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open2c / pairtools

Extract 3D contacts (.pairs) from sequencing alignments
MIT License
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most likely due to a circular import #234

Open stephrom opened 7 months ago

stephrom commented 7 months ago

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 commented 6 months ago

Same issue here

aowenson-imm commented 4 months ago

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- commented 3 months ago

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 commented 2 months ago

I also have the same problem with version 1.1.0. Based on the traceback, the culprit is this line: https://github.com/open2c/pairtools/blob/8c41a26b3f3a3905e307f3baa4b547203394dca1/pairtools/lib/dedup.py#L9 It does seem to be a circular import.

dmitrymyl commented 2 months ago

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.