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You should be able to update this setting from the Update a repository endpoint. You'll pass that configuration using the allow_auto_merge parameter on the body of that request.
The GitHub Actions bot should be able to merge pull requests if it has write permission on pull requests. If you need to grant write permissions to GitHub Actions workflow through the API, you can do that using the following endpoints(both organizational and repository level):
Allow for configuring auto-merge on a repository, it should be under the generic tests.
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