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bio2bel / hmdb

A Bio2BEL package for converting the Human Metabolite Database (HMDB) to BEL
http://bio2bel-hmdb.rtfd.io/
MIT License
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Error Alchemy bio2bel hmdb #8

Open wgarzon opened 2 years ago

wgarzon commented 2 years ago

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 commented 2 years ago

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 commented 2 years ago

Please let me know if that solves the issue

wgarzon commented 2 years ago

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 commented 2 years ago

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 https://github.com/bio2bel/bio2bel/commit/bd2f2bdcd63ce52041b2cde27bfb5ba7c4f014be and just released a new version of Bio2BEL (v0.4.2) with the fix