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How to setup logging

NPLinker 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 NPLinker, you can set up logging in different ways.

NPLinker as an application

If you're using NPLinker as an application, you're running the whole workflow of NPLinker as described in the Quickstart. In this case, you can set up logging in the nplinker configuration file nplinker.toml.

NPLinker as a library

If you're using NPLinker as a library, you're using only some functions and classes of NPLinker in your script. By default, NPLinker will not log any messages. However, you can set up logging in your script to log messages.

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

setup_logging(level="DEBUG", file="nplinker.log", use_console=True) # (1)!

# Your business code here
# e.g. download and extract nplinker example data
from nplinker.utils import download_and_extract_archive

download_and_extract_archive(
    url="https://zenodo.org/records/10822604/files/nplinker_local_mode_example.zip",
    download_root=".",
)
  1. The setup_logging function sets up the logging configuration. The level argument sets the logging level. The file argument sets the log file. The use_console argument sets whether to log messages to the console.

The log messages will be written to the log file nplinker.log and displayed in the console with a format like this: [Date Time] Level Log-message Module:Line.

Run your script in a terminal
# Run your script
$ python your_script.py
Downloading nplinker_local_mode_example.zip ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100.0% • 195.3/195.3 MB • 2.6 MB/s • 0:00:00 • 0:01:02 # (1)!
[2024-05-10 15:14:48] INFO     Extracting nplinker_local_mode_example.zip to .                      utils.py:401

# Check the log file
$ cat nplinker.log
[2024-05-10 15:14:48] INFO     Extracting nplinker_local_mode_example.zip to .                      utils.py:401
  1. This is a progress bar but not a log message.