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

[GNU bug Tracking System]

Your message dated Sun, 21 Jan 2024 13:31:18 -0500
with message-id <87r0ia8rnt.fsf@gmail.com>
and subject line Re: bug#53258: Python unable to find modules within a 
Singularity container created with guix pack
has caused the debbugs.gnu.org bug report #53258,
regarding Python unable to find modules within a Singularity container created 
with guix pack
to be marked as done.

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help-debbugs@gnu.org.)


-- 
53258: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=53258
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> --- Begin Message ---
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> Subject: 
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> Python unable to find modules within a Singularity container created with guix pack
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> Date: 
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> Fri, 14 Jan 2022 15:20:46 +0100
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> User-agent: 
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> Mozilla/5.0 (X11; Linux x86_64; rv:68.0) Gecko/20100101 Firefox/68.0 SeaMonkey/2.53.10.2
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>
>
>
> 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
>
>
>
>
> --- End Message ---
> --- Begin Message ---
>
>
>
> Subject: 
>
> Re: bug#53258: Python unable to find modules within a Singularity container created with guix pack
>
>
>
>
> Date: 
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> Sun, 21 Jan 2024 13:31:18 -0500
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>
>
>
> User-agent: 
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> Gnus/5.13 (Gnus v5.13)
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>
>
>
> Hi Konrad,
>
> Konrad Hinsen <konrad.hinsen@fastmail.net> writes:
>
> > Konrad Hinsen <konrad.hinsen@fastmail.net> writes:
> >
> >> Patch at https://issues.guix.gnu.org/68241
> >
> > If you want to test it without rebuilding tons of packages, here is a
> > version that grafts a patched Python onto the existing ones (as substitutes):
> >
> > https://codeberg.org/khinsen/guix/src/branch/graft-fix-python-sitecustomize
>
> I've applied your patch to core-updates.  I trust that it fixed this
> issue based on your own testing.
>
> Closing; we can always reopen if we find it didn't fix every use cases
> or create a fresh issue.
>
> -- 
> Thanks,
> Maxim
>
>
> --- End Message ---