Issue with colorlog logging

[alexweisberg]

Version of Integron_Finder:

integron_finder version 2-2021-09-27 Using:

• Python 3.7.2 (default, Feb 9 2019, 23:04:15) [GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
• numpy 1.20.2
• pandas 1.1.3
• matplolib 3.0.3
• biopython 1.76

Authors:

• Jean Cury, Bertrand Neron, Eduardo Rocha,

Citation:

Identification and analysis of integrons and cassette arrays in bacterial genomes Jean Cury; Thomas Jove; Marie Touchon; Bertrand Neron; Eduardo PC Rocha Nucleic Acids Research 2016; doi: 10.1093/nar/gkw319

OS

• [X] Linux
• [ ] Windows
• [ ] Mac

Expected behavior

Running of integron_finder

Actual behavior

Running integron_finder with python3 after installing with pip from github gives the following error:

python3 /myhomefolder/.local/bin/integron_finder -v genome.fa
Traceback (most recent call last):
  File "/myhomefolder/.local/bin/integron_finder", line 8, in <module>
    sys.exit(main())
  File "/myhomefolder/.local/lib/python3.7/site-packages/integron_finder/scripts/finder.py", line 521, in main
    out=not config.mute)
  File "/myhomefolder/.local/lib/python3.7/site-packages/integron_finder/__init__.py", line 78, in init_logger
    logging = colorlog.logging.logging
AttributeError: module 'colorlog' has no attribute 'logging'

The colorlog module appears to be up to date (version 6.4.1). Thank you!

[alexweisberg]

It turns out this issue is due to changes in a recent version of colorlog. Colorlog version 6.4.1 has renamed the colorlog.logging function to colorlog.wrappers. Installing an earlier version of colorlog doesn't have this issue.