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liguowang / CrossMap

CrossMap is a python program to lift over genome coordinates from one genome version to another.
https://crossmap.readthedocs.io/en/latest/
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Installing v0.7.0 makes python 3.11 coredump when help('modules') is called #67

Open t-kreitler opened 5 months ago

t-kreitler commented 5 months ago

Hi,

After installing CrossMap with pip, running python -c 'help("modules")' yields:

Please wait a moment while I gather a list of all available modules...
Segmentation fault (core dumped)

I suspect that src/__init__.py is misplaced. It gets installed directly in site_packages and may cause some trouble when python tries to find all modules via pkgutil.walk_packages().

Removing the file and a pip install . from the repo did solve the issue in my case.

Best, Thomas

liguowang commented 5 months ago

Thanks, Thomas. What is the appropriate place to put the src/__init__.py?

t-kreitler commented 5 months ago

I would say the __init__.py in src/cmmodule should be sufficient, and the empty one in src can just go.