Resolving python import loop error?

[vickietr]

When running pairtools parse, it leads to a python import loop error! Help with resolving? Thank you!

Error:
File "/home/vtrinh2/.local/bin/pairtools", line 5, in
from pairtools.cli import cli
File "/home/vtrinh2/.local/lib/python3.8/site-packages/pairtools/cli/init.py", line 188, in
from . import (
File "/home/vtrinh2/.local/lib/python3.8/site-packages/pairtools/cli/dedup.py", line 12, in
from ..lib import fileio, pairsam_format, headerops
File "/home/vtrinh2/.local/lib/python3.8/site-packages/pairtools/lib/init.py", line 2, in
from . import dedup
File "/home/vtrinh2/.local/lib/python3.8/site-packages/pairtools/lib/dedup.py", line 8, in
from . import dedup_cython, pairsam_format
ImportError: cannot import name 'dedup_cython' from partially initialized module 'pairtools.lib' (most likely due to a circular import) (/home/vtrinh2/.local/lib/python3.8/site-packages/pairtools/lib/init.py)

[agalitsyna]

Hi Vickie, I reproduced your problem in a fresh environment, it seems to be problem with pip dependencies. Meanwhile, you can try re-installing pairtools with:

pip install cython
pip install git+https://github.com/open2c/pairtools

[vickietr]

This worked! Thank you so much!! 🙏