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How to setup logging

TaxoTagger uses the standard library logging module for managing log messages and the python library rich to colorize the log messages. Depending on how you use TaxoTagger, you can set up logging in different ways.

TaxoTagger as an application

If you're using TaxoTagger as an application, you are using the TaxoTagger class, like the example described in the Quickstart. In this case, you can set up logging with the configuration.

TaxoTagger as a library

If you're using TaxoTagger as a library, you're using some other functions or classes in your script. By default, TaxoTagger will not log any messages. However, you can set up logging in your script with the setup_logging function:

Set up logging in 'your_script.py'
# Set up logging configuration first
from TaxoTagger import setup_logging

setup_logging(level="DEBUG", file="taxotagger.log", to_console=True) # (1)!

# Your business code here
# e.g. download a model from the internet to `~/temp_dir` folder
from TaxoTagger.utils import download_from_url

url = "https://zenodo.org/records/10904344/files/MycoAI-CNN.pt"
download_from_url(url, "~/temp_dir")
  1. The setup_logging function sets up the logging settings:
    • The level sets the logging level, e.g. NONSET, DEBUG, INFO, WARNING, ERROR, and CRITICAL.
    • The file sets the path to the log file.
    • The to_console sets whether to log messages to your console.

Run the script above, you will see the log messages in the console and the log file taxotagger.log in the current working directory.