Switch to nbclassic and Python 3.12.11 by danielhollas · Pull Request #479 · aiidalab/aiidalab-docker-stack

danielhollas · 2024-07-14T19:35:12Z

fixes #552

This is just a test if we can switch to nbclassic interface, which is now supported in appmode.

Notebook v7 is currently not supported in Appmode.

yakutovicha · 2026-03-16T11:05:51Z

@edan-bainglass, @danielhollas - this one is ready, please test 🙏

edan-bainglass

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edan-bainglass · 2026-03-16T11:49:09Z

 PSQL_START_CMD="pg_ctl --timeout=180 -w -l ${PSQL_LOGFILE} start"

-MAMBA_RUN="mamba run -n aiida-core-services"
+CONDA_RUN="conda run -n aiida-core-services"


The time I tried, Mamba was just hanging and not moving forward, so I switched to conda to make it work.

I can try to revert it and see how it goes this time.

Please try. If it fails, good to understand why.

Here it is: #479 (comment)

danielhollas · 2026-03-27T12:21:32Z

I've merged in main to get aiida-core 2.8.0

For some reason, mamba now lists this package in canonicalize form as `aiidalab_home`

yakutovicha · 2026-04-02T16:03:11Z

For the record, the failing tests are because we are constraining ipywidgets~=8.0, which means we won't be able to make the tests run before apps (QE app in this case) migrate to ipywidgets 8.x.

yakutovicha · 2026-04-08T09:17:32Z

@edan-bainglass, @danielhollas: Here is the result of the investigation regarding mamba run vs conda activate.

By default, conda run sets up pipes for stdout/stderr to capture the subprocess output. The flow is:

mamba run -n aiida-core-services pg_ctl start spawns pg_ctl as a child process
pg_ctl's stdout/stderr are connected to pipes back to mamba run
mamba run reads from those pipes until EOF, then exits

What happens when starting the deamons

When pg_ctl starts or rabbitmq-server -detached runs:

The command forks a long-running daemon process.
The daemon inherits the pipe file descriptors from its parent (stdout/stderr).
The parent process exits normally.
mamba run sees the parent exit, but it's still waiting for EOF on the pipe.
EOF on a pipe only occurs when every process holding the write end closes it.
The daemon still holds the pipe's write end open (inherited at fork).
The daemon never exits -> pipe never gets EOF -> mamba run hangs forever

An alternative solution is suggested here is to use --no-capture-output

Here is the summary of all tries:

Approach	Result	Notes
mamba run (original)	HANGS	Pipe inheritance by forked daemons
mamba run --no-capture-output	BROKEN	Generates exec (in wrapper script -> exec): invalid option (mamba bug)
conda run --no-capture-output	WORKS	Avoids pipe capture without the exec bug
conda activate + direct commands	WORKS	To me, this is the cleanest way.

yakutovicha · 2026-04-08T09:18:51Z

@danielhollas, @edan-bainglass - to me, the PR is ready to go, please re-review.

danielhollas · 2026-04-08T09:27:56Z

@yakutovicha thanks so much, I'll have a look (but will not have time today). Note that this is still blocked on the RabbitMQ upgrade, we need to resolve #510 first. But I agree that otherwise this looks ready.

Can you please merge main? That should remove some of the changes to the docker compose files.

danielhollas · 2026-04-09T12:11:16Z

@yakutovicha I just launched the latest image from this PR and I am seeing a Notebook v7 warning banner:

I believe it was hidden in the earlier versions of this PR, perhaps that change got lost?

edan-bainglass

LGTM. Just a few comments, but good to go.

edan-bainglass · 2026-04-10T03:17:03Z

    },
    "AIIDALAB_HOME_TAG": {
-      "default": "v25.02.0"
+      "default": "main"


We should make a new release of aiidalab-home

edan-bainglass · 2026-04-10T03:17:31Z


 variable "JUPYTER_BASE_IMAGE" {
-  default = "jupyter/minimal-notebook:python-${PYTHON_VERSION}"
+  default = "quay.io/jupyter/minimal-notebook:python-${PYTHON_VERSION}"


edan-bainglass · 2026-04-10T03:20:48Z


 def test_correct_aiidalab_home_version_installed(package_info, aiidalab_home_tag):
-    info = package_info("aiidalab-home")
+    info = package_info("aiidalab_home")


Was this a typo before?

Newer mamba version in this image uses this canonicalized package name in its mamba list output

We've been manually updating traitlets to 5.9 for performance reasons, but the new python3.12 base image contains newer traitlets version already.

danielhollas · 2026-04-10T10:23:19Z

Pushed some small changes, hope that's okay. Disabled QeApp integration tests for now, but before this is merged it would be good to have at least a rough idea what it would take to upgrade QeApp for this image.

May I ask, what kind of testing has been done on this image so far? I think at the very least we should test individual AWB widgets.

Marking this as blocked until #510 is merged (hope to make some progress on that over weekend) and we need to first release the 2.8 based image anyway.

danielhollas · 2026-04-10T23:27:52Z

This is very minor, but I am seeing this warning when using pip in this image

We can add ENV PIP_USE_FEATURE="build-constraint" in the base image to get rid of it (where we set PIP_CONSTRAINT).

danielhollas added 3 commits July 14, 2024 20:33

WIP: Switch to nbclassic

4605af7

Python 3.11

f1afae2

Fix integration test

9f351bc

danielhollas force-pushed the nbclassic branch from e25098b to 9f351bc Compare July 17, 2024 09:26

danielhollas and others added 6 commits February 11, 2025 12:52

Merge branch 'main' into nbclassic

c2f2802

Python 3.11.14

2dde592

Merge branch 'main' into nbclassic

d956705

Change jupyter base image.

05767b0

Python 3.11.10

28cd153

Select branch with migrated home app

0980742

yakutovicha force-pushed the nbclassic branch from ae183b7 to 0980742 Compare November 10, 2025 12:29

yakutovicha added 3 commits November 10, 2025 14:16

Working version (tested locally)

95eaa25

Replace mamba run with conda run, otherwise hangs.

175c1ec

First working version

684b52c

yakutovicha changed the title ~~WIP: Switch to nbclassic~~ Switch to nbclassic and Python 3.11.10 Nov 11, 2025

yakutovicha mentioned this pull request Nov 11, 2025

Update base image to python-3.11.3 #455

Closed

yakutovicha added 3 commits November 19, 2025 13:44

Merge branch 'main' into nbclassic

8f2ed31

Merge branch 'main' into nbclassic

82b5cbb

Bump appmode to 1.1.0

1865f09

yakutovicha force-pushed the nbclassic branch from 43d88f9 to 368487b Compare March 9, 2026 22:10

Python 3.12.11

be2f192

yakutovicha force-pushed the nbclassic branch from 368487b to be2f192 Compare March 9, 2026 22:20

yakutovicha added 2 commits March 10, 2026 14:23

Remove appmode enabling, it is enabled automatically.

c6edc7b

Change aiidalab-home version (branch).

c9e6f25

yakutovicha changed the title ~~Switch to nbclassic and Python 3.11.10~~ Switch to nbclassic and Python 3.12.11 Mar 10, 2026

Fix logo and rotating gears.

b1f8f0f

yakutovicha requested a review from edan-bainglass March 16, 2026 11:05

yakutovicha marked this pull request as ready for review March 16, 2026 11:05

edan-bainglass reviewed Mar 16, 2026

View reviewed changes

danielhollas mentioned this pull request Mar 25, 2026

Cleanup docker-compose config files #556

Merged

Merge branch 'main' into nbclassic

1ba7f90

danielhollas commented Mar 27, 2026

View reviewed changes

Comment thread build.json Outdated

danielhollas added 2 commits March 27, 2026 12:20

point aiidalab_home to main branch

f53ce41

Merge branch 'main' into nbclassic

0668263

danielhollas and others added 2 commits March 27, 2026 13:04

Fix test_correct_aiidalab_home_version_installed test

19c5ec5

For some reason, mamba now lists this package in canonicalize form as `aiidalab_home`

Merge branch 'main' into nbclassic

c2ddd10

yakutovicha mentioned this pull request Apr 2, 2026

🔍 Try running CI vs 5.0.0rc1 aiidalab/aiidalab-qe#1471

Draft

Remove zstandard package

0fe29f2

yakutovicha added 5 commits April 4, 2026 08:26

Merge branch 'main' into nbclassic

bd841b1

Remove pip install appmode

060ed4a

Remove ~/.tmp_notebooks folder creation

8a51479

Revert test_base.py to original state

bd7992a

start_rabbitmq.sh: removed sleep 2 and the outdated arm64 comment

d9609f9

yakutovicha requested review from edan-bainglass and yakutovicha April 8, 2026 09:18

edan-bainglass approved these changes Apr 10, 2026

View reviewed changes

danielhollas added 3 commits April 10, 2026 06:32

Merge branch 'main' into nbclassic

4f16079

Temporarily Remove QeApp from integration tests

cd4b1f5

Remove traitlets install in base image

7d566e0

We've been manually updating traitlets to 5.9 for performance reasons, but the new python3.12 base image contains newer traitlets version already.

danielhollas added blocked This issue/PR is blocked by another issue/PR. labels Apr 10, 2026

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