rework logic of `_yml_to_dict`

[hovey]

Updated pixel but need update on mesh

       # has_required_keys = all(tuple(map(lambda x: db.get(x) != None, required_keys)))
        # keys_tuple = tuple(map(lambda x: db.get(x), required_keys))
        # has_required_keys = all(tuple(map(lambda x: db.get(x), required_keys)))
        found_keys = tuple(db.keys())
        keys_exist = tuple(map(lambda x: x in found_keys, required_keys))
        has_required_keys = all(keys_exist)
        if not has_required_keys:
            raise KeyError(f"Input files must have these keys defined: {required_keys}")

[hovey]

Fixed on both the pixel and mesh repos.