Hi Guannan,
The 'rU' mode (universal newline mode) was deprecated in Python 3.4 and later removed in Python 3.11.
I tested that changing all "rU" to "r" gives the same results under python 3.12 (e.g. fin_obo = open(OBOInput,"rU"))

I attached the modified python3 files.
GOMCL-py3.12.zip
Best regards,
Beery Yaakov
(Simon Barak lab)