'Failed to create commit: current tip is not the first parent' for basic commit

I am trying to do something relatively simple which is just add and commit file changes to an existing repository as i would through the command line. The one complicating caveat is i am calling the code to do this from inside a submodule, however everything seems to be okay until the commit part.

In the folder above the code/submodule folder i have another which is the main git repo and which also has a folder of data i wish to monitor and commit changes of.

The code is

data_repo = pygit2.Repository('../')

index = data_repo.index
index.add_all(pathspecs=["tables/"]) # Because of the data repo path we are already in that repo local path so all paths relative to that
index.write()
tree = index.write_tree()
modified_tables = [ x for x in data_repo.status().keys() if 'tables' in x]

author = pygit2.Signature('Alice Author', 'alice@authors.tld')
committer = pygit2.Signature('GitRateWatcher', 'me@internet.com')
msg  = f"GitRateWatcher commit on {datetime.datetime.today().date()} modified tables: {', '.join(modified_tables)}"
oid = data_repo.create_commit('refs/heads/master', author, committer, msg, tree, [] )
data_repo.head.set_target(oid)

However when I try this i get

_pygit2.GitError: failed to create commit: current tip is not the first parent

if i remove the 'refs/heads/master' part it works but it basically does a rebase and wipes all previous stuff which is no good either. What am I missing?

Start with the shown data_repo.create_commit call and the refs/heads/master target, then inspect how its parent list relates to the repository's current tip. Reproduce the submodule and parent-repository layout from the issue and verify that a new commit preserves the existing history rather than rebasing it. Done means the commit succeeds while retaining the prior branch history.