T023/25/26: ImportError: cannot import name 'ParamSpec' from 'typing_extensions'

[dominiquesydow]

In our CI, T023/25/26 fails (but not T012 and T014 that also use the same import), see traceback below.

I cannot reproduce this behaviour locally (MacOS/M1) 🙄

---

___ teachopencadd/talktorials/T023_what_is_a_kinase/talktorial.ipynb::Cell 5 ___
[gw1] darwin -- Python 3.8.15 /usr/local/miniconda/envs/teachopencadd/bin/python
Notebook cell execution failed
Cell 5: Cell execution caused an exception

Input:
from opencadd.databases.klifs import setup_remote

klifs = setup_remote()
structures_df = klifs.structures.all_structures()

# Get number of structures per kinase
n_structures_per_kinase = (
    structures_df.groupby(["structure.pdb_id", "kinase.klifs_name"])
    .first()
    .reset_index()
    .groupby("kinase.klifs_name")
    .size()
)

# Save in KinMap format
kinmap_n_structures_per_kinase = format_for_kinmap(
    n_structures_per_kinase.index, n_structures_per_kinase.values
)
kinmap_n_structures_per_kinase.to_csv(DATA / "kinmap_n_structures_per_kinase.csv", index=None)
# Some kinases will not be resolved in KinMap and will be simply dropped

Traceback:

---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
Cell In[6], line 1
----> 1 from opencadd.databases.klifs import setup_remote
      3 klifs = setup_remote()
      4 structures_df = klifs.structures.all_structures()

File /usr/local/miniconda/envs/teachopencadd/lib/python3.8/site-packages/opencadd/databases/klifs/__init__.py:5
      1 """
      2 opencadd.databases.klifs module
      3 """
----> 5 from .api import setup_local, setup_remote

File /usr/local/miniconda/envs/teachopencadd/lib/python3.8/site-packages/opencadd/databases/klifs/api.py:11
      7 import logging
      9 import pandas as pd
---> 11 from .session import Session
     13 # Set logger
     14 _logger = logging.getLogger(__name__)

File /usr/local/miniconda/envs/teachopencadd/lib/python3.8/site-packages/opencadd/databases/klifs/session.py:11
      7 from pathlib import Path
      9 import pandas as pd
---> 11 from . import remote
     12 from . import local
     13 from .remote import KLIFS_CLIENT

File /usr/local/miniconda/envs/teachopencadd/lib/python3.8/site-packages/opencadd/databases/klifs/remote.py:12
      9 from pathlib import Path
     11 import pandas as pd
---> 12 from bravado.client import SwaggerClient
     14 from .core import (
     15     KinasesProvider,
     16     LigandsProvider,
   (...)
     24     StructureModifiedResiduesProvider,
     25 )
     26 from .schema import FIELDS

File /usr/local/miniconda/envs/teachopencadd/lib/python3.8/site-packages/bravado/client.py:53
     51 from bravado_core.exception import SwaggerMappingError
     52 from bravado_core.formatter import SwaggerFormat  # noqa
---> 53 from bravado_core.param import marshal_param
     54 from bravado_core.spec import Spec
     55 from six import iteritems

File /usr/local/miniconda/envs/teachopencadd/lib/python3.8/site-packages/bravado_core/param.py:13
     11 from bravado_core.content_type import APP_JSON
     12 from bravado_core.exception import SwaggerMappingError
---> 13 from bravado_core.marshal import marshal_schema_object
     14 from bravado_core.unmarshal import unmarshal_schema_object
     15 from bravado_core.validate import validate_schema_object

File /usr/local/miniconda/envs/teachopencadd/lib/python3.8/site-packages/bravado_core/marshal.py:11
      9 from bravado_core import schema
     10 from bravado_core.exception import SwaggerMappingError
---> 11 from bravado_core.model import Model
     12 from bravado_core.model import MODEL_MARKER
     13 from bravado_core.schema import collapsed_properties

File /usr/local/miniconda/envs/teachopencadd/lib/python3.8/site-packages/bravado_core/model.py:13
     11 from six import iteritems
     12 from six import string_types
---> 13 from swagger_spec_validator.ref_validators import attach_scope
     15 from bravado_core.schema import collapsed_properties
     16 from bravado_core.schema import is_dict_like

File /usr/local/miniconda/envs/teachopencadd/lib/python3.8/site-packages/swagger_spec_validator/__init__.py:1
----> 1 from swagger_spec_validator.common import SwaggerValidationError
      2 from swagger_spec_validator.util import validate_spec_url
      4 __all__ = [
      5     "SwaggerValidationError",
      6     "validate_spec_url",
      7 ]

File /usr/local/miniconda/envs/teachopencadd/lib/python3.8/site-packages/swagger_spec_validator/common.py:17
     15 import yaml
     16 from pkg_resources import resource_filename
---> 17 from typing_extensions import ParamSpec
     19 try:
     20     from yaml import CSafeLoader as SafeLoader

ImportError: cannot import name 'ParamSpec' from 'typing_extensions' (/usr/local/miniconda/envs/teachopencadd/lib/python3.8/site-packages/typing_extensions.py)
`
``

[dominiquesydow]

I do not know what happened but this issue disappeared for now from our CI.