search

EI-CoreBioinformatics / mikado

Mikado is a lightweight Python3 pipeline whose purpose is to facilitate the identification of expressed loci from RNA-Seq data * and to select the best models in each locus.
https://mikado.readthedocs.io/en/stable/
GNU Lesser General Public License v3.0
97 stars 18 forks source link

SQLAlchemy warning #182

Closed cschu closed 5 years ago

cschu commented 5 years ago

https://github.com/kvesteri/sqlalchemy-utils/issues/374

I don't think this causes a major problem, but it is an annoying warning. Need to update SQLAlchemy version?

cschu commented 5 years ago

[schudomc@EI-HPC mikado]$ singularity exec container.img mikado -h /usr/local/lib/python3.7/site-packages/sqlalchemy/sql/functions.py:68: SAWarning: The GenericFunction 'array_agg' is already registered and is going to be overriden. "is going to be overriden.".format(identifier))

lucventurini commented 5 years ago

This should be fixed in sqlalchemy-utils 0.34.0 (released yesterday). I am installing sqlalchemy and sqlalchemy-utils through Conda, so this issue should fix itself once they update things over there. Not much I can do on the codebase here ..

cschu commented 5 years ago

I am installing sqlalchemy and sqlalchemy-utils through Conda

Well, yea, but your environment.yaml states (or have you updated it?)

- conda-forge::sqlalchemy-utils>=0.33.11

, which means it will not necessary use 0.34.0, depending on how it solves the interdependencies.

lucventurini commented 5 years ago

I cannot update it yet, version 0.34 has not been ported to Conda. If I were to update the environment.yml file now, it would cause a break. I can keep this open until Conda is updated, I guess.

lucventurini commented 5 years ago

I have now created a pull request for updating sqlalchemy-utils in conda-forge, see here. Once it has been accepted and merged into the main repo, I will update our yml and close the issue.

lucventurini commented 5 years ago

Both Portcullis and sqlalchemy-utils are now updated, so the annoying message has disappeared. Updated the environment.yml file for good measure, to ensure that the message will not appear again.

Closing.