Error Alchemy bio2bel hmdb

[wgarzon]

I'm trying to run bio2bel_hmdb in Python 3.7 and 3.8, but I got an error message, and I don't find how to solve it.
The error message:

from .abstract_manager import AbstractManager, get_bio2bel_manager_classes
File "/home/wgarzon/bio2bel/src/bio2bel/manager/abstract_manager.py", line 14, in
from sqlalchemy.ext.declarative.api import DeclarativeMeta
ModuleNotFoundError: No module named 'sqlalchemy.ext.declarative.api'

I appreciate knowing the tested versions libraries required to use bio2bel_hmdb. I'm using a Debian version. I tried with conda and local environments.

Thanks

[cthoyt]

I'm guessing the issue is SQLAlchemy version 1.4 did a lot of reorganizing preparing for a 2.0 release. If you can upgrade to the 1.3.* series, this might resolve the issue. I haven't touched the bio2bel code in a while so unfortunately this will be a pain to update the whole series :/

[cthoyt]

Please let me know if that solves the issue

[wgarzon]

The SQLAlchemy problem was solved.

Now, new error:
File "/home/wgarzon/anaconda3/envs/metabol/lib/python3.7/site-packages/bio2bel/utils.py", line 40, in get_data_dir return BIO2BEL_MODULE.get(module_name.lower()) AttributeError: 'Module' object has no attribute 'get'

I imagine another version badly installed in my environment.

[cthoyt]

The SQLAlchemy problem was solved.

Now, new error: File "/home/wgarzon/anaconda3/envs/metabol/lib/python3.7/site-packages/bio2bel/utils.py", line 40, in get_data_dir return BIO2BEL_MODULE.get(module_name.lower()) AttributeError: 'Module' object has no attribute 'get'

I imagine another version badly installed in my environment.

This is because the interface in pystow changed. I fixed it in bio2bel/bio2bel@bd2f2bd and just released a new version of Bio2BEL (v0.4.2) with the fix