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{lib}[foss/2023a] nnU-Net v2.4.2, MedPy v0.5.1, dicom2nifti v2.4.10, python-gdcm v3.0.23.1 w/ CUDA 12.1.1#20664

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lexming merged 14 commits intoeasybuilders:developfrom
WilleBell:20240527174514_new_pr_nnU-Net242
Jun 16, 2025
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{lib}[foss/2023a] nnU-Net v2.4.2, MedPy v0.5.1, dicom2nifti v2.4.10, python-gdcm v3.0.23.1 w/ CUDA 12.1.1#20664
lexming merged 14 commits intoeasybuilders:developfrom
WilleBell:20240527174514_new_pr_nnU-Net242

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@WilleBell WilleBell commented May 27, 2024 •
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(created using eb --new-pr)
Depends on:

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github-actions Bot commented Mar 31, 2025 •
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Updated software batchgenerators-0.25-foss-2023a.eb

Diff against batchgenerators-0.25.1-foss-2023a.eb

easybuild/easyconfigs/b/batchgenerators/batchgenerators-0.25.1-foss-2023a.eb

diff --git a/easybuild/easyconfigs/b/batchgenerators/batchgenerators-0.25.1-foss-2023a.eb b/easybuild/easyconfigs/b/batchgenerators/batchgenerators-0.25-foss-2023a.eb
index 729d4072a7..6fdd72371a 100644
--- a/easybuild/easyconfigs/b/batchgenerators/batchgenerators-0.25.1-foss-2023a.eb
+++ b/easybuild/easyconfigs/b/batchgenerators/batchgenerators-0.25-foss-2023a.eb
@@ -1,7 +1,7 @@
 easyblock = 'PythonPackage'
 
 name = 'batchgenerators'
-version = '0.25.1'
+version = '0.25'
 
 homepage = 'https://github.com/MIC-DKFZ/batchgenerators'
 description = """Data augmentation toolkit developed at the Division of Medical
@@ -11,7 +11,7 @@ deep learning data augmentation needs."""
 toolchain = {'name': 'foss', 'version': '2023a'}
 
 sources = [SOURCE_TAR_GZ]
-checksums = ['4663a7f393bf1681d7675648362ba3f11b2a9474fb17228a92aac5d1ad28bb39']
+checksums = ['38a67413e847ff367e64abac36331fcb065494202d526ae96f7644de3a0e5495']
 
 dependencies = [
     ('Python', '3.11.3'),
@@ -21,6 +21,6 @@ dependencies = [
 ]
 
 # remove requirement on Pillow and unittest2, which are not actually used
-preinstallopts = "sed -i '13d;20d' setup.py &&"
+preinstallopts = "sed -i '13d;19d' setup.py &&"
 
 moduleclass = 'vis'
Diff against batchgenerators-0.25-foss-2021a.eb

easybuild/easyconfigs/b/batchgenerators/batchgenerators-0.25-foss-2021a.eb

diff --git a/easybuild/easyconfigs/b/batchgenerators/batchgenerators-0.25-foss-2021a.eb b/easybuild/easyconfigs/b/batchgenerators/batchgenerators-0.25-foss-2023a.eb
index b062814054..6fdd72371a 100644
--- a/easybuild/easyconfigs/b/batchgenerators/batchgenerators-0.25-foss-2021a.eb
+++ b/easybuild/easyconfigs/b/batchgenerators/batchgenerators-0.25-foss-2023a.eb
@@ -8,16 +8,16 @@ description = """Data augmentation toolkit developed at the Division of Medical
 Image Computing at the German Cancer Research Center (DKFZ) to suit all our
 deep learning data augmentation needs."""
 
-toolchain = {'name': 'foss', 'version': '2021a'}
+toolchain = {'name': 'foss', 'version': '2023a'}
 
 sources = [SOURCE_TAR_GZ]
 checksums = ['38a67413e847ff367e64abac36331fcb065494202d526ae96f7644de3a0e5495']
 
 dependencies = [
-    ('Python', '3.9.5'),
-    ('SciPy-bundle', '2021.05'),
-    ('scikit-image', '0.18.3'),
-    ('scikit-learn', '0.24.2'),
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('scikit-image', '0.22.0'),
+    ('scikit-learn', '1.3.1'),
 ]
 
 # remove requirement on Pillow and unittest2, which are not actually used

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WilleBell commented Mar 31, 2025

Test report by @WilleBell
SUCCESS
Build succeeded for 5 out of 5 (5 easyconfigs in total)
node402.hydra.os - Linux Rocky Linux 8.10, x86_64, AMD EPYC 7282 16-Core Processor, 1 x NVIDIA NVIDIA A100-PCIE-40GB, 570.124.06, Python 3.6.8
See https://gist.github.com/WilleBell/f8db09cbcb033a0da5f52afec684ff92 for a full test report.

verdurin
verdurin previously requested changes Jun 10, 2025
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Comment thread easybuild/easyconfigs/n/nnU-Net/nnU-Net-2.4.2-foss-2023a-CUDA-12.1.1.eb
@github-actions github-actions Bot removed the update label Jun 16, 2025
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lexming commented Jun 16, 2025

@boegelbot please test @ jsc-zen3

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boegelbot commented Jun 16, 2025

@lexming: 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=20664 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_20664 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

  • exit code: 0
  • output:
Submitted batch job 6766

Test results coming soon (I hope)...

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- notification for comment with ID 2976784908 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).

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boegelbot commented Jun 16, 2025

Test report by @boegelbot
SUCCESS
Build succeeded for 4 out of 4 (4 easyconfigs in total)
jsczen3c1.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/c26112913568e383f42ae9293a6dd194 for a full test report.

lexming
lexming approved these changes Jun 16, 2025
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LGTM

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lexming commented Jun 16, 2025

Merging, thanks @WilleBell !

@lexming lexming enabled auto-merge June 16, 2025 14:36
@lexming lexming dismissed verdurin’s stale review June 16, 2025 14:36

review addressed by author

@lexming lexming merged commit cbeaf42 into easybuilders:develop Jun 16, 2025
5 checks passed
@lexming lexming added this to the next release (5.1.1?) milestone Jun 16, 2025
@boegel boegel changed the title {lib}[foss/2023a] nnU-Net v2.4.2, MedPy v0.5.1, dicom2nifti v2.4.10, ... w/ CUDA 12.1.1 {lib}[foss/2023a] nnU-Net v2.4.2, MedPy v0.5.1, dicom2nifti v2.4.10, python-gdcm v3.0.23.1 w/ CUDA 12.1.1 Jul 5, 2025
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