There is also a failure because there are two versions of scikit-learn in the toolchain. Should I use the more common one rather than the latest?

FAIL: test_dep_versions_per_toolchain_generation (test.easyconfigs.easyconfigs.EasyConfigTest.test_dep_versions_per_toolchain_generation)
Check whether there's only one dependency version per toolchain generation actively used.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/runner/work/easybuild-easyconfigs/easybuild-easyconfigs/test/easyconfigs/easyconfigs.py", line 1075, in test_dep_versions_per_toolchain_generation
    self.fail("Should not have multi-variant dependencies in easyconfigs:\n%s" % multi_dep_vars_msg)
AssertionError: Should not have multi-variant dependencies in easyconfigs:

found 2 variants of 'scikit-learn' dependency in easyconfigs using '2024a' toolchain generation
* version: 1.5.2; versionsuffix:  as dep for {'Extra-P-4.2.3-gfbf-2024a.eb', 'pycomlink-0.4.1-foss-2024a.eb', 'pyrosm-0.6.2-foss-2024a.eb', 'TEtrimmer-1.5.4-foss-2024a.eb', 'bayesian-optimization-2.0.3-foss-2024a.eb', 'geopandas-1.0.1-foss-2024a.eb', 'MACS3-3.0.3-gfbf-2024a.eb', 'clisops-0.15.0-foss-2024a.eb', 'xclim-0.58.1-foss-2024a.eb', 'MDAnalysis-2.9.0-foss-2024a.eb', 'xclim-0.55.1-foss-2024a.eb', 'NLTK-3.9.1-foss-2024a.eb', 'pyOpenRiverCam-0.8.6-foss-2024a.eb', 'umap-learn-0.5.7-foss-2024a.eb', 'imbalanced-learn-0.14.0-gfbf-2024a.eb', 'r5py-1.0.6-foss-2024a-Java-21.eb', 'nglview-3.1.4-foss-2024a.eb', 'imbalanced-learn-0.12.4-gfbf-2024a.eb', 'librosa-0.10.2.post1-foss-2024a.eb', 'Optuna-4.1.0-foss-2024a.eb', 'regionmask-0.13.0-foss-2024a.eb', 'SnapATAC2-2.9.0-dev0-20250630-foss-2024a.eb', 'koopmans-1.1.0-foss-2024a.eb', 'hmmlearn-0.3.3-gfbf-2024a.eb', 'EasyPQP-0.1.53-foss-2024a.eb'}
* version: 1.6.1; versionsuffix:  as dep for {'LightGBM-4.6.0-foss-2024a.eb', 'CheckM2-1.1.0-foss-2024a.eb', 'tslearn-0.6.4-foss-2024a.eb'}

There is also a failure because there are two versions of scikit-learn in the toolchain. Should I use the more common one rather than the latest?

FAIL: test_dep_versions_per_toolchain_generation (test.easyconfigs.easyconfigs.EasyConfigTest.test_dep_versions_per_toolchain_generation)
Check whether there's only one dependency version per toolchain generation actively used.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/runner/work/easybuild-easyconfigs/easybuild-easyconfigs/test/easyconfigs/easyconfigs.py", line 1075, in test_dep_versions_per_toolchain_generation
    self.fail("Should not have multi-variant dependencies in easyconfigs:\n%s" % multi_dep_vars_msg)
AssertionError: Should not have multi-variant dependencies in easyconfigs:

found 2 variants of 'scikit-learn' dependency in easyconfigs using '2024a' toolchain generation
* version: 1.5.2; versionsuffix:  as dep for {'Extra-P-4.2.3-gfbf-2024a.eb', 'pycomlink-0.4.1-foss-2024a.eb', 'pyrosm-0.6.2-foss-2024a.eb', 'TEtrimmer-1.5.4-foss-2024a.eb', 'bayesian-optimization-2.0.3-foss-2024a.eb', 'geopandas-1.0.1-foss-2024a.eb', 'MACS3-3.0.3-gfbf-2024a.eb', 'clisops-0.15.0-foss-2024a.eb', 'xclim-0.58.1-foss-2024a.eb', 'MDAnalysis-2.9.0-foss-2024a.eb', 'xclim-0.55.1-foss-2024a.eb', 'NLTK-3.9.1-foss-2024a.eb', 'pyOpenRiverCam-0.8.6-foss-2024a.eb', 'umap-learn-0.5.7-foss-2024a.eb', 'imbalanced-learn-0.14.0-gfbf-2024a.eb', 'r5py-1.0.6-foss-2024a-Java-21.eb', 'nglview-3.1.4-foss-2024a.eb', 'imbalanced-learn-0.12.4-gfbf-2024a.eb', 'librosa-0.10.2.post1-foss-2024a.eb', 'Optuna-4.1.0-foss-2024a.eb', 'regionmask-0.13.0-foss-2024a.eb', 'SnapATAC2-2.9.0-dev0-20250630-foss-2024a.eb', 'koopmans-1.1.0-foss-2024a.eb', 'hmmlearn-0.3.3-gfbf-2024a.eb', 'EasyPQP-0.1.53-foss-2024a.eb'}
* version: 1.6.1; versionsuffix:  as dep for {'LightGBM-4.6.0-foss-2024a.eb', 'CheckM2-1.1.0-foss-2024a.eb', 'tslearn-0.6.4-foss-2024a.eb'}

If the package supports using scikit-learn/1.5.2, then yes. Looking at our test suite, "CheckM2 and its dep LightGBM require scikit-learn-1.6.1". That's probably why we have two versions of scikit-learn in that toolchain

@boegelbot please test @ jsc-zen3

@Thyre: 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=24339 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_24339 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

• exit code: 0
• output:

Submitted batch job 8521

Test results coming soon (I hope)...

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
jsczen3c1.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/6d2fa67c96af4a41e10d20a3a59d58e5 for a full test report.

Test report by @WilleBell
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
node710.hydra.os - Linux Rocky Linux 9.6, x86_64, AMD EPYC 9535 64-Core Processor, Python 3.9.21
See https://gist.github.com/WilleBell/b06c6fb9fc3d0a0a1b6eb2b49d23bd71 for a full test report.

Going in, thanks @JarneRenders!