Logging issue

[Nummi83]

Importing MakeGenerator from descriptastorus.descriptors.DescriptorGenerator messes up how logging works. Below is an MWE demoing this unwanted behavior.

import logging

from descriptastorus.descriptors.DescriptorGenerator import MakeGenerator

logging.basicConfig(handlers=[logging.FileHandler("temp.log", "a", "utf-8"),
                              logging.StreamHandler()], level=logging.INFO,
                    format="%(asctime)s %(levelname)s [%(module)s.%(funcName)s]: %(message)s")

def status():
    logging.info("Hello!")

if __name__ == '__main__':
    status()

Running this code does not result in "Hello!" being written to the log file "temp.log" as is expected. If you comment out the row from descriptastorus.descriptors.DescriptorGenerator import MakeGenerator the log entry is written without error.

To verify this issue I created a new conda environment, first installing rdkit conda install -c rdkit rdkit, followed by pip install git+https://github.com/bp-kelley/descriptastorus and pip install scipy.

[bp-kelley]

The generator does "work" upon import which interfaces with logging. I'm in the process of moving logging to it's own namespace which will help somewhat, but your solution here is to configure logging before importing descriptastorus

import logging

logging.basicConfig(handlers=[logging.FileHandler("temp.log", "a", "utf-8"),
                              logging.StreamHandler()], level=logging.INFO,
                    format="%(asctime)s %(levelname)s [%(module)s.%(funcName)s]: %(message)s")

from descriptastorus.descriptors.DescriptorGenerator import MakeGenerator

def status():
    logging.info("Hello!")

if __name__ == '__main__':
    status()

Not the best solution but I think until I make the data loading "lazy" you will always need to do this.

[bp-kelley]

I'll consider making the data loading lazy in 3.0.0 but I kind of like the fast failure for descriptastorus right now.

[bp-kelley]

All the logging is now in the "descriptastorus" logger.

pip install descriptastorus>=2.6.1