patterns: List[str]

elif root_path not in dirpath.parents:

len(set(path.parents).intersection(exclude_paths)) != 0 is equivalent to set(path.parents).intersection(exclude_paths) when coerced to bool.

(also, shorter version if you prefer: set(path.parents) & exclude_paths)

Jenkins reports this code is never ran by the tests

Instead of duplicating the code to call Directory.from_disk, you could define dir_filter like this:

if exclude_paths:
    def dir_filter(dirpath, *args):
        return directory_filter(dirpath, exclude_paths)
else:
    dir_filter = None

(mypy might pout, but adding type annotations should work)

should just be else, to handle non-regular files.

same here

Does this really need to be a separate case? Doesn't Directory.from_disk handle roots that are a file?

exclude_paths: Set[PosixPath]

Avoid mutables as default value. It's fine here; but it's a bad habit (it's instantiated on function declaration, not on function call; so mutating it once affects all future calls)

this test doesn't fail if get_subpaths returns nothing, which is what happens here.

You should assign the return value of get_subpaths, check the length, then iterate on it.

Could you write test(s) for this function?

You could compile patterns here, so fnmatch doesn't need to recompile for each call to directory_filter.