Create lockfile for Cargo package if missing #3995

Flamefire · 2025-11-21T08:07:52Z

(created using eb --new-pr)

Requires/Includes for easier testing:

enhance Cargo easyblock to merge Cargo.toml file with workspace file #4016
Explictly call PythonPackage and Cargo configure step in CargoPythonPackage easyblock #3996
Make CargoPythonPackage the default class for extensions/components of CargoPythonBundle #3993

boegel · 2025-12-13T13:00:25Z

@Flamefire This will need to be re-worked on top of:

enhance Cargo easyblock to merge Cargo.toml file with workspace file #4016

Flamefire · 2025-12-13T13:04:21Z

Shall I wait until that is merged and rebase then?

boegel · 2025-12-13T16:30:43Z

Shall I wait until that is merged and rebase then?

Yes, makes sense.

boegel · 2025-12-14T11:17:58Z

@Flamefire #4016 is merged...

boegel · 2025-12-15T19:15:45Z

@boegelbot please test @ jsc-zen3
CORE_CNT=16
EB_ARGS="--installpath /tmp/$USER/pr3995 bamtofastq-1.4.1-GCCcore-12.3.0.eb bcrypt-4.0.1-GCCcore-12.3.0.eb chopper-0.9.0-GCCcore-12.3.0.eb cramino-0.14.5-GCC-12.3.0.eb cramjam-2.9.0-GCCcore-12.3.0.eb cryptography-41.0.1-GCCcore-12.3.0.eb elfx86exts-0.6.2-GCC-12.3.0.eb Evcxr-REPL-0.14.2-GCCcore-12.2.0-Rust-1.65.0.eb jiter-0.4.1-GCCcore-12.3.0.eb juliaup-1.17.9-GCCcore-12.3.0.eb jupyter-server-2.7.2-GCCcore-12.3.0.eb JupyterLab-4.0.3-GCCcore-12.2.0.eb kyber-0.4.0-GCC-12.3.0.eb Longshot-0.4.5-GCCcore-11.3.0.eb Longshot-1.0.0-GCCcore-12.3.0.eb maturin-1.1.0-GCCcore-12.3.0.eb maturin-1.4.0-GCCcore-12.3.0-Rust-1.75.0.eb maturin-1.7.8-GCCcore-12.3.0-Rust-1.81.0.eb mfqe-0.5.0-GCC-12.3.0.eb modkit-0.3.3-GCCcore-12.3.0.eb orjson-3.9.15-GCCcore-12.3.0.eb phasius-0.2.0-GCC-12.3.0.eb poetry-1.7.1-GCCcore-12.3.0.eb pydantic-2.5.3-GCCcore-12.2.0.eb pydantic-2.5.3-GCCcore-12.3.0.eb pydantic-2.6.4-GCCcore-13.2.0.eb pydantic-2.7.4-GCCcore-13.2.0.eb python-jellyfish-1.1.0-GCCcore-12.3.0.eb SKA2-0.3.7-GCCcore-12.3.0.eb skani-0.2.2-GCCcore-12.3.0.eb smafa-0.8.0-GCC-12.3.0.eb Spyder-5.5.1-GCCcore-12.3.0.eb tiktoken-0.6.0-GCCcore-12.3.0.eb tokenizers-0.13.3-GCCcore-12.2.0.eb tokenizers-0.15.2-GCCcore-12.3.0.eb Python-bundle-PyPI-2024.06-GCCcore-13.3.0.eb "

boegelbot · 2025-12-15T19:33:10Z

@boegel: 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=3995 EB_ARGS="--installpath /tmp/$USER/pr3995 bamtofastq-1.4.1-GCCcore-12.3.0.eb bcrypt-4.0.1-GCCcore-12.3.0.eb chopper-0.9.0-GCCcore-12.3.0.eb cramino-0.14.5-GCC-12.3.0.eb cramjam-2.9.0-GCCcore-12.3.0.eb cryptography-41.0.1-GCCcore-12.3.0.eb elfx86exts-0.6.2-GCC-12.3.0.eb Evcxr-REPL-0.14.2-GCCcore-12.2.0-Rust-1.65.0.eb jiter-0.4.1-GCCcore-12.3.0.eb juliaup-1.17.9-GCCcore-12.3.0.eb jupyter-server-2.7.2-GCCcore-12.3.0.eb JupyterLab-4.0.3-GCCcore-12.2.0.eb kyber-0.4.0-GCC-12.3.0.eb Longshot-0.4.5-GCCcore-11.3.0.eb Longshot-1.0.0-GCCcore-12.3.0.eb maturin-1.1.0-GCCcore-12.3.0.eb maturin-1.4.0-GCCcore-12.3.0-Rust-1.75.0.eb maturin-1.7.8-GCCcore-12.3.0-Rust-1.81.0.eb mfqe-0.5.0-GCC-12.3.0.eb modkit-0.3.3-GCCcore-12.3.0.eb orjson-3.9.15-GCCcore-12.3.0.eb phasius-0.2.0-GCC-12.3.0.eb poetry-1.7.1-GCCcore-12.3.0.eb pydantic-2.5.3-GCCcore-12.2.0.eb pydantic-2.5.3-GCCcore-12.3.0.eb pydantic-2.6.4-GCCcore-13.2.0.eb pydantic-2.7.4-GCCcore-13.2.0.eb python-jellyfish-1.1.0-GCCcore-12.3.0.eb SKA2-0.3.7-GCCcore-12.3.0.eb skani-0.2.2-GCCcore-12.3.0.eb smafa-0.8.0-GCC-12.3.0.eb Spyder-5.5.1-GCCcore-12.3.0.eb tiktoken-0.6.0-GCCcore-12.3.0.eb tokenizers-0.13.3-GCCcore-12.2.0.eb tokenizers-0.15.2-GCCcore-12.3.0.eb Python-bundle-PyPI-2024.06-GCCcore-13.3.0.eb " EB_CONTAINER= EB_REPO=easybuild-easyblocks EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_3995 --ntasks="16" ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 9187

Test results coming soon (I hope)...

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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).

boegel · 2025-12-15T19:44:06Z

@Flamefire Looks like HERRO-0.1.0_20240808-foss-2023a.eb fails with this updated Cargo easyblock?

Build step fails with:

error: failed to parse lock file at: /tmp/vsc40023/easybuild_build/HERRO/0.1.0_20240808/foss-2023a/herro-deccc46823615577f6fcda4ec9469f592fc3ffcb/Cargo.lock

Caused by:
  lock file version `2` was found, but this version of Cargo does not understand this lock file, perhaps Cargo needs to be updated?

boegel · 2025-12-15T21:14:01Z

There's also trouble with other easyconfigs:

For poetry-1.8.3-GCCcore-13.3.0.eb:

ERROR: Installation of poetry-1.8.3-GCCcore-13.3.0.eb failed: Extension 'six' cannot have crates. You can add them to the top-level config parameters when using e.g.the Cargo or CargoPythonBundle easyblock.

For pydantic-2.9.1-GCCcore-13.3.0.eb:

ERROR: Installation of pydantic-2.9.1-GCCcore-13.3.0.eb failed: Extension 'annotated_types' cannot have crates. You can add them to the top-level config parameters when using e.g.the Cargo or CargoPythonBundle easyblock.

@Flamefire It seems like this needs more work, so this won't make it in for EasyBuild v5.2.0...

boegelbot · 2025-12-15T22:25:43Z

Test report by @boegelbot

Overview of tested easyconfigs (in order)

SUCCESS bamtofastq-1.4.1-GCCcore-12.3.0.eb
SUCCESS bcrypt-4.0.1-GCCcore-12.3.0.eb
SUCCESS chopper-0.9.0-GCCcore-12.3.0.eb
SUCCESS cramino-0.14.5-GCC-12.3.0.eb
SUCCESS cryptography-41.0.1-GCCcore-12.3.0.eb
SUCCESS elfx86exts-0.6.2-GCC-12.3.0.eb
SUCCESS Evcxr-REPL-0.14.2-GCCcore-12.2.0-Rust-1.65.0.eb
SUCCESS juliaup-1.17.9-GCCcore-12.3.0.eb
FAIL JupyterLab-4.0.3-GCCcore-12.2.0.eb (build issue)
(partial log available at https://gist.github.com/boegelbot/abcd080fd74e6540ccc9b1e426b73e36)
SUCCESS kyber-0.4.0-GCC-12.3.0.eb
FAIL Longshot-0.4.5-GCCcore-11.3.0.eb (build issue)
(partial log available at https://gist.github.com/boegelbot/e5a54176fe660f57530d876c72f80771)
FAIL Longshot-1.0.0-GCCcore-12.3.0.eb (build issue)
(partial log available at https://gist.github.com/boegelbot/c3f1ea23577b76593ad4cc687d8aaec3)
SUCCESS maturin-1.1.0-GCCcore-12.3.0.eb
SUCCESS maturin-1.4.0-GCCcore-12.3.0-Rust-1.75.0.eb
SUCCESS maturin-1.7.8-GCCcore-12.3.0-Rust-1.81.0.eb
SUCCESS mfqe-0.5.0-GCC-12.3.0.eb
FAIL modkit-0.3.3-GCCcore-12.3.0.eb (build issue)
(partial log available at https://gist.github.com/boegelbot/5dbd35dfcf8b5f5a406c242643f561b8)
FAIL orjson-3.9.15-GCCcore-12.3.0.eb (build issue)
(partial log available at https://gist.github.com/boegelbot/b1b9817421fa969e4d249f997a2018ed)
SUCCESS phasius-0.2.0-GCC-12.3.0.eb
FAIL poetry-1.7.1-GCCcore-12.3.0.eb (build issue)
(partial log available at https://gist.github.com/boegelbot/571af7a9b8ab87c325f9d1cb28bba3cd)
FAIL pydantic-2.5.3-GCCcore-12.2.0.eb (build issue)
(partial log available at https://gist.github.com/boegelbot/059c4f002f84c3a6cd21957a74b80dca)
FAIL pydantic-2.5.3-GCCcore-12.3.0.eb (build issue)
(partial log available at https://gist.github.com/boegelbot/af5114946f1bd589c04c48f5cf4c2e2d)
FAIL pydantic-2.6.4-GCCcore-13.2.0.eb (build issue)
(partial log available at https://gist.github.com/boegelbot/9edd813cb3918f2d98ae737a9c546d8c)
FAIL pydantic-2.7.4-GCCcore-13.2.0.eb (build issue)
(partial log available at https://gist.github.com/boegelbot/e92a48b2ad6676a8068b247f89e29c9c)
SUCCESS python-jellyfish-1.1.0-GCCcore-12.3.0.eb
SUCCESS SKA2-0.3.7-GCCcore-12.3.0.eb
SUCCESS skani-0.2.2-GCCcore-12.3.0.eb
FAIL smafa-0.8.0-GCC-12.3.0.eb (build issue)
(partial log available at https://gist.github.com/boegelbot/4939fa47e64f7fde5823a827e390091e)
FAIL tiktoken-0.6.0-GCCcore-12.3.0.eb (build issue)
(partial log available at https://gist.github.com/boegelbot/d1ba1a6a0b82a535d9840b7812e3b933)
FAIL tokenizers-0.13.3-GCCcore-12.2.0.eb (build issue)
(partial log available at https://gist.github.com/boegelbot/8836b26e4bc0ee361d82cc24f1b0ccb1)
FAIL tokenizers-0.15.2-GCCcore-12.3.0.eb (build issue)
(partial log available at https://gist.github.com/boegelbot/25e078dc6b3aa0cee148b5eba599999f)
FAIL Python-bundle-PyPI-2024.06-GCCcore-13.3.0.eb (build issue)
(partial log available at https://gist.github.com/boegelbot/1f30d01bdf9fb9cd0943b44e8ce2c8e2)
SUCCESS cramjam-2.9.0-GCCcore-12.3.0.eb
FAIL jiter-0.4.1-GCCcore-12.3.0.eb (build issue)
(partial log available at https://gist.github.com/boegelbot/581340dae8bbeaf6a1e6e3afbeb1a7a6)
FAIL jupyter-server-2.7.2-GCCcore-12.3.0.eb (build issue)
(partial log available at https://gist.github.com/boegelbot/42f5181d5b1260ecad9b72fcace10eb7)
SUCCESS Spyder-5.5.1-GCCcore-12.3.0.eb

Build succeeded for 19 out of 36 (total: 1 hour 5 mins 29 secs) (36 easyconfigs in total)
jsczen3c2.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.6, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.21
See https://gist.github.com/boegelbot/593ab131ec81464c230ef82184d98389 for a full test report.

Flamefire · 2025-12-16T07:52:49Z

There's also trouble with other easyconfigs:

For poetry-1.8.3-GCCcore-13.3.0.eb:

ERROR: Installation of poetry-1.8.3-GCCcore-13.3.0.eb failed: Extension 'six' cannot have crates. You can add them to the top-level config parameters when using e.g.the Cargo or CargoPythonBundle easyblock.

For pydantic-2.9.1-GCCcore-13.3.0.eb:

ERROR: Installation of pydantic-2.9.1-GCCcore-13.3.0.eb failed: Extension 'annotated_types' cannot have crates. You can add them to the top-level config parameters when using e.g.the Cargo or CargoPythonBundle easyblock.

Those errors are real, somehow. They only get detected through the recent change in #3993, prior to that the crates specified in those easyconfigs are silently ignored unless there is something happening that I'm missing.
In this case the crates are actually from the top-level EC and "only" copied to extensions which they should not. This so far only caused errors when sources of an extension was a dict and the extension derived from Cargo, like CargoPythonPackage

So that needs to be fixed first.

lock file version 2 was found, but this version of Cargo does not understand this lock file, perhaps Cargo needs to be updated?

That is weird. Then I'll need to recheck which cargo version has which lockfile version

…f CargoPythonBundle

We cannot have multiple sources for extensions, see easybuilders/easybuild-framework#3463

…ythonbundle

That does additional configuration required for Rust crates

Flamefire · 2025-12-19T17:24:31Z

lock file version 2 was found, but this version of Cargo does not understand this lock file, perhaps Cargo needs to be updated?

That is weird. Then I'll need to recheck which cargo version has which lockfile version

Found it: Versions 1 and 2 were internal versions only, not reflected in the lockfile, so version = 1/2 must not be added.

Also fixed an issue where cargo might output warnings that confuse the code expecting a path.

I started a job with 40 random easyconfigs using Rust as a dependency and the ECs you used above. That will take a while but should succeed now.

Flamefire · 2025-12-20T11:43:33Z

Test report by @Flamefire

Overview of tested easyconfigs (in order)

SUCCESS bamtofastq-1.4.1-GCCcore-12.3.0.eb
SUCCESS bcrypt-4.0.1-GCCcore-12.3.0.eb
SUCCESS bcrypt-4.3.0-GCCcore-14.3.0.eb
SUCCESS chopper-0.9.0-GCCcore-12.3.0.eb
SUCCESS cramino-0.14.5-GCC-12.3.0.eb
SUCCESS cryptography-41.0.1-GCCcore-12.3.0.eb
SUCCESS cryptography-42.0.8-GCCcore-13.3.0.eb
SUCCESS cryptography-44.0.2-GCCcore-14.2.0.eb
SUCCESS cryptography-45.0.5-GCCcore-14.3.0.eb
SUCCESS DeltaLake-0.25.5-gfbf-2023b.eb
SUCCESS elfx86exts-0.6.2-GCC-12.3.0.eb
SUCCESS Evcxr-REPL-0.14.2-GCCcore-12.2.0-Rust-1.65.0.eb
SUCCESS gsutil-5.10-GCCcore-11.2.0.eb
SUCCESS HERRO-0.1.0_20240808-foss-2023a.eb
SUCCESS isONclust3-0.3.0-GCCcore-13.3.0.eb
SUCCESS juliaup-1.17.9-GCCcore-12.3.0.eb
SUCCESS jupyter-collaboration-2.1.1-GCCcore-13.2.0.eb
SUCCESS kyber-0.4.0-GCC-12.3.0.eb
SUCCESS libavif-1.0.4-GCCcore-12.3.0.eb
FAIL librsvg-2.58.0-GCCcore-13.2.0.eb (build issue)
(partial log available at https://gist.github.com/Flamefire/537dbc7f58a92ec8323b8cce6b23ed40)
FAIL librsvg-2.60.0-GCCcore-13.3.0.eb (build issue)
(partial log available at https://gist.github.com/Flamefire/3160204ffc60638bf435358c41731eda)
FAIL librsvg-2.61.0-GCCcore-14.3.0.eb (build issue)
(partial log available at https://gist.github.com/Flamefire/cf4f1773e7fbe07652a9b221416859b3)
SUCCESS Longshot-0.4.5-GCCcore-11.3.0.eb
SUCCESS Longshot-1.0.0-GCCcore-12.3.0.eb
SUCCESS maturin-1.1.0-GCCcore-12.3.0.eb
SUCCESS maturin-1.3.2-GCCcore-11.3.0-Rust-1.65.0.eb
SUCCESS maturin-1.4.0-GCCcore-12.3.0-Rust-1.75.0.eb
SUCCESS maturin-1.7.8-GCCcore-12.3.0-Rust-1.81.0.eb
SUCCESS mfqe-0.5.0-GCC-12.3.0.eb
SUCCESS modkit-0.3.3-GCCcore-12.3.0.eb
SUCCESS orjson-3.9.15-GCCcore-12.3.0.eb
SUCCESS phasius-0.2.0-GCC-12.3.0.eb
SUCCESS poetry-1.7.1-GCCcore-12.3.0.eb
SUCCESS poetry-1.8.3-GCCcore-13.3.0.eb
SUCCESS poetry-2.1.2-GCCcore-14.2.0.eb
SUCCESS poetry-2.1.3-GCCcore-14.3.0.eb
FAIL polars-0.15.6-foss-2022a.eb (build issue)
(partial log available at https://gist.github.com/Flamefire/d0c0d08e5f8b638710c400a0974adb14)
SUCCESS pydantic-2.5.3-GCCcore-12.3.0.eb
SUCCESS pydantic-2.6.4-GCCcore-13.2.0.eb
SUCCESS pydantic-2.7.4-GCCcore-13.2.0.eb
FAIL Python-3.10.8-GCCcore-12.2.0.eb (build issue)
(partial log available at https://gist.github.com/Flamefire/8f0e380cc79a62a995739be90839ffe3)
SUCCESS Python-bundle-PyPI-2024.06-GCCcore-13.3.0.eb
SUCCESS Python-bundle-PyPI-2025.07-GCCcore-14.3.0.eb
SUCCESS python-jellyfish-1.1.0-GCCcore-12.3.0.eb
SUCCESS rav1e-0.8.1-GCCcore-14.3.0.eb
FAIL retworkx-0.9.0-foss-2021a.eb (build issue)
(partial log available at https://gist.github.com/Flamefire/1fe4d18c707d47606c810a9df9fbf885)
SUCCESS retworkx-0.9.0-foss-2023a.eb
SUCCESS rustworkx-0.12.1-foss-2022a.eb
SUCCESS rustworkx-0.15.1-gfbf-2023a.eb
SUCCESS rustworkx-0.16.0-gfbf-2024a.eb
SUCCESS SKA2-0.3.7-GCCcore-12.3.0.eb
SUCCESS skani-0.2.2-GCCcore-12.3.0.eb
SUCCESS smafa-0.8.0-GCC-12.3.0.eb
SUCCESS tiktoken-0.6.0-GCCcore-12.3.0.eb
SUCCESS tiktoken-0.7.0-GCCcore-12.3.0.eb
SUCCESS timm-0.6.13-foss-2022a-CUDA-11.7.0.eb
SUCCESS tokenizers-0.13.3-GCCcore-12.2.0.eb
SUCCESS tokenizers-0.15.2-GCCcore-12.3.0.eb
SUCCESS tokenizers-0.19.1-GCCcore-13.2.0.eb
SUCCESS uv-0.4.20-GCCcore-13.3.0.eb
SUCCESS vLLM-0.4.0-foss-2023a-CUDA-12.1.1.eb
SUCCESS yacrd-1.0.0-foss-2023a.eb
SUCCESS cramjam-2.9.0-GCCcore-12.3.0.eb
SUCCESS jiter-0.4.1-GCCcore-12.3.0.eb
SUCCESS JupyterLab-4.0.3-GCCcore-12.2.0.eb
SUCCESS jupyter-server-2.7.2-GCCcore-12.3.0.eb
SUCCESS pydantic-2.5.3-GCCcore-12.2.0.eb
FAIL Qiskit-2.0.2-foss-2023a.eb (build issue)
(partial log available at https://gist.github.com/Flamefire/0ff203ea5f6664f3abcf4ea76cb516d1)
SUCCESS Spyder-5.5.1-GCCcore-12.3.0.eb

Build succeeded for 62 out of 69 (total: 19 hours 9 mins 11 secs) (75 easyconfigs in total)
i7095 - Linux Rocky Linux 9.6, x86_64, AMD EPYC 7702 64-Core Processor (zen2), Python 3.9.21
See https://gist.github.com/Flamefire/8df3a3453f13b50ed09a326319c8abfb for a full test report.

Flamefire force-pushed the 20251121090749_new_pr_cargo branch from de3fe7d to 66b2862 Compare November 21, 2025 08:11

This was referenced Nov 21, 2025

Explictly call PythonPackage and Cargo configure step in CargoPythonPackage easyblock #3996

Open

Use downloaded crates in SnapATAC2-2.9.0 easybuilders/easybuild-easyconfigs#24643

Open

boegel added the enhancement label Dec 3, 2025

boegel added this to the release after 5.2.0 milestone Dec 3, 2025

Flamefire force-pushed the 20251121090749_new_pr_cargo branch from 66b2862 to a0c5b67 Compare December 15, 2025 08:56

boegel modified the milestones: release after 5.2.0, next release (5.2.0) Dec 15, 2025

boegel modified the milestones: next release (5.2.0), release after 5.2.0 Dec 15, 2025

Flamefire added 3 commits December 17, 2025 13:20

Make CargoPythonPackage the default class for extensions/components o…

3e85845

…f CargoPythonBundle

Disallow using crates when Cargo is used as an extension.

eaa9818

We cannot have multiple sources for extensions, see easybuilders/easybuild-framework#3463

Don't inherit crates from parent when Cargo is an extension

e325a7d

Flamefire force-pushed the 20251121090749_new_pr_cargo branch from 806ad6d to 3f95cfa Compare December 18, 2025 16:52

Flamefire and others added 4 commits December 19, 2025 14:45

Merge branch 'easybuilders:develop' into 20251118151816_new_pr_cargop…

8d17841

…ythonbundle

Call Cargo configure step from CargoPythonPackage

9dd0fcf

That does additional configuration required for Rust crates

Create lockfile for Cargo package if missing

146bda1

Handle warnings in cargo output

d491dee

Flamefire force-pushed the 20251121090749_new_pr_cargo branch from a13f9bf to d491dee Compare December 19, 2025 13:46

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Create lockfile for Cargo package if missing #3995

Create lockfile for Cargo package if missing #3995

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Create lockfile for Cargo package if missing #3995

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Overview of tested easyconfigs (in order)

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Flamefire commented Nov 21, 2025 •

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