Update the jupyterhub/repo2docker image

[jtpio]

Update the jupyterhub/repo2docker Docker image to point to a pinned version by default.

The tag is made configurable in case so it's easier to override if needed, without having to update this repo.

Having a default pinned version makes it easier to reason about which version is being installed when the playbook is run multiple times.

Fixes #211

• Pick the latest stable tag as default: 2023.06.0-41.g57d229e
• Add / update the documentation: https://plasmabio--217.org.readthedocs.build/en/217/
• Fix custom entrypoint with the newer repo2docker
• Fix tests

[jtpio]

Environments seems to be building fine locally:

Although servers time out on startup. Wondering if it could be related to the custom entrypoint used in Plasma, and the fact that it has since changed in repo2docker to be implemented in Python instead of being a Bash script: jupyterhub/repo2docker#1014

tornado.web.HTTPError: HTTP 500: Internal Server Error (Spawner failed to start [status=0]. The logs for jtp may contain details.)

[jtpio]

This is now opt-in in dockerspawner>=12.0: https://jupyterhub-dockerspawner.readthedocs.io/en/latest/changelog.html#id3

Not sure why we didn't have to set it explicitly before, as it was updated in #193.

[jtpio]

OK this seems to be doing the trick for being able able to launch the server.

If I understand correctly, specifying - would be equivalent to starting the process with --login, which conflicts with -m / --preserve-environment.

As hinted by the the error logs:

su: ignoring --preserve-environment, it's mutually exclusive with --login
--root-prefix: 1 required TEXT missing
Run with --help for more information.
/srv/conda/envs/notebook/bin/jupyterhub-singleuser: 7: /etc/profile.d/activate-conda.sh: [[: not found
/srv/conda/envs/notebook/bin/jupyterhub-singleuser: 20: /etc/profile.d/activate-conda.sh: mamba: not found
JUPYTERHUB_API_TOKEN env is required to run jupyterhub-singleuser. Did you launch it manually?

[jtpio]

I guess this is related to recent update of the mamba activation scripts in repo2docker. Removing the - seems to be working fine locally so we should be able to do without now:

[jtpio]

Need to do a bit more testing on a test VM, but this change might break compatibility with existing environments built with an older version of repo2docker.

[atrawog]

This issue is quite likely caused by jupyterhub/repo2docker#1287 and the latest version of repo2docker using Ubuntu 22.04 instead of 18.04 and should be fixed by using repo2docker --build-arg BASE_IMAGE=ubuntu:18.04 or adding BASE_IMAGE=ubuntu:18.04 to the build args in the tljh-repo2docker web gui when craeting the environment.