improve compatibility w. singularity sandbox mode

[espenhgn]

Describe the bug
Many tests fail in "singularity sandbox" mode:
gwas_pytest_errors.txt

To Reproduce
Steps to reproduce the behavior:

1. micromamba create -n containers python=3.11 pytest singularity -Y && micromamba activate containers
2. py.test -v tests

Setup (please complete the following information - if applicable):

• OS: Ubuntu 22.04.3 LTS
• singularity version 3.8.6
• Container file and version: gwas.sif (latest)

[github-actions]

This issue appears to be stale due to non-activity

[espenhgn]

Furthermore, it could be beneficial to spawn instances of the containers in the background and invoke binaries in the foreground when needed, as converting to temporary sandboxes for each call is infeasibly slow; similar to:

$ apptainer instance start -B $TMPDIR singularity/gwas.sif gwas
INFO:    Environment variable SINGULARITY_TMPDIR is set, but APPTAINER_TMPDIR is preferred
INFO:    squashfuse not found, will not be able to mount SIF or other squashfs files
INFO:    fuse2fs not found, will not be able to mount EXT3 filesystems
INFO:    gocryptfs not found, will not be able to use gocryptfs
INFO:    Converting SIF file to temporary sandbox...
INFO:    instance started successfully

$ apptainer instance list
INSTANCE NAME    PID        IP    IMAGE
gwas             3059372          /mnt/scratch/tmp/rootfs-3445735741/root

$ apptainer exec instance://gwas plink --version
INFO:    Environment variable SINGULARITY_TMPDIR is set, but APPTAINER_TMPDIR is preferred
PLINK v1.90b7.2 64-bit (11 Dec 2023)

$ apptainer instance stop gwas
INFO:    Stopping gwas instance of /mnt/scratch/tmp/rootfs-3445735741/root (PID=3059372)