Cannot Import Any Embedder "load()" has been removed, use yaml = YAML(typ='rt') yaml.load(...)

[wijuliano]

Hello everyone,

I tried to import both SeqVecEmbedder and ProtTransBertBFDEmbedder and it keeps giving the same error.
I have tried uninstalling/installing again and changing Python versions. None solved my issue.

Let me know if anyone is facing the same issue and how to solve it.

`---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
Cell In[2], line 1
----> 1 from bio_embeddings.embed import ProtTransBertBFDEmbedder
2 from Bio import SeqIO

File ~/.local/lib/python3.8/site-packages/bio_embeddings/init.py:12
1 """
2 The functionality of bio_embeddings is split into 5 different modules
3
(...)
9 bio_embeddings.visualize
10 """
---> 12 import bio_embeddings.embed
13 import bio_embeddings.extract
14 import bio_embeddings.project

File ~/.local/lib/python3.8/site-packages/bio_embeddings/embed/init.py:67
64 import logging
65 from typing import Dict, Type
---> 67 from bio_embeddings.embed.embedder_interfaces import EmbedderInterface
68 from bio_embeddings.embed.fasttext_embedder import FastTextEmbedder
69 from bio_embeddings.embed.glove_embedder import GloveEmbedder

File ~/.local/lib/python3.8/site-packages/bio_embeddings/embed/embedder_interfaces.py:17
14 import torch
15 from numpy import ndarray
---> 17 from bio_embeddings.utilities import (
18 get_model_file,
19 get_model_directories_from_zip,
20 get_device,
21 )
23 logger = logging.getLogger(name)
26 class EmbedderInterface(abc.ABC):

File ~/.local/lib/python3.8/site-packages/bio_embeddings/utilities/init.py:12
8 from bio_embeddings.utilities.filemanagers.FileManagerInterface import (
9 FileManagerInterface,
10 )
11 from bio_embeddings.utilities.helpers import *
---> 12 from bio_embeddings.utilities.remote_file_retriever import (
13 get_model_file,
14 get_model_directories_from_zip,
15 )
17 all = [
18 "FileManagerInterface",
19 "FileSystemFileManager",
(...)
31 "write_fasta_file",
32 ]

File ~/.local/lib/python3.8/site-packages/bio_embeddings/utilities/remote_file_retriever.py:18
15 from bio_embeddings.utilities.config import read_config_file
17 _module_dir: Path = Path(os.path.dirname(os.path.abspath(file)))
---> 18 _defaults: Dict[str, Dict[str, str]] = read_config_file(_module_dir / "defaults.yml")
20 logger = logging.getLogger(name)
23 class TqdmUpTo(tqdm):

File ~/.local/lib/python3.8/site-packages/bio_embeddings/utilities/config.py:58, in read_config_file(config_path, preserve_order)
56 try:
57 if preserve_order:
---> 58 return yaml.load(fp, Loader=yaml.RoundTripLoader)
59 else:
60 return yaml.safe_load(fp)

File /opt/jupyterhub/lib/python3.8/site-packages/ruamel/yaml/main.py:1085, in load(stream, Loader, version, preserve_quotes)
1078 def load(
1079 stream: Any, Loader: Any = None, version: Any = None, preserve_quotes: Any = None,
1080 ) -> Any:
1081 """
1082 Parse the first YAML document in a stream
1083 and produce the corresponding Python object.
1084 """
-> 1085 error_deprecation('load', 'load', arg=_error_dep_arg, comment=_error_dep_comment)

File /opt/jupyterhub/lib/python3.8/site-packages/ruamel/yaml/main.py:1037, in error_deprecation(fun, method, arg, comment)
1035 s += '\n'
1036 if sys.version_info < (3, 10):
-> 1037 raise AttributeError(s)
1038 else:
1039 raise AttributeError(s, name=None)

AttributeError:
"load()" has been removed, use

yaml = YAML(typ='rt')
yaml.load(...)

and register any classes that you use, or check the tag attribute on the loaded data,
instead of file "/home/juliano/.local/lib/python3.8/site-packages/bio_embeddings/utilities/config.py", line 58

            return yaml.load(fp, Loader=yaml.RoundTripLoader)