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Bug#1012469: singularity-container: Broken handling of Docker environment variables in Singularity

Package: singularity-container
Version: 3.9.9+ds1-1+b1
Severity: important
X-Debbugs-Cc: offringa@gmail.com

Dear Maintainer,

Using Debian's singularity to pull a Docker container somehow removes the
environment variables that are set in the Dockerfile (using ENV) from the
container. This bug is not present in 3.9.9 upstream, so it has to do with how
it is packaged in Debian.

The issue is also discussed here, and there is concluded it is a Debian issue:

An example run that displays the problems:

$ singularity pull --name astronrd_linc.sif docker://astronrd/linc
$ singularity exec --contain --cleanenv astronrd_linc.sif bash
Singularity> echo $PYTHONPATH

Singularity> echo $LINC_DATA_ROOT


Both these variables are set in the Docker container, but are no longer set
when the docker container is pulled using Debian's singularity. The correct
output should be:

Singularity> echo $PYTHONPATH
Singularity> echo $LINC_DATA_ROOT

Singularity's own package for 3.9.9 does this correctly (and various other
versions were tested as well, see link to github issue above)

Kind regards,

-- System Information:
Debian Release: bookworm/sid
  APT prefers testing
  APT policy: (500, 'testing')
Architecture: amd64 (x86_64)
Foreign Architectures: i386

Kernel: Linux 5.17.0-1-amd64 (SMP w/16 CPU threads; PREEMPT)
Locale: LANG=en_GB.UTF-8, LC_CTYPE=en_GB.UTF-8 (charmap=UTF-8), LANGUAGE=en_GB:en
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled

Versions of packages singularity-container depends on:
ii  ca-certificates              20211016
ii  containernetworking-plugins  1.1.0+ds1-1+b1
ii  libc6                        2.33-7
ii  libseccomp2                  2.5.4-1
ii  squashfs-tools               1:4.5.1-1

Versions of packages singularity-container recommends:
ii  e2fsprogs  1.46.5-2

singularity-container suggests no packages.

-- no debconf information

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