Thanks a lot for the lead, it seems indeed that this bash profile is not
loaded. You're right that the GUIX_PYTHONPATH is properly defined in the
profile file.
Although I don't know yet where the current python2 path comes from if
the bash profile is not loaded.
I'll try to look at how it's handled in the docker format.
On 03/06/2025 19:55, Rutherther wrote:
Hi Alexis,
I don't know what apptainer is, and I don't currently have time to
investigate it or test it, so just what I found so far:
apptainer is the new name of singularity, a container platform mainly
used on HPC clusters. So very much like docker.
Alexis Simon <[email protected]> writes:
a little addition to this, to reproduce you can do
```
guix pack -f squashfs bash python | \
xargs -I % sh -c 'apptainer exec % bash -c "echo \$GUIX_PYTHONPATH"'
guix pack -f squashfs bash python python2 | \
xargs -I % sh -c 'apptainer exec % bash -c "echo \$GUIX_PYTHONPATH"'
```
First one gives
/gnu/store/rxfshmxwk8pas52lpmhhnqys8apwynpr-profile/lib/python3.11/site-packages
Second one gives
/gnu/store/rxfshmxwk8pas52lpmhhnqys8apwynpr-profile/lib/python2.7/site-packages
My initial guess is that this is problem of apptainer / its
configuration, not Guix. Guix puts the export of GUIX_PYTHONPATH to
etc/profile of the used profile in store.
```
ruther:/tmp/b/squashfs-root]└2 %
cat gnu/store/99p9q3g8g7gri8klhkj983hjxn6fi215-profile/etc/profile
# Source this file to define all the relevant environment variables in Bash
# for this profile. You may want to define the 'GUIX_PROFILE' environment
# variable to point to the "visible" name of the profile, like this:
#
# GUIX_PROFILE=/path/to/profile ; \
# source /path/to/profile/etc/profile
#
# When GUIX_PROFILE is undefined, the various environment variables refer
# to this specific profile generation.
export
PATH="${GUIX_PROFILE:-/gnu/store/99p9q3g8g7gri8klhkj983hjxn6fi215-profile}/bin${PATH:+:}$PATH"
export
BASH_LOADABLES_PATH="${GUIX_PROFILE:-/gnu/store/99p9q3g8g7gri8klhkj983hjxn6fi215-profile}/lib/bash${BASH_LOADABLES_PATH:+:}$BASH_LOADABLES_PATH"
export
GUIX_PYTHONPATH="${GUIX_PROFILE:-/gnu/store/99p9q3g8g7gri8klhkj983hjxn6fi215-profile}/lib/python3.11/site-packages${GUIX_PYTHONPATH:+:}$GUIX_PYTHONPATH"
export
GUIX_PYTHONPATH="${GUIX_PROFILE:-/gnu/store/99p9q3g8g7gri8klhkj983hjxn6fi215-profile}/lib/python2.7/site-packages${GUIX_PYTHONPATH:+:}$GUIX_PYTHONPATH"
```
As can be observed, both are exported, and they should be appended if
this file was sourced by bash, as can be seen with:
```
unset GUIX_PYTHONPATH
[ruther:/tmp/b/squashfs-root]└2 %
source gnu/store/99p9q3g8g7gri8klhkj983hjxn6fi215-profile/etc/profile
[ruther:/tmp/b/squashfs-root]└2 %
printenv GUIX_PYTHONPATH
/gnu/store/99p9q3g8g7gri8klhkj983hjxn6fi215-profile/lib/python2.7/site-packages:/gnu/store/99p9q3g8g7gri8klhkj983hjxn6fi215-profile/lib/python3.11/site-packages
```
So it seems to me apptainer is doing something strange here with the
etc/profile file.
Rutherther
