{tools}[GCCcore/12.3.0] PycURL v7.45.2, PyZMQ v25.1.1, jupyter-server v2.7.2, ... by casparvl · Pull Request #18617 · easybuilders/easybuild-easyconfigs

casparvl · 2023-08-22T12:48:22Z

(created using eb --new-pr)

Depends on:

{lib}[GCCcore/12.3.0] tornado v6.3.2 w/ Python 3.11.3 #18511
{tools}[GCCcore/12.3.0] maturin v1.1.0 + switch to CargoPythonPackage in existing maturin easyconfig #18596
{tools}[GCCcore/12.3.0] Python-bundle-PyPI v2023.06, hatchling v1.18.0, poetry v1.5.1, setuptools-rust v1.6.0, virtualenv v20.23.1, ... w/ Python 3.11.3 #18208
{devel,lib,system,tools}[GCCcore/12.3.0] IPython v8.14.0, ZeroMQ v4.3.4, libsodium v1.0.18, ... #18570

This PR provides the Jupyter stack. I have rearranged a little compared to what we had for GCCcore-12.2.0 to reflect what makes sense in the curren ecosystem. For more info, see e.g. https://jupyter-notebook.readthedocs.io/en/latest/migrate_to_notebook7.html

In my view, there are three possible interfaces that people might want:

JupyterLab: for people who want a modern, IDE-like interface.
Notebook 7: for people who want a simpel interface, similar to the 'classic' notebook interface. But: modernized and now runs on top of JupyterLab. It does break compatibility with many old extensions (see this warning).
nbclassic: the old 'notebook' interface, but running on top of jupyter-server. It is there for backwards compatibility (see https://github.com/jupyter/nbclassic)

According to https://jupyter-notebook.readthedocs.io/en/latest/migrating/multiple-interfaces.html it makes perfect sense to have any combination of nbclassic, notebook 7 and jupyterlab (well, you can't have notebook 7 without jupyterlab). Depending on what is installed, jupyter-server will serve these at different endpoints:

if you only have notebook 7, it will be served at /tree
if you only have nbclassic, it will be served at /tree
if you have both nbclassic and notebook 7, they will be served at /nbclassic/tree and /tree respectively
Jupyterlab will always be served at /lab

Seeing as how having JupyterLab, JupyterLab + notebook 7, nbclassic, and JupyterLab + notebook 7 + nbclassic are all sensible installations one might be willing to offer, I figured it made sense to make separate EasyConfigs for each.

I'll probably follow-up with a PR that bundles a ton of Jupyter stuff together, including some common extensions (e.g. jupyterlmod, jupyter-resource-usage). This bundle can then be used whenever you want to install all functionality. EDIT: I did, that follow-up PR is here

…core-12.3.0.eb, jupyter-server-2.7.2-GCCcore-12.3.0.eb, JupyterHub-4.0.2-GCCcore-12.3.0.eb, JupyterLab-4.0.5-GCCcore-12.3.0.eb, notebook-7.0.2-GCCcore-12.3.0.eb, nbclassic-1.0.0-GCCcore-12.3.0.eb, jupyter-server-proxy-4.0.0-GCCcore-12.3.0.eb

This PR depends on easybuilders#18596 Shouldn't re-add this

Depends on easybuilders#18511 , shouldn't re-add this

…asyconfigs into 20230822144632_new_pr_PycURL7452

…classic. Set download_dep_fail in notebook.

Is in dependent PR already

casparvl · 2023-08-22T15:28:44Z

Test report by @casparvl
SUCCESS
Build succeeded for 9 out of 9 (9 easyconfigs in total)
tcn1.local.snellius.surf.nl - Linux RHEL 8.6, x86_64, AMD EPYC 7H12 64-Core Processor, Python 3.6.8
See https://gist.github.com/casparvl/4d14a27757392bdbf380ffa9e4557404 for a full test report.

casparvl · 2023-08-22T15:31:08Z

@boegelbot please test @ generoso

boegelbot · 2023-08-22T15:35:09Z

@casparvl: Request for testing this PR well received on login1

PR test command 'EB_PR=18617 EB_ARGS= EB_CONTAINER= /opt/software/slurm/bin/sbatch --job-name test_PR_18617 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 11529

Test results coming soon (I hope)...

Details

- notification for comment with ID 1688441957 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

casparvl · 2023-08-23T16:06:54Z

@boegelbot please test @ generoso

boegelbot · 2023-08-23T16:10:12Z

@casparvl: Request for testing this PR well received on login1

PR test command 'EB_PR=18617 EB_ARGS= EB_CONTAINER= /opt/software/slurm/bin/sbatch --job-name test_PR_18617 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 11535

Test results coming soon (I hope)...

Details

- notification for comment with ID 1690236154 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

casparvl · 2023-08-23T16:16:09Z

@boegelbot please test @ jsc-zen2

boegelbot · 2023-08-23T16:17:07Z

@casparvl: Request for testing this PR well received on jsczen2l1.int.jsc-zen2.easybuild-test.cluster

PR test command 'EB_PR=18617 EB_ARGS= /opt/software/slurm/bin/sbatch --mem-per-cpu=4000M --job-name test_PR_18617 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen2.sh' executed!

exit code: 0
output:

Submitted batch job 3228

Test results coming soon (I hope)...

Details

- notification for comment with ID 1690251788 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

…asyconfigs into 20230822144632_new_pr_PycURL7452

… JupyterHub, but so are JupyterLab, notebook, etc. I'll make a Jupyter-bundle that bundles all these together for convenience in a follow-up PR. It does mean I need to add tornado here as a dependency, previously that was provided through jupyter-server-proxy.

casparvl · 2023-08-23T17:42:35Z

@boegelbot please test @ generoso

boegelbot · 2023-08-23T17:45:09Z

@casparvl: Request for testing this PR well received on login1

PR test command 'EB_PR=18617 EB_ARGS= EB_CONTAINER= /opt/software/slurm/bin/sbatch --job-name test_PR_18617 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 11537

Test results coming soon (I hope)...

Details

- notification for comment with ID 1690376546 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

casparvl · 2023-08-23T17:52:22Z

Test report by @casparvl
FAILED
Build succeeded for 8 out of 9 (9 easyconfigs in total)
tcn1.local.snellius.surf.nl - Linux RHEL 8.6, x86_64, AMD EPYC 7H12 64-Core Processor, Python 3.6.8
See https://gist.github.com/casparvl/7fb4d9209233a326d2860e5b88fb1f4e for a full test report.

casparvl · 2023-08-23T17:54:04Z

Checksum failure, I'll update it...

casparvl · 2023-08-23T17:56:19Z

Ah, it's because I use the git_config, the checksum is not reproducible...

boegelbot · 2023-08-23T17:58:39Z

Test report by @boegelbot
FAILED
Build succeeded for 8 out of 9 (9 easyconfigs in total)
cns1 - Linux Rocky Linux 8.5, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/boegelbot/53df003612540f14fbc52b3f67736649 for a full test report.

…to a reproducible checksum.

…commit

casparvl · 2023-08-23T18:20:58Z

@boegelbot please test @ generoso

boegelbot · 2023-08-23T18:25:09Z

@casparvl: Request for testing this PR well received on login1

PR test command 'EB_PR=18617 EB_ARGS= EB_CONTAINER= /opt/software/slurm/bin/sbatch --job-name test_PR_18617 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 11538

Test results coming soon (I hope)...

Details

- notification for comment with ID 1690427375 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

casparvl · 2023-08-23T18:33:54Z

Test report by @casparvl
SUCCESS
Build succeeded for 9 out of 9 (9 easyconfigs in total)
tcn1.local.snellius.surf.nl - Linux RHEL 8.6, x86_64, AMD EPYC 7H12 64-Core Processor, Python 3.6.8
See https://gist.github.com/casparvl/7aa471e53e2d99ab7194d76cca1a4873 for a full test report.

boegelbot · 2023-08-23T18:43:09Z

Test report by @boegelbot
SUCCESS
Build succeeded for 9 out of 9 (9 easyconfigs in total)
cns1 - Linux Rocky Linux 8.5, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/boegelbot/ef4ddaa1e414c86d53436fc418a7ba6a for a full test report.

casparvl · 2023-08-24T11:24:23Z

@boegelbot please test @ jsc-zen2

boegelbot · 2023-08-24T11:27:12Z

@casparvl: Request for testing this PR well received on jsczen2l1.int.jsc-zen2.easybuild-test.cluster

PR test command 'EB_PR=18617 EB_ARGS= /opt/software/slurm/bin/sbatch --mem-per-cpu=4000M --job-name test_PR_18617 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen2.sh' executed!

exit code: 0
output:

Submitted batch job 3237

Test results coming soon (I hope)...

Details

- notification for comment with ID 1691496200 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

boegelbot · 2023-08-24T11:40:15Z

Test report by @boegelbot
SUCCESS
Build succeeded for 9 out of 9 (9 easyconfigs in total)
jsczen2c1.int.jsc-zen2.easybuild-test.cluster - Linux Rocky Linux 8.5, x86_64, AMD EPYC 7742 64-Core Processor (zen2), Python 3.6.8
See https://gist.github.com/boegelbot/c50199acad0d1048ff06ad258e85bff3 for a full test report.

verdurin · 2023-08-29T18:09:03Z

Test report by @verdurin
SUCCESS
Build succeeded for 34 out of 34 (9 easyconfigs in total)
easybuild-c7.novalocal - Linux CentOS Linux 7.9.2009, x86_64, Intel Xeon Processor (Skylake, IBRS), Python 3.6.8
See https://gist.github.com/verdurin/264ca00f8ae3c96fc59af218021c2f66 for a full test report.

verdurin

Looks fine.

verdurin · 2023-08-30T15:59:34Z

Going in, thanks @casparvl!

boegel · 2023-09-07T10:16:47Z

@@ -0,0 +1,41 @@
+easyblock = 'PythonPackage'
+
+name = 'notebook'


Note: this was renamed to JupyterNotebook in #18735

casparvl added new update labels Aug 22, 2023

casparvl and others added 6 commits August 22, 2023 15:03

Delete maturin-1.1.0-GCCcore-12.3.0.eb

ae7cc5b

This PR depends on easybuilders#18596 Shouldn't re-add this

Delete tornado-6.3.2-GCCcore-12.3.0.eb

d794d51

Depends on easybuilders#18511 , shouldn't re-add this

Merge branch 'develop' of https://github.com/easybuilders/easybuild-e…

42e215e

…asyconfigs into 20230822144632_new_pr_PycURL7452

Fix style issue JupyterHub. Fix checksums PyZMQ. Fix missing patch nb…

a142655

…classic. Set download_dep_fail in notebook.

Set download_dep_fail in nbclassic.

ef66f77

Delete tornado-6.3.2-GCCcore-12.3.0.eb

463b628

Is in dependent PR already

Caspar van Leeuwen added 2 commits August 23, 2023 19:37

Merge branch 'develop' of https://github.com/easybuilders/easybuild-e…

20af44b

…asyconfigs into 20230822144632_new_pr_PycURL7452

casparl added 3 commits August 23, 2023 20:08

Make sure the batchspawner tarball is downloaded in a way that leads …

586de11

…to a reproducible checksum.

Re-added explaination of why we install batchspawner from a specific …

6406490

…commit

Fix typo

600f599

casparvl mentioned this pull request Aug 24, 2023

{tools}[GCCcore/12.3.0] Jupyter-bundle v20230823, jupyter-resource-usage v1.0.0, jupyterlmod v4.0.3 #18634

Merged

1 task

casparvl added the 2023a label Aug 25, 2023

verdurin reviewed Aug 30, 2023

View reviewed changes

Comment thread easybuild/easyconfigs/j/JupyterLab/JupyterLab-4.0.5-GCCcore-12.3.0.eb

verdurin added this to the next release (4.8.1?) milestone Aug 30, 2023

verdurin approved these changes Aug 30, 2023

View reviewed changes

verdurin merged commit 82bc474 into easybuilders:develop Aug 30, 2023

boegel mentioned this pull request Sep 7, 2023

rename notebook to JupyterNotebook #18735

Merged

boegel reviewed Sep 7, 2023

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easybuilders deleted a comment from boegelbot Sep 11, 2023

trz42 mentioned this pull request Oct 23, 2023

{tools}[intel/2020a] udocker v1.1.4 w/ Python 2.7.18 #11235

Closed

		@@ -0,0 +1,41 @@
		easyblock = 'PythonPackage'

		name = 'notebook'

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casparvl commented Aug 22, 2023 •

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