Update base image to python-3.11.3

[danielhollas]

Closes #265

NOTE: Upgrading Python is a breaking change since the python dependencies of installed AiiDAlab Apps need to be reinstalled due, see #317

[danielhollas]

Blocked on aiidalab/aiidalab#428

[unkcpz]

Hi @danielhollas, I reconsidered if use jupyter stack as the base image is a good option, instead if we move to using aiida-core images could gaining more flexibility. Major two reasons are:

1. The jupyter/minimal-notebook we use now as you did in this PR, we using python version tag, therefore has no control on the notebook version. If fact the python version is not we really care but mostly the aiida-core version and jupyter backend version.
2. We cannot set the system username which is minor but still not so good. Plus we can not using s6-overlay which I think manage well for the services when we need more.

Let me know your opinion.

[danielhollas]

Blocked on aiidalab/aiidalab#429

@unkcpz I've created #471, we shouldn't be discussing these foundational thing in PRs.

[unkcpz]

Yep, just came to this PR when I start to try with notebook v7. Great you open an issue for this, I agree it is premature to move to that, this is just things come to my mind and want to get to know your opinions. Let’s have follow up discussion on the issue you opened. Gesendet von Outlook für iOS<https://aka.ms/o0ukef>

…

________________________________ Von: Daniel Hollas ***@***.***> Gesendet: Saturday, June 22, 2024 7:12:18 PM An: aiidalab/aiidalab-docker-stack ***@***.***> Cc: Jusong Yu ***@***.***>; Mention ***@***.***> Betreff: Re: [aiidalab/aiidalab-docker-stack] Update base image to python-3.10.11 (PR #455) Blocked on aiidalab/aiidalab#429<aiidalab/aiidalab#429> @unkcpz<https://github.com/unkcpz> I've created #471<#471>, we shouldn't be discussing these foundational thing in PRs. — Reply to this email directly, view it on GitHub<#455 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ACDMFRJIEIKK6TADBBHT2JLZIWV7FAVCNFSM6AAAAABHVEF3JGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCOBUGEYTGMJSGI>. You are receiving this because you were mentioned.Message ID: ***@***.***>

[danielhollas]

Yeah, if you want to start to play with NB7, you can start with this PR and set python=3.11.4 which is the first version with v7.

[danielhollas]

The base image already comes with traitlets==5.9.0

[danielhollas]

This is now ready for review and testing. I don't want to merge yet, since we should deploy this change together with #483 and #482 so that we bundle all possibly breaking changes in single release.

[yakutovicha]

Thanks, @danielhollas. I just tried to run the container on my laptop, but it failed. My aiidalab-launch config looks as follows:

port = 8892
default_apps = []
system_user = "jovyan"
image = "ghcr.io/aiidalab/full-stack:pr-455"
home_mount = "aiidalab_test-python-311_home"
extra_mounts = []

Here is the log containing the error:

...


+ _log '/usr/local/bin/start.sh: running script /usr/local/bin/before-notebook.d/20_start-postgresql.sh'
+ [[ /usr/local/bin/start.sh: running script /usr/local/bin/before-notebook.d/20_start-postgresql.sh == \E\R\R\O\R\:* ]]
+ [[ /usr/local/bin/start.sh: running script /usr/local/bin/before-notebook.d/20_start-postgresql.sh == \W\A\R\N\I\N\G\:* ]]
+ [[ '' == '' ]]
+ echo '/usr/local/bin/start.sh: running script /usr/local/bin/before-notebook.d/20_start-postgresql.sh'
+ source /usr/local/bin/before-notebook.d/20_start-postgresql.sh
/usr/local/bin/start.sh: running script /usr/local/bin/before-notebook.d/20_start-postgresql.sh
++ set -x
++ [[ -z /home/jovyan/.postgresql ]]
++ PSQL_LOGFILE=/home/jovyan/.postgresql/logfile
++ PSQL_START_CMD='pg_ctl --timeout=180 -w -l /home/jovyan/.postgresql/logfile start'
++ MAMBA_RUN='mamba run -n aiida-core-services'
++ [[ ! -d /home/jovyan/.postgresql ]]
++ chmod -R g-rwxs /home/jovyan/.postgresql
++ [[ -f /home/jovyan/.postgresql/logfile ]]
++ rm -f /home/jovyan/.postgresql/logfile.1.gz
++ mv /home/jovyan/.postgresql/logfile /home/jovyan/.postgresql/logfile.1
++ gzip /home/jovyan/.postgresql/logfile.1
++ rm -vf /home/jovyan/.postgresql/postmaster.pid
removed '/home/jovyan/.postgresql/postmaster.pid'
++ mamba run -n aiida-core-services pg_ctl --timeout=180 -w -l /home/jovyan/.postgresql/logfile start
pg_ctl: could not start server
Examine the log output.

ERROR conda.cli.main_run:execute(125): `conda run pg_ctl --timeout=180 -w -l /home/jovyan/.postgresql/logfile start` failed. (See above for error)
waiting for server to start.... stopped waiting

For your information: I have ARM architecture, but I doubt it is related.

[danielhollas]

@yakutovicha strange, it works for me. Have you pulled the latest version of the image? Can you dig up the postgres logs to see why it is failing?

[danielhollas]

I just enabled the arm tests on this branch and they all passed.