Sqlalchemy v2.0.0 bug causes cells.SingleCells to not work: ObjectNotExecutableError with read_sql

[jenna-tomkinson]

I noticed that when I pip installed Pycytominer to use in a project yesterday that I was getting this error when trying to run cells.SingleCells from the cells.py file.

ObjectNotExecutableError: Not an executable object: 'select * from Per_Image'

This error is caused by a bug between Pandas and the newest release of Sqlalchemy from a few days ago. It is described further in this issue from the Pandas GitHub.

I noticed that in the requirements.txt that it states:

sqlalchemy>=1.3.6

This means it is installing the latest version of Sqlalchemy when pip installing. This means a new user if they wanted to use the cells.SingleCells function or any function in Pycytominer that uses Sqlalchemy read_sql function using a string, then it will not work.

The only work around I have that works is a conda environment that installs Sqlalchemy v1.4.42 (which is the last version that works) and pip installs Pycytominer. The conda install override the pip install.

Once this bug is fixed, then this won't be a worry, but I wanted to make this issue for others to be aware in case they get this same error.

[bethac07]

Thanks Jenna! Put in a PR to solve the immediate issue, and another issue to remind us to keep an eye out for the pandas fix.