most likely due to a circular import

[stephrom]

Dear,

I systematically get the following error:

ImportError: cannot import name 'dedup_cython' from partially initialized module 'pairtools.lib' (most likely due to a circular import) (/shared/clssoft/apps/x86_64/pairtools/1.0.3/lib/python3.8/site-pack

could one advice, please

Best regards
Stephane

[xscapintime]

Same issue here

[aowenson-imm]

You have to PIP install from source after installing the dependencies:

git clone -b "v1.1.0" https://github.com/open2c/pairtools.git
cd pairtools && pip install .

Indicates a problem with the precompiled wheel in PyPI.

[liviu-]

You have to PIP install from source after installing the dependencies:

git clone -b "v1.1.0" https://github.com/open2c/pairtools.git
cd pairtools && pip install .

Indicates a problem with the precompiled wheel in PyPI.

This didn't work for me; anyone got it working? I get the error for all package versions, different python versions, different environments, on bioconda it's not found...

[dmitrymyl]

I also have the same problem with version 1.1.0. Based on the traceback, the culprit is this line:

pairtools/pairtools/lib/dedup.py

Line 9 in 8c41a26

from . import dedup_cython, pairsam_format

It does seem to be a circular import.

[dmitrymyl]

But this advice

You have to PIP install from source after installing the dependencies:

git clone -b "v1.1.0" https://github.com/open2c/pairtools.git
cd pairtools && pip install .

Indicates a problem with the precompiled wheel in PyPI.

worked for me.