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How to fix ‘fatal: refusing to merge unrelated histories’ Git error

What is the ‘fatal: refusing to merge unrelated histories’ error?

The fatal: refusing to merge histories error is a fairly common Git error. It appears when a developer tries to merge two unrelated projects into a single branch.

This error appears when the branch has its commit histories and tags incompatible with the pull request or clone.

Why does ‘fatal: refusing to merge unrelated histories’ happen?

Here are some common scenarios where fatal: refusing to merge unrelated histories can occur.

  1. You have a new Git repository with some commits. You then try to pull from an existing remote repo. The merge becomes incompatible because the histories for branch and remote pull are different. Git sees the situation as you trying to merge two completely unrelated branches, and it doesn’t know what to do.
  2. There’s something wrong with the .git directory. It may have been accidentally deleted at some point or got corrupted. This can happen if you’ve cloned or cleaned a project. Here the error occurs because Git doesn’t have the necessary information about your local project’s history.
  3. The branches are at different HEAD positions when you try to push or pull data from a remote repo and cannot be matched due to a lack of commonality.

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How to resolve ‘fatal: refusing to merge unrelated histories’

There are two ways of solving the fatal: refusing to merge unrelated histories error.

Option 1: Use ‘–allow-unrelated-histories’

One way to solve the issue is to use the --allow-unrelated-histories git flag.

Here the git command will look something like this: git pull origin master --allow-unrelated-histories.

You can substitute origin with the remote repository you are pulling from. You can also replace the master branch with whatever branch you want the pull request to merge into.

The idea behind --allow-unrelated-histories is that git lets you merge unrelated branches. This git flag works seamlessly when there are no file conflicts.

However, in reality, at least one thing pops up, and you will need to use the normal Git resolution flow to resolve them.

Here is an example of what a common conflict may look like when trying to merge branches:

 Auto-merging package.json
 CONFLICT (add/add): Merge conflict in package.json
 Auto-merging package-lock.json
 CONFLICT (add/add): Merge conflict in package-lock.json
 CONFLICT (add/add): Merge conflict in
 Auto-merging .gitignore
 CONFLICT (add/add): Merge conflict in .gitignore
 Automatic merge failed; fix conflicts and then commit the result.

Option 2: unstage, stash, clone, unstash, and then commit

The alternative (and longer) way of fixing the fatal: refusing to merge unrelated histories issues is to unstage your current commits, stash them, clone your required remote repository, and then place your stashed branch contents into the new clone.

This will ensure that any conflicts that you may encounter in the code are addressed before merging and prevent application errors from occurring.
To unstage all the files in your last commit, use the following git command: git reset HEAD~.

To stash your unsaved files, use the following git command: git stash.

This will give you a clean working tree to pull your remote repository into. Once you’ve successfully pulled into your branch, you can unstash your files, commit them as a separate commit and resolve any file conflicts that you may have.

To unstash your files, use git pop. This will move the changes stashed and reapplies them to your current working copy.

Alternatively, you can use git stash apply to add the changes to your current working copy of code.

Here is a quick summary of differences between git stash apply and <code”>git pop:

  • git pop: ‘pops’ the changes from the stash and applies them to the current code
  • git stash apply: keeps the changes in the stash and applies the changes to the current code

How to prevent ‘fatal: refusing to merge unrelated histories’

The easiest way to prevent the fatal: refusing to merge unrelated histories error is to avoid pulling remote repositories into branches that already have commits on them.
However, sometimes you just want to keep the commits. One way to prevent the error is to create a brand new branch, pull your required code in, and then manually merge your local branch into your main flow.

Here is a git example of the flow:

# branch A is where your current code is
# clone in your remote repo into a new and separate branch. 
# For our purposes, it's branch B
git clone -b [branch] [remote_repo]
# to merge A into B, you need to be on B
# merge your branches together
git merge A

The only thing about merges is that if there is a conflict in the code, there is no way around it other than resolving it as usual.
Here’s what your merge branch looks like on Git:

          C1---C2---C3 branch A
  Ca---Cb---Cc---Ce---Cf branch B

Kubernetes Troubleshooting with Komodor

The above guide should help you through the troubleshooting steps you need to follow in order to resolve the fatal: refusing to merge unrelated histories Git error.

This is, of course, just one of many Git errors that you may come across in your K8s logs. Such deceptively minor and often easy-to-miss issues can cause serious issues and detecting them could be time-consuming, stressful, and often downright impossible.

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