Automatically refactor the code in an entire github organization

run.sh

#!/bin/bash
set -ex

# Define your GitHub username and organization name
YOUR_USERNAME="pepijndevos"
ORG_NAME="SciML"

# Iterate through the organization's repositories
REPO_LIST=$(gh repo list $ORG_NAME --json name --limit 1000 --no-archived)

for repo in $(echo "$REPO_LIST" | jq -r '.[].name'); do
  if [ -d "$repo" ]; then
    echo "Skipping $repo. Directory already exists."
    continue
  fi

  git clone "https://github.com/$ORG_NAME/$repo.git" 


  cd "$repo"

  # Run the specified command
  git ls-files -z | xargs -0 sed -i -e 's/typeof(\([^)]*\)) <:/\1 isa/g'

  # Check if the diff is empty
  if [[ -z $(git diff --color) ]]; then
    echo "No changes in $repo. Skipping pull request."
  else
    # Ask for confirmation before creating the pull request
    read -p "Do you want to create a pull request for $repo? (y/n): " confirm
    if [[ $confirm == "y" ]]; then
      git branch new-branch
      git checkout new-branch

      # Commit changes
      git commit -am "Change typeof(x) <: y to x isa y"

      # Fork the repository to your account
      gh repo fork "$ORG_NAME/$repo" --clone=false
      sleep 5 # let it finish or something?
 
      # Push changes to a new branch
      git remote add fork git@github.com:$YOUR_USERNAME/$repo.git
      git push fork new-branch

      # Create a pull request in the original repository
      gh repo set-default "$ORG_NAME/$repo"
      gh pr create --head "$YOUR_USERNAME:new-branch" --title "Change typeof(x) <: y to x isa y" --body "This PR has been automatically generated by a script co-authored by ChatGPT"
    fi
  fi

  # Go back to the original directory
  cd ..
done