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

[Marek Felšöci]

Hello folks,

Recently, I have come around this issue. I created a Singularity container using 
the following `guix pack` command:

`guix pack -f squashfs bash coreutils python python-numpy`

Then, I run a bash shell within the container:

`singularity exec test.gz.squashfs bash`

Now, if I want to use numpy,

`python3 -m numpy`

it gives me the following error and the numpy module IS NOT found:

Error in sitecustomize; set PYTHONVERBOSE for traceback:
ValueError: 
'/gnu/store/2dyd6rlcc9m68k3mvkw86k8dygkbg025-profile/bin/../../p5fgysbcnnp8b1d91mrvjvababmczga0-python-3.9.6/lib/python3.9/site-packages' 
is not in list
/gnu/store/2dyd6rlcc9m68k3mvkw86k8dygkbg025-profile/bin/python3: No module named 
numpy

However, if I do,

`export PYTHONPATH=$GUIX_PYTHONPATH`

the numpy module IS found:

Error in sitecustomize; set PYTHONVERBOSE for traceback:
ValueError: 
'/gnu/store/2dyd6rlcc9m68k3mvkw86k8dygkbg025-profile/bin/../../p5fgysbcnnp8b1d91mrvjvababmczga0-python-3.9.6/lib/python3.9/site-packages' 
is not in list
/gnu/store/2dyd6rlcc9m68k3mvkw86k8dygkbg025-profile/bin/python3: No module named 
numpy.__main__; 'numpy' is a package and cannot be directly executed

Still, the sitecustomize error persists.

See the output of `guix describe` below (only the guix channel):

Pokolenie 3    14. január 2022 14:33:06    (súčasné)
  guix 5c5d9e5
    zdroj repozitára: https://git.savannah.gnu.org/git/guix.git
    vetva: master
    úprava: 5c5d9e5a3208fa51351c6ad8267eba3d96fa2232

Thanks,

Marek