`_apptainer_shell.sh` missing?

[Filip-K]

Hi! The FAQ says we can use the "--shell /usr/local/bin/_apptainer_shell.sh option to apptainer exec to activate the base environment". That doesn't seem to work for me (the base environment is not activated) and I noticed that /usr/local/bin/_apptainer_shell.sh is not present in the image. I think the file would have to be present for this to work, or am I misunderstanding something?

To check, do apptainer pull micromamba.sif docker://mambaorg/micromamba:2.5.0, apptainer exec micromamba.sif ls /usr/local/bin/ and notice that _apptainer_shell.sh is not there.

Also, I think the FAQ should say "--shell /usr/local/bin/_apptainer_shell.sh option to apptainer shell to activate the base environment" apptainer exec has no --shell option as of apptainer version 1.4.5.

[wholtz]

Hello @Filip-K - It appears that back in Sept 2024 I performed a refactor and the COPY of _apptainer_shell.sh was lost. Thank you for the report. I'm restoring it in PR #705 .

I also need to look into the documentation issue....

[Filip-K]

That's perfect, thanks a lot!

[wholtz]

@Filip-K - there was a problem with the image builds, but they are now in the repos.

[Filip-K]

Thanks! I just verified that _apptainer_shell.sh is there in the new 2.5 and the --shell /usr/local/bin/_apptainer_shell.sh argument to apptainer shell works as intended (it drops the user into a shell with the base environment activated).