bug#53258: Python unable to find modules within a Singularity container created with guix pack

[Konrad Hinsen]

Hi everyone,

I found this issue while investigating a related one (the error
message). It looks like the core problem discussed here has been solved
in the meantime:

   Singularity> python3 -m numpy
   Error in sitecustomize; set PYTHONVERBOSE for traceback:
   ValueError: 
'/gnu/store/kx98dz2vc3gdpjficy4nbd7rscnkvz4s-profile/bin/../../h855kddqbay0pcbwr8a7i8m6ilz67cfn-python-3.10.7/lib/python3.10/site-packages'
 is not in list
   /gnu/store/kx98dz2vc3gdpjficy4nbd7rscnkvz4s-profile/bin/python3: No module 
named numpy.__main__; 'numpy' is a package and cannot be directly executed

This error message is to be expected, and NumPy can be imported:

   Singularity> python3
   Error in sitecustomize; set PYTHONVERBOSE for traceback:
   ValueError: 
'/gnu/store/kx98dz2vc3gdpjficy4nbd7rscnkvz4s-profile/bin/../../h855kddqbay0pcbwr8a7i8m6ilz67cfn-python-3.10.7/lib/python3.10/site-packages'
 is not in list
   Python 3.10.7 (main, Jan  1 1970, 00:00:01) [GCC 11.3.0] on linux
   Type "help", "copyright", "credits" or "license" for more information.
   >>> import numpy
   >>> 

What remains is the error message, which comes from a bug in Guix'
sitecustomize.py. It compares a raw path (sys.prefix) with paths that
have been normalized (os.path.normpath). That comparison fails if
sys.prefix contains "../", as it does when run from a Singularity
container. I will submit a patch for this.

Cheers,
  Konrad