATH), which is useful for tools like git-filter-repo that you might want available regardless of the active user.
  • Avoids Overwriting System Binaries: By using /usr/local/bin, you reduce the risk of overwriting system binaries or creating conflicts with system-managed files in /usr/bin and /bin.

Steps to install git-filter-repo in /usr/local/bin
Download git-filter-repo (if you haven't already):

curl -O https://raw.githubusercontent.com/newren/git-filter-repo/main/git-filter-repo

Move and rename (optional) the script to /usr/local/bin:

sudo mv git-filter-repo /usr/local/bin/git-filter-repo

Make it executable:

sudo chmod +x /usr/local/bin/git-filter-repo

Verify installation:

git-filter-repo --version

By following these steps, you'll install git-filter-repo in a standard, system-wide accessible location that aligns with Unix conventions for user-installed software.



What is the new-repo-url for a repository I have created?

Relevant discussion with GPT4

Relevant discussion with GPT4

Me
How can I figure out what is the new-repo-url for a repository I have created?

E.g., with respect to this command:

git remote set-url origin new-repo-url

GPT4
To figure out the new-repo-url for a repository you've created, you'll need to obtain the URL provided by GitHub (or another Git hosting service) for that repository. Here's how you can do it on GitHub, which is a common scenario:

Finding the Repository URL on GitHub

  1. Navigate to Your GitHub Repository: Open your web browser and go to your GitHub account. Then, navigate to the repository you've created.
  2. Locate the "Code" Button: On the repository's main page, you'll see a green button labeled "Code" near the top right, just above the file list.
  3. Get the Repository URL: Click the "Code" button. A dropdown menu will appear, offering you options to clone the repository with HTTPS, SSH, or GitHub CLI. Here are your options:
  • HTTPS: If you're using HTTPS, simply copy the URL shown (it will look something like https://github.com/username/repo-name.git).
  • SSH: If you're using SSH, switch to the SSH tab and copy the SSH URL (it will look like [email protected]:username/repo-name.git).
  • GitHub CLI: For using the GitHub CLI, it shows a command rather than a URL, so you'd typically use HTTPS or SSH URLs for setting remote URLs.

Using the Repository URL in Git
Once you've copied the repository URL, use it in your command to set the new remote URL:

git remote set-url origin <new-repo-url>

Replace with the URL you just copied. For example:

git remote set-url origin https://github.com/username/repo-name.git

or with SSH:

git remote set-url origin [email protected]:username/repo-name.git

Confirming the Change
After changing the remote URL, you can confirm that the operation was successful by listing the remote URLs associated with your repository:

git remote -v

This command will show you the URLs for fetching and pushing for each remote associated with your local repository. After executing the set-url command, you should see the remote URL for origin has been updated to the new URL you provided.

This process applies to GitHub, but the steps are similar for other Git hosting services like GitLab or Bitbucket, with differences mainly in how they structure their repository URLs and where the clone URL can be found on their respective web interfaces.



On where to run git remote set-url origin new-repo-url

Relevant discussion with GPT4

Relevant discussion with GPT4

Me
Currently, I am in the following directory,

/Users/kalavattam/repos/bak/2023_rDNA

and I have just run the following command,

git-filter-repo --subdirectory-filter "results/2023-0406_tutorial_ChIP-seq_analyses"

which printed the following to my console,

Parsed 229 commits
New history written in 0.48 seconds; now repacking/cleaning...
Repacking your repo and cleaning out old unneeded objects
HEAD is now at ecf547c Finally pushing the last couple weeks of work (but not the scratch work) to the tutorial repo; this work concerned various set operations with ChIP-seq MACS3 peak sets (Rachel's data: Esa1, Gcn5, and Rpd3)
Enumerating objects: 170, done.
Counting objects: 100% (170/170), done.
Delta compression using up to 8 threads
Compressing objects: 100% (98/98), done.
Writing objects: 100% (170/170), done.
Total 170 (delta 76), reused 130 (delta 72), pack-reused 0
Completely finished after 0.70 seconds.

According to your instructions, the next step is as follows:

Step 4: Change the Remote Repository URL
Now, you'll want to push the filtered local repository to the new GitHub repository you just created. First, change the remote URL to the new repository's URL:

git remote set-url origin new-repo-url

Replace new-repo-url with the URL of the new repository you created on GitHub.

Am I to run git remote set-url origin new-repo-url, where new-repo-url is https://github.com/kalavattam/2023_teaching.git from my current directory, /Users/kalavattam/repos/bak/2023_rDNA?



Install git-filter-rep to /usr/local/bin

Relevant discussion with GPT4

Relevant discussion with GPT4

Me

cd /usr/local/bin

sudo curl -O https://raw.githubusercontent.com/newren/git-filter-repo/main/git-filter-repo

sudo chmod +x git-filter-repo

git-filter-repo --version
# ae71fad1d03f

GPT4
Yes, based on your current directory (/Users/kalavattam/repos/bak/2023_rDNA) and the steps you've followed so far with git-filter-repo, you should run the git remote set-url origin new-repo-url command with new-repo-url being https://github.com/kalavattam/2023_teaching.git from your current directory. This command will change the remote URL of the repository located in your current directory to point to the new repository on GitHub, allowing you to push the filtered history to the new repository.

Here's how to do it:

  1. Ensure you are in the correct directory (/Users/kalavattam/repos/bak/2023_rDNA). If you're not sure, you can verify your current directory by running:
pwd

Change the remote URL to the new repository's URL:

git remote set-url origin https://github.com/kalavattam/2023_teaching.git

You can confirm that the remote URL was successfully updated by listing the current remotes with their URLs:

git remote -v

You should see the URL for the origin remote has been updated to https://github.com/kalavattam/2023_teaching.git.

After updating the remote URL, you're ready to push the changes to the new repository. Since git-filter-repo has rewritten the history, it is a good practice to use git push --force to overwrite the history in the remote repository with your newly filtered history:

git push --force origin master

If you're using a different default branch (such as main), replace master with the name of your default branch in the command above.



What if there is no such remote as origin?

Relevant discussion with GPT4

Relevant discussion with GPT4

Me
How can I troubleshoot this? How can I find the name I should use instead of origin?

❯ git remote set-url origin https://github.com/kalavattam/2023_teaching.git
error: No such remote 'origin'

GPT4
The error message No such remote 'origin' indicates that there is no remote repository with the name origin currently associated with your local Git repository. You can troubleshoot and resolve this issue by following these steps:

List Existing Remotes
First, check the current remotes associated with your repository to see what they're named:

git remote -v

This command will list all the remote repositories your local repository knows about, along with the URLs associated with the fetch and push actions for each remote.

Add a New Remote
If the output of git remote -v does not list an origin (or if there are no remotes listed at all), you need to add a new remote with the name origin pointing to your GitHub repository URL:

git remote add origin https://github.com/kalavattam/2023_teaching.git

Rename an Existing Remote
If there is a remote, but it's not named origin (for example, if it's named upstream or some other name), and you want to rename it to origin, you can use the git remote rename command:

git remote rename existing_remote_name origin

Replace existing_remote_name with the actual name of the remote you found using git remote -v.

Set the URL for an Existing Remote
If there's already a remote with a different name, and you simply want to change its URL without renaming it to origin, you can replace origin in the original command with the actual name of your remote:

git remote set-url existing_remote_name https://github.com/kalavattam/2023_teaching.git

Again, replace existing_remote_name with the name of the remote you're intending to update.

Confirm the Changes
After adding, renaming, or updating the remote, run git remote -v again to confirm that the changes were made successfully. You should now see the origin remote (or whichever name you've chosen to use) listed with the correct URL to your GitHub repository.

With the remote correctly set up, you can proceed with pushing your changes to the repository using git push (you might need to use --force or --set-upstream options depending on your situation).



Is it enough to run git remote add origin prior to running git push -u origin master?

Relevant discussion with GPT4

Relevant discussion with GPT4

Me
I have run the following command:

git remote add origin https://github.com/kalavattam/2023_teaching.git

Having done so, can I proceed with Step #5?

Step 5: Push to the New Repository Finally, push the local repository's content to the new GitHub repository:

git push -u origin master

If you're using a branch name other than master (such as main or something else), adjust the command accordingly.

GPT4
Yes, after successfully adding a remote named origin with the command you've run:

git remote add origin https://github.com/kalavattam/2023_teaching.git

You can proceed with Step #5 and push the local repository's content to the new GitHub repository. However, you should check which branch you are currently on, especially since many repositories now use main as the default branch name instead of master.

To check your current branch, use:

git branch

The branch you're currently on will be marked with an asterisk (*).

If your current branch is master, you can follow the step as written:

git push -u origin master

If your branch is named differently, such as main or any other name, you should replace master with the name of your current branch:

git push -u origin main

The -u flag sets the upstream for your branch, linking your local branch with the remote one, which will make future pushes (simply git push) and pulls automatically refer to this upstream setting without needing to specify the remote and branch names.

If you have just filtered your repository and it's the first time you are pushing to this new repository, you may need to use the --force flag because git-filter-repo rewrites the history, which can cause discrepancies with the remote history:

git push -u origin main --force

Replace main with your actual branch name if it's different.



On encountering an error with git push -u origin main

Relevant discussion with GPT4

Relevant discussion with GPT4

Me
After running this command,

git push -u origin main

I got the following error message:

❯ git push -u origin main
To https://github.com/kalavattam/2023_teaching.git
 ! [rejected]        main -> main (fetch first)
error: failed to push some refs to 'https://github.com/kalavattam/2023_teaching.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.
hint: See the 'Note about fast-forwards' in 'git push --help' for details.

Regarding 2023_teaching, I don't care about any "work that [I] do not have locally". How can I move forward? Is it possible for me to force the push?

GPT4
Yes, you can force the push if you're sure that you don't need any commits that are currently on the remote repository and that overwriting the history on the remote is safe in your context. This situation often arises after using tools like git-filter-repo, where you've intentionally rewritten the history of your repository and need the remote repository to reflect these changes.

To force the push to the remote repository and overwrite its history with your local history, you can use the --force flag with git push:

git push -u origin main --force

Or, as a safer alternative, you can use --force-with-lease, which ensures you do not overwrite the work of others on the remote repository in case there have been updates to it since you last fetched:

git push -u origin main --force-with-lease

The --force-with-lease option is generally recommended over --force because it provides an extra level of safety, ensuring that you do not accidentally overwrite remote changes you're unaware of. However, if you're absolutely certain that it's safe to overwrite the remote repository (for instance, if it's a new repository or you're the only one working on it), using --force is acceptable.

Remember, using --force or --force-with-lease will overwrite the history on the remote. This action cannot be undone and may result in loss of work if not used carefully. Always make sure that this is what you really intend to do before proceeding.



On actually filtering the repository subdirectory—i.e., moving a GitHub repository subdirectory to its own new repository

Code

Code 
#!/bin/bash

cd /usr/local/bin

sudo curl -O https://raw.githubusercontent.com/newren/git-filter-repo/main/git-filter-repo

sudo chmod +x git-filter-repo

git-filter-repo --version

cd ~/repos

mkdir bak

cd bak

gh repo clone kalavattam/2023_rDNA

cd 2023_rDNA

git-filter-repo --subdirectory-filter "results/2023-0406_tutorial_ChIP-seq_analyses"

git remote set-url origin https://github.com/kalavattam/2023_teaching.git
#  Error

git remote -v
#  Returns nothing

git remote add origin https://github.com/kalavattam/2023_teaching.git
#  Seems to have worked 

git branch
# * main

# git push -u origin main  # See question below
git push -u origin main --force
# Enumerating objects: 170, done.
# Counting objects: 100% (170/170), done.
# Delta compression using up to 8 threads
# Compressing objects: 100% (94/94), done.
# Writing objects: 100% (170/170), 2.97 MiB | 3.40 MiB/s, done.
# Total 170 (delta 76), reused 170 (delta 76), pack-reused 0
# remote: Resolving deltas: 100% (76/76), done.
# To https://github.com/kalavattam/2023_teaching.git
#  + 6236e05...ecf547c main -> main (forced update)
# branch 'main' set up to track 'origin/main'.