{vis}[foss/2023a] napari v0.4.19.post1, VisPy v0.14.1 w/ Python v3.11.3 by ThomasHoffmann77 · Pull Request #19664 · easybuilders/easybuild-easyconfigs

ThomasHoffmann77 · 2024-01-22T09:12:16Z

(created using eb --new-pr)

…ydantic v2.5.3 w/ Python v3.11.3

del pydantic (easybuilders#19647)

jfgrimm · 2024-01-22T10:39:33Z

see also: #19652
Assuming you're also working on RELION 5, I have more PRs coming

ThomasHoffmann77 · 2024-01-22T14:19:36Z

see also: #19652 Assuming you're also working on RELION 5, I have more PRs coming

see #19240 - did not port it to 2023a, yet. looking forward to your PRs.

regarding napari 0.4.18 vs 0.4.19rc3. The pydantic < 2 requirement might lead to conflicts. 4.19 uses pydantic_compat.

jfgrimm · 2024-01-22T17:46:37Z

see also: #19652 Assuming you're also working on RELION 5, I have more PRs coming

see #19240 - did not port it to 2023a, yet. looking forward to your PRs.

regarding napari 0.4.18 vs 0.4.19rc3. The pydantic < 2 requirement might lead to conflicts. 4.19 uses pydantic_compat.

made a draft here: #19678

remove download_dep_fail

…s-2023a.eb 0.4.19rc3 -> 0.4.19

add checksum for pydantic_compat

update napari-plugin-engine2 to version 0.7.4

adjust dependency imageio to ver 2.33.1

jfgrimm · 2024-02-29T15:30:34Z

@ThomasHoffmann77 can you fix the conflicts please?

….0.eb

ThomasHoffmann77 · 2024-03-01T09:12:48Z

@ThomasHoffmann77 can you fix the conflicts please?
@jfgrimm I deleted PyOpenGL, Qtconsole, and QtPy. I updated some extensions and to 0.4.19.post1.
I opened a new PR #20007 to add PyOpenGL-accelerate.

ThomasHoffmann77 · 2024-03-01T09:56:12Z

@jfgrimm I downgraded the VisPy dependency from 0.14.1 to 0.12.2 since there was a conflict with the napari 0.4.18 easyconfig. Preferably I'd like to keep the newer version of VisPy.

ThomasHoffmann77 · 2024-03-25T11:15:30Z

Test report by @ThomasHoffmann77
FAILED
Build succeeded for 1 out of 3 (6 easyconfigs in total)
srv-mahamid-01.embl.de - Linux AlmaLinux 8.8, x86_64, AMD EPYC 7513 32-Core Processor, 2 x NVIDIA NVIDIA GeForce RTX 3090, 535.113.01, Python 3.6.8
See https://gist.github.com/ThomasHoffmann77/dfcccd87696ced64a8cad347055edad6 for a full test report.

ThomasHoffmann77 · 2024-03-25T11:16:02Z

Test report by @ThomasHoffmann77
FAILED
Build succeeded for 0 out of 2 (6 easyconfigs in total)
srv-mahamid-01.embl.de - Linux AlmaLinux 8.8, x86_64, AMD EPYC 7513 32-Core Processor, 2 x NVIDIA NVIDIA GeForce RTX 3090, 535.113.01, Python 3.6.8
See https://gist.github.com/ThomasHoffmann77/9f8d87068c021bbbee47eeb18df266e0 for a full test report.

ThomasHoffmann77 · 2024-03-25T11:18:45Z

Test report by @ThomasHoffmann77
FAILED
Build succeeded for 0 out of 2 (7 easyconfigs in total)
srv-mahamid-01.embl.de - Linux AlmaLinux 8.8, x86_64, AMD EPYC 7513 32-Core Processor, 2 x NVIDIA NVIDIA GeForce RTX 3090, 535.113.01, Python 3.6.8
See https://gist.github.com/ThomasHoffmann77/1ef026d81ffb48d4265e348c2321a22a for a full test report.

ThomasHoffmann77 · 2024-03-25T15:18:02Z

Test report by @ThomasHoffmann77
FAILED
Build succeeded for 2 out of 3 (7 easyconfigs in total)
srv-mahamid-01.embl.de - Linux AlmaLinux 8.8, x86_64, AMD EPYC 7513 32-Core Processor, 2 x NVIDIA NVIDIA GeForce RTX 3090, 535.113.01, Python 3.6.8
See https://gist.github.com/ThomasHoffmann77/0885fe8e76a35d337f40b0230390a594 for a full test report.

fix python shebang

ThomasHoffmann77 · 2024-03-27T10:41:29Z

Test report by @ThomasHoffmann77
SUCCESS
Build succeeded for 5 out of 5 (5 easyconfigs in total)
srv-mahamid-01.embl.de - Linux AlmaLinux 8.8, x86_64, AMD EPYC 7513 32-Core Processor, 2 x NVIDIA NVIDIA GeForce RTX 3090, 535.113.01, Python 3.6.8
See https://gist.github.com/ThomasHoffmann77/b0a2112a1f875e261fc111fdcf7465a7 for a full test report.

jfgrimm

sorry for not looking at this again sooner

easybuild/easyconfigs/v/VisPy/VisPy-0.14.1-foss-2023a.eb

jfgrimm · 2024-05-16T14:48:07Z

Test report by @jfgrimm
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in total)
node086.viking2.yor.alces.network - Linux Rocky Linux 8.9, x86_64, AMD EPYC 7643 48-Core Processor, Python 3.6.8
See https://gist.github.com/jfgrimm/5e5fc117102596c1ce98dd8b4db9cc7a for a full test report.

Co-authored-by: Jasper Grimm <65227842+jfgrimm@users.noreply.github.com>

jfgrimm · 2024-05-16T14:58:28Z

@boegelbot: please test @ generoso

boegelbot · 2024-05-16T15:00:05Z

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

PR test command 'EB_PR=19664 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_19664 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 13476

Test results coming soon (I hope)...

Details

- notification for comment with ID 2115485749 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).

jfgrimm · 2024-05-16T15:02:33Z

Test report by @jfgrimm
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in total)
node086.viking2.yor.alces.network - Linux Rocky Linux 8.9, x86_64, AMD EPYC 7643 48-Core Processor, Python 3.6.8
See https://gist.github.com/jfgrimm/6935c9f6f279db28017d86eccdee10ce for a full test report.

jfgrimm

LGTM (just waiting on the bot reports + CI)

boegelbot · 2024-05-16T15:07:45Z

Test report by @boegelbot
FAILED
Build succeeded for 1 out of 2 (2 easyconfigs in total)
cns1 - Linux Rocky Linux 8.9, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/boegelbot/63ff5316550ee8de14cd6a506a8a238a for a full test report.

jfgrimm · 2024-05-16T15:14:15Z

jsc-zen3 build failed with:

asyncpg 0.29.0 has requirement async-timeout>=4.0.3; python_version < "3.12.0", but you have async-timeout 4.0.2.

jfgrimm · 2024-05-17T09:34:01Z

@boegelbot: please test @ generoso

boegelbot · 2024-05-17T09:35:09Z

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

PR test command 'EB_PR=19664 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_19664 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 13484

Test results coming soon (I hope)...

Details

- notification for comment with ID 2117145510 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 · 2024-05-17T09:42:12Z

Test report by @boegelbot
FAILED
Build succeeded for 1 out of 2 (2 easyconfigs in total)
cns1 - Linux Rocky Linux 8.9, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/boegelbot/0d2eb8172fea56eac14fef4f0b308065 for a full test report.

issues

jfgrimm · 2024-05-17T10:43:34Z

I've traced the difference between my installations and the bots to the following PR: #20511

jfgrimm · 2024-05-17T13:57:07Z

@boegelbot: please test @ generoso

boegelbot · 2024-05-17T14:00:05Z

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

PR test command 'EB_PR=19664 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_19664 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 13493

Test results coming soon (I hope)...

Details

- notification for comment with ID 2117669847 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 · 2024-05-17T14:09:11Z

Test report by @boegelbot
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in total)
cns1 - Linux Rocky Linux 8.9, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/boegelbot/fc234641e4e50576d2410325037742df for a full test report.

jfgrimm · 2024-05-17T14:09:20Z

@boegelbot: please test @ jsc-zen3

ThomasHoffmann77 · 2024-05-17T14:09:59Z

@jfgrimm are the sanity pip check messages about missing hatchling related to 20546 and jupyter-server?

boegelbot · 2024-05-17T14:10:08Z

@jfgrimm: Request for testing this PR well received on jsczen3l1.int.jsc-zen3.fz-juelich.de

PR test command 'if [[ develop != 'develop' ]]; then EB_BRANCH=develop ./easybuild_develop.sh 2> /dev/null 1>&2; EB_PREFIX=/home/boegelbot/easybuild/develop source init_env_easybuild_develop.sh; fi; EB_PR=19664 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_19664 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 4150

Test results coming soon (I hope)...

Details

- notification for comment with ID 2117694597 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 · 2024-05-17T14:15:46Z

Test report by @boegelbot
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.4, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.18
See https://gist.github.com/boegelbot/5ae390c56fde5d9056cfc5999c9fe908 for a full test report.

jfgrimm

LGTM

will merge once #20553 is merged

jfgrimm · 2024-05-20T13:11:01Z

Going in, thanks @ThomasHoffmann77!

ThomasHoffmann77 and others added 3 commits January 22, 2024 10:11

{vis}[foss/2023a] napari v4.19rc3, Qtconsole v5.5.1, VisPy v0.14.1, p…

042a42a

…ydantic v2.5.3 w/ Python v3.11.3

Delete easybuild/easyconfigs/p/pydantic/pydantic-2.5.3-GCCcore-12.3.0.eb

baf14f2

del pydantic (easybuilders#19647)

add PyOpenGL and QtPy

a3b5164

ThomasHoffmann77 changed the title ~~{vis}[foss/2023a] napari v4.19rc3, Qtconsole v5.5.1, VisPy v0.14.1, pydantic v2.5.3 w/ Python v3.11.3~~ {vis}[foss/2023a] napari v4.19rc3, Qtconsole v5.5.1, VisPy v0.14.1, PyOpenGL v3.1.7, QtPy v2.4.1, w/ Python v3.11.3 Jan 22, 2024

ThomasHoffmann77 added 2 commits February 1, 2024 15:19

Update PyOpenGL-3.1.7-GCCcore-12.3.0.eb

84accc3

remove download_dep_fail

Update and rename napari-0.4.19rc3-foss-2023a.eb to napari-0.4.19-fos…

6977868

…s-2023a.eb 0.4.19rc3 -> 0.4.19

ThomasHoffmann77 changed the title ~~{vis}[foss/2023a] napari v4.19rc3, Qtconsole v5.5.1, VisPy v0.14.1, PyOpenGL v3.1.7, QtPy v2.4.1, w/ Python v3.11.3~~ {vis}[foss/2023a] napari v0.4.19, Qtconsole v5.5.1, VisPy v0.14.1, PyOpenGL v3.1.7, QtPy v2.4.1, w/ Python v3.11.3 Feb 1, 2024

ThomasHoffmann77 added 3 commits February 1, 2024 15:48

Update napari-0.4.19-foss-2023a.eb

28c2316

add checksum for pydantic_compat

Update napari-0.4.19-foss-2023a.eb

263d506

update napari-plugin-engine2 to version 0.7.4

Update napari-0.4.19-foss-2023a.eb

6573517

adjust dependency imageio to ver 2.33.1

This was referenced Feb 26, 2024

{bio}[foss/2023a] RELION v5.0.0 w/ CUDA 12.1.1 #19678

Merged

{bio}[foss/2023a] pyTME v0.2.1, pyFFTW v0.13.1, PyWavelets v1.5.0 /w CUDA 12.1.1 #19684

Open

ThomasHoffmann77 and others added 3 commits March 1, 2024 09:54

update to 0.4.19.post1

63d31f1

Delete easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.7-GCCcore-12.3.0.eb

6a4d9da

Delete easybuild/easyconfigs/q/Qtconsole/Qtconsole-5.5.1-GCCcore-12.3…

2867be2

….0.eb

ThomasHoffmann77 changed the title ~~{vis}[foss/2023a] napari v0.4.19, Qtconsole v5.5.1, VisPy v0.14.1, PyOpenGL v3.1.7, QtPy v2.4.1, w/ Python v3.11.3~~ {vis}[foss/2023a] napari v0.4.19.post1, VisPy v0.14.1 w/ Python v3.11.3 Mar 1, 2024

Delete easybuild/easyconfigs/q/QtPy/QtPy-2.4.1-GCCcore-12.3.0.eb

d2d5836

downgrad VisPy dependency from 0.14.1 to 0.12.2

3206533

Delete easybuild/easyconfigs/n/napari/napari-0.4.19-foss-2023a.eb

c216037

Update napari-0.4.19.post1-foss-2023a.eb

7aa0ef2

fix python shebang

jfgrimm requested changes May 16, 2024

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easybuild/easyconfigs/v/VisPy/VisPy-0.14.1-foss-2023a.eb Outdated Show resolved Hide resolved

Update easybuild/easyconfigs/v/VisPy/VisPy-0.14.1-foss-2023a.eb

2be9cb0

Co-authored-by: Jasper Grimm <65227842+jfgrimm@users.noreply.github.com>

jfgrimm added this to the release after 4.9.1 milestone May 16, 2024

jfgrimm added the update label May 16, 2024

jfgrimm previously approved these changes May 16, 2024

View reviewed changes

jfgrimm mentioned this pull request May 17, 2024

bump async-timeout to 4.0.3 in aiohttp 3.8.5 #20553

Merged

jfgrimm approved these changes May 17, 2024

View reviewed changes

jfgrimm merged commit e142610 into easybuilders:develop May 20, 2024

easybuilders deleted a comment from boegelbot Jun 10, 2024

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