make Rust a build dependency for maturin 1.1.0 (2023a generation) #22983

boegel · 2025-05-31T09:34:03Z

(created using eb --new-pr)

partial fix for #22763

boegel · 2025-05-31T09:42:53Z

@boegelbot please test @ jsc-zen3
EB_ARGS="Rust-1.70.0-GCCcore-12.3.0.eb maturin-1.1.0-GCCcore-12.3.0.eb jupyter-server-2.7.2-GCCcore-12.3.0.eb nbclassic-1.0.0-GCCcore-12.3.0.eb polars-0.19.19-gfbf-2023a.eb pymatgen-2023.12.18-foss-2023a.eb torch-em-0.7.1-foss-2023a.eb"
CORE_CNT=16

boegelbot · 2025-05-31T09:50:09Z

@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=22983 EB_ARGS="Rust-1.70.0-GCCcore-12.3.0.eb maturin-1.1.0-GCCcore-12.3.0.eb jupyter-server-2.7.2-GCCcore-12.3.0.eb nbclassic-1.0.0-GCCcore-12.3.0.eb polars-0.19.19-gfbf-2023a.eb pymatgen-2023.12.18-foss-2023a.eb torch-em-0.7.1-foss-2023a.eb" EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_22983 --ntasks="16" ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 6534

Test results coming soon (I hope)...

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boegelbot · 2025-05-31T11:48:32Z

Test report by @boegelbot
SUCCESS
Build succeeded for 7 out of 7 (7 easyconfigs in total)
jsczen3c4.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.5, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.21
See https://gist.github.com/boegelbot/00afeff63652b038ee9266894a461560 for a full test report.

…build dependency

boegel · 2025-05-31T13:08:11Z

@boegelbot please test @ jsc-zen3
CORE_CNT=16

boegelbot · 2025-05-31T13:10:09Z

@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=22983 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_22983 --ntasks="16" ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 6537

Test results coming soon (I hope)...

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boegel · 2025-05-31T13:51:17Z

Test report by @boegel
SUCCESS
Build succeeded for 6 out of 6 (6 easyconfigs in total)
node3902.accelgor.os - Linux RHEL 9.4, x86_64, AMD EPYC 7413 24-Core Processor (zen3), 1 x NVIDIA NVIDIA A100-SXM4-80GB, 570.133.20, Python 3.9.18
See https://gist.github.com/boegel/50db15646b3ef9bc5ec2dc6e6003c003 for a full test report.

…f crates

boegelbot · 2025-05-31T14:01:44Z

Test report by @boegelbot
FAILED
Build succeeded for 2 out of 6 (6 easyconfigs in total)
jsczen3c2.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.5, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.21
See https://gist.github.com/boegelbot/7f3694c55b8a65f65b92f7408ffbbcd1 for a full test report.

boegel · 2025-05-31T14:21:30Z

@boegelbot please test @ jsc-zen3-a100
CORE_CNT=16

boegelbot · 2025-05-31T14:30:08Z

@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=22983 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_22983 --ntasks="16" --partition=jsczen3g --gres=gpu:1 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 6543

Test results coming soon (I hope)...

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boegelbot · 2025-05-31T15:21:25Z

Test report by @boegelbot
FAILED
Build succeeded for 5 out of 6 (6 easyconfigs in total)
jsczen3g1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.5, x86_64, AMD EPYC-Milan Processor (zen3), 1 x NVIDIA NVIDIA A100 80GB PCIe, 555.42.06, Python 3.9.21
See https://gist.github.com/boegelbot/c00fdb95c0653dfcabb1b2b57e2b4a4f for a full test report.

boegel · 2025-05-31T20:21:20Z

@boegelbot please test @ jsc-zen3-a100
CORE_CNT=16

boegelbot · 2025-05-31T20:30:08Z

@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=22983 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_22983 --ntasks="16" --partition=jsczen3g --gres=gpu:1 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 6551

Test results coming soon (I hope)...

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boegelbot · 2025-05-31T21:18:36Z

Test report by @boegelbot
FAILED
Build succeeded for 5 out of 6 (6 easyconfigs in total)
jsczen3g1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.5, x86_64, AMD EPYC-Milan Processor (zen3), 1 x NVIDIA NVIDIA A100 80GB PCIe, 555.42.06, Python 3.9.21
See https://gist.github.com/boegelbot/5d27737b4ea1cb8bb8b4498d36e241d4 for a full test report.

boegel · 2025-05-31T21:42:14Z

Test report by @boegel
SUCCESS
Build succeeded for 5 out of 5 (5 easyconfigs in total)
node3534.doduo.os - Linux RHEL 9.4, x86_64, AMD EPYC 7552 48-Core Processor (zen2), Python 3.9.18
See https://gist.github.com/boegel/3678d1897c1df1122973586f26fc5a60 for a full test report.

…t required at all) + use PythonPackage easyblock

boegel · 2025-06-02T10:19:20Z

@boegelbot please test @ jsc-zen3-a100
CORE_CNT=16

boegelbot · 2025-06-02T10:20:09Z

@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=22983 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_22983 --ntasks="16" --partition=jsczen3g --gres=gpu:1 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 6577

Test results coming soon (I hope)...

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boegelbot · 2025-06-02T11:15:08Z

Test report by @boegelbot
FAILED
Build succeeded for 5 out of 6 (6 easyconfigs in total)
jsczen3g1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.5, x86_64, AMD EPYC-Milan Processor (zen3), 1 x NVIDIA NVIDIA A100 80GB PCIe, 555.42.06, Python 3.9.21
See https://gist.github.com/boegelbot/337ea60988210e20d2b16e513795084c for a full test report.

boegel · 2025-06-02T12:30:20Z

Taking a look why pymatgen-2023.12.18-foss-2023a.eb failed, I'm not seeing that on our systems... 🤔

edit: error is pretty clear, when installing orjson extension:

ModuleNotFoundError: No module named 'maturin'

So maturin is required for installing pymatgen.

Same problem locally (I was using pymatgen-2024.5.1-foss-2023b.eb instead of pymatgen-2023.12.18-foss-2023a.eb before...), so will fix by adding back maturin for pymatgen.
Problem doesn't occur with pymatgen-2024.5.1-foss-2023b.eb because orjson is a separate installation there (via orjson-3.10.10-GCCcore-13.2.0.eb).

edit: pymatgen only requires maturin, not Rust, so no need to use CargoPythonPackage

boegel · 2025-06-03T08:21:48Z

@boegelbot please test @ jsc-zen3-a100
CORE_CNT=16

boegelbot · 2025-06-03T08:30:10Z

@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=22983 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_22983 --ntasks="16" --partition=jsczen3g --gres=gpu:1 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 6588

Test results coming soon (I hope)...

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easybuild/easyconfigs/p/pymatgen/pymatgen-2023.12.18-foss-2023a.eb

boegelbot · 2025-06-03T09:25:38Z

Test report by @boegelbot
FAILED
Build succeeded for 5 out of 6 (6 easyconfigs in total)
jsczen3g1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.5, x86_64, AMD EPYC-Milan Processor (zen3), 1 x NVIDIA NVIDIA A100 80GB PCIe, 555.42.06, Python 3.9.21
See https://gist.github.com/boegelbot/c0daabfae39863e21a90a380329c1295 for a full test report.

…12.18

boegel · 2025-06-06T17:08:28Z

@boegelbot please test @ jsc-zen3-a100
CORE_CNT=16

boegelbot · 2025-06-06T17:10:09Z

@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=22983 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_22983 --ntasks="16" --partition=jsczen3g --gres=gpu:1 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 6624

Test results coming soon (I hope)...

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boegelbot · 2025-06-06T18:13:59Z

Test report by @boegelbot
SUCCESS
Build succeeded for 6 out of 6 (6 easyconfigs in total)
jsczen3g1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.5, x86_64, AMD EPYC-Milan Processor (zen3), 1 x NVIDIA NVIDIA A100 80GB PCIe, 555.42.06, Python 3.9.21
See https://gist.github.com/boegelbot/8866c22b695235133ba38bfbffa407ef for a full test report.

Micket · 2025-06-06T20:10:11Z

easybuild/easyconfigs/p/pymatgen/pymatgen-2023.12.18-foss-2023a.eb

@@ -1,4 +1,4 @@
-easyblock = 'PythonBundle'
+easyblock = 'CargoPythonBundle'


orjson is a rust package

crates = [ ('ahash', '0.8.6'), ('arrayvec', '0.7.4'), ('associative-cache', '2.0.0'), ('autocfg', '1.1.0'), ('beef', '0.5.2'), ('bytecount', '0.6.7'), ('castaway', '0.2.2'), ('cc', '1.0.83'), ('cfg-if', '1.0.0'), ('chrono', '0.4.31'), ('compact_str', '0.7.1'), ('encoding_rs', '0.8.33'), ('itoa', '1.0.9'), ('itoap', '1.0.1'), ('libc', '0.2.149'), ('libm', '0.2.8'), ('no-panic', '0.1.26'), ('num-traits', '0.2.17'), ('once_cell', '1.18.0'), ('packed_simd', '0.3.9'), ('proc-macro2', '1.0.69'), ('pyo3-build-config', '0.20.0'), ('pyo3-ffi', '0.20.0'), ('quote', '1.0.33'), ('rustversion', '1.0.14'), ('ryu', '1.0.15'), ('serde', '1.0.190'), ('serde_derive', '1.0.190'), ('serde_json', '1.0.107'), ('simdutf8', '0.1.4'), ('smallvec', '1.11.1'), ('static_assertions', '1.1.0'), ('syn', '2.0.38'), ('target-lexicon', '0.12.12'), ('unicode-ident', '1.0.12'), ('version_check', '0.9.4'), ('zerocopy', '0.7.15'), ('zerocopy-derive', '0.7.15'), ]

I.. really don't understand how this could pass a build without this. We should be setting cargo to offline mode, but maybe the maturin/pip wrapper thing overrides those environment variables, allowing it to go online?

Yeah, I was also a bit puzzled about how this could work without providing a list of crates...

I guess this explains it?

== 2025-05-31 23:13:07,252 easyblock.py:3091 DEBUG Installing extension orjson with default class PythonPackage (from easybuild.easyblocks.generic.pythonpackage)

In pymatgen-2024.5.1-foss-2023b.eb, orjson has been lifted in a proper dependency, so situation is different there.

@Micket CargoPythonBundle should make sure that CargoPythonPackage is used for all extensions, so Cargo.extract_step (which ends up setting $CARGO_NET_OFFLINE to true is used for every extension?

Hmm, no, should be fine, the log tells me that $CARGO_NET_OFFLINE is being set to true right before the installation of every extension, including orjson

Well, it's being set, but then later being unset again, before the actual pip install happens:

egrep 'installing.*extension|CARGO_NET_OFFLINE|Running shell command.*pip install.*orjson' /software/pymatgen/2023.12.18-foss-2023a/easybuild/*log* ... == 2025-05-31 23:15:56,812 environment.py:93 INFO Environment variable CARGO_NET_OFFLINE set to true (previously undefined) == 2025-05-31 23:15:56,852 build_log.py:322 INFO installing extension orjson 3.9.10 (13/25)... == 2025-05-31 23:15:57,920 environment.py:172 DEBUG Key in old environment found that is not in new one: CARGO_NET_OFFLINE (true) == 2025-05-31 23:16:05,368 run.py:500 INFO Running shell command '/user/gent/400/vsc40023/eb_arcaninescratch/RHEL9/zen2-ib/software/Python/3.11.3-GCCcore-12.3.0/bin/python -m pip install --prefix=/user/gent/400/vsc40023/eb_arcaninescratch/RHEL9/zen2-ib/software/pymatgen/2023.12.18-foss-2023a --verbose --no-deps --ignore-installed --no-build-isolation .' in /tmp/vsc40023/easybuild_build/pymatgen/2023.12.18/foss-2023a/orjson/orjson-3.9.10

I think the problem is that $CARGO_NET_OFFLINE is not being set by Cargo.set_cargo_vars, which results in it not being set anymore when the actual installation of extensions is done.

That's probably an unexpected side effect from the changes implemented in easybuilders/easybuild-framework#4868

For the specific version of orjson being used here (3.9.10), it seems like cargo doesn't need to download anything at all, because the sources of the requires crates are included in the source tarball or orjson:

eb-shell> pwd /tmp/vsc40023/easybuild_build/pymatgen/2023.12.18/foss-2023a/orjson/orjson-3.9.10 eb-shell> ls include/cargo/ ahash-0.8.6 bytecount-0.6.7 compact_str-0.7.1 libm-0.2.8 proc-macro2-1.0.69 ryu-1.0.15 smallvec-1.11.1 version_check-0.9.4 arrayvec-0.7.4 castaway-0.2.2 encoding_rs-0.8.33 no-panic-0.1.26 pyo3-build-config-0.20.0 serde-1.0.190 static_assertions-1.1.0 zerocopy-0.7.15 associative-cache-2.0.0 cc-1.0.83 itoa-1.0.9 num-traits-0.2.17 pyo3-ffi-0.20.0 serde_derive-1.0.190 syn-2.0.38 zerocopy-derive-0.7.15 autocfg-1.1.0 cfg-if-1.0.0 itoap-1.0.1 once_cell-1.18.0 quote-1.0.33 serde_json-1.0.107 target-lexicon-0.12.12 beef-0.5.2 chrono-0.4.31 libc-0.2.149 packed_simd-0.3.9 rustversion-1.0.14 simdutf8-0.1.4 unicode-ident-1.0.12

So although easybuilders/easybuild-easyblocks#3764 is a correct fix, we don't actually need to provide a list of crates at all for this pymatgen easyconfig, since all crates required by the orjson extension included in it are shipped/vendored with it...

Lets make a comment that explains that this specific older version of orjson used vendored crates.
Updating to newer versions will require adding the crates.

@Micket OK, makes sense, done in f21d6b6

boegel · 2025-06-07T08:14:55Z

@boegelbot please test @ jsc-zen3
EB_ARGS="--include-easyblocks-from-pr 3764 pymatgen-2023.12.18-foss-2023a.eb --installpath /tmp/$USER/pr22983"

boegelbot · 2025-06-07T08:20:09Z

@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=22983 EB_ARGS="--include-easyblocks-from-pr 3764 pymatgen-2023.12.18-foss-2023a.eb --installpath /tmp/$USER/pr22983" EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_22983 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 6633

Test results coming soon (I hope)...

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boegelbot · 2025-06-07T08:37:56Z

Test report by @boegelbot
Using easyblocks from PR(s) easybuilders/easybuild-easyblocks#3764
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
jsczen3c2.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.5, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.21
See https://gist.github.com/boegelbot/fe0dfb964b8a722c75ffffa70f250ab4 for a full test report.

…requires in source tarball

boegel · 2025-06-07T13:29:49Z

@boegelbot please test @ jsc-zen3-a100
CORE_CNT=16

boegelbot · 2025-06-07T13:30:09Z

@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=22983 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_22983 --ntasks="16" --partition=jsczen3g --gres=gpu:1 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 6635

Test results coming soon (I hope)...

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boegelbot · 2025-06-07T14:30:57Z

Test report by @boegelbot
SUCCESS
Build succeeded for 6 out of 6 (6 easyconfigs in total)
jsczen3g1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.5, x86_64, AMD EPYC-Milan Processor (zen3), 1 x NVIDIA NVIDIA A100 80GB PCIe, 555.42.06, Python 3.9.21
See https://gist.github.com/boegelbot/f13b7fcabb491b2c3c1d492b38b5819a for a full test report.

Micket

lgtm

make Rust a build dependency for maturin 1.1.0 (2023a generation)

cc78ff6

boegel added the change label May 31, 2025

boegel mentioned this pull request May 31, 2025

use Rust with nightly channel as build dependency for polars 0.19.19 + 0.20.2 #22984

Merged

boegel added this to the next release (5.1.1?) milestone May 31, 2025

boegel mentioned this pull request May 31, 2025

Remove Rust runtime dependency of maturin #22763

Closed

use CargoPythonBundle or CargoPythonPackage easyblock when Rust is a …

1d968e9

…build dependency

use CargoPythonBundle easyblock for jupyter-server 2.7.2 + add list o…

70242e7

…f crates

boegel added 2 commits May 31, 2025 16:20

add list of crates to easyconfig for torch-em 0.7.1

600597f

add list of crates to easyconfig for vLLM 0.4.0

20fd2f8

boegel added 2 commits May 31, 2025 18:31

add additional crates required by torch-em 0.7.1 extensions

2d44fc3

fix order of checksums in torcm-em easyconfig

90b6618

easybuilders deleted a comment from boegelbot May 31, 2025

remove maturin + Rust build dependencies for nbclassic & pymatgen (no…

ed6e8f8

…t required at all) + use PythonPackage easyblock

add back maturin as build dependency for pymatgen

293e133

Micket reviewed Jun 3, 2025

View reviewed changes

easybuild/easyconfigs/p/pymatgen/pymatgen-2023.12.18-foss-2023a.eb Show resolved Hide resolved

add Rust build dependency + use CargoPythonBundle for pymatgen v2023.…

2e4f299

…12.18

Micket requested changes Jun 6, 2025

View reviewed changes

add comment to clarify that orjson 3.9.10 vendors the Rust crates it …

f21d6b6

…requires in source tarball

Micket approved these changes Jun 10, 2025

View reviewed changes

Micket merged commit c43994b into easybuilders:develop Jun 11, 2025
8 checks passed

boegel deleted the 20250531113359_new_pr_maturin110 branch June 11, 2025 17:43

		@@ -1,4 +1,4 @@
		easyblock = 'PythonBundle'
		easyblock = 'CargoPythonBundle'

make Rust a build dependency for maturin 1.1.0 (2023a generation) #22983

make Rust a build dependency for maturin 1.1.0 (2023a generation) #22983

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