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{bio,devel}[GCCcore/12.3.0,gfbf/2023a] TBProfiler v6.6.3 and deps - black, python-docx, and samclip#23014

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smoors merged 3 commits intoeasybuilders:developfrom
verdurin:20250603144814_new_pr_TBProfiler663
Jul 2, 2025
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{bio,devel}[GCCcore/12.3.0,gfbf/2023a] TBProfiler v6.6.3 and deps - black, python-docx, and samclip#23014
smoors merged 3 commits intoeasybuilders:developfrom
verdurin:20250603144814_new_pr_TBProfiler663

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@verdurin
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@verdurin verdurin commented Jun 3, 2025

(created using eb --new-pr)

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github-actions Bot commented Jun 3, 2025 •
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Updated software black-24.1.1-GCCcore-12.3.0.eb

Diff against black-24.10.0-GCCcore-13.2.0.eb

easybuild/easyconfigs/b/black/black-24.10.0-GCCcore-13.2.0.eb

diff --git a/easybuild/easyconfigs/b/black/black-24.10.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/b/black/black-24.1.1-GCCcore-12.3.0.eb
index 716af8bc41..b888a5350f 100644
--- a/easybuild/easyconfigs/b/black/black-24.10.0-GCCcore-13.2.0.eb
+++ b/easybuild/easyconfigs/b/black/black-24.1.1-GCCcore-12.3.0.eb
@@ -1,7 +1,7 @@
 easyblock = 'PythonBundle'
 
 name = 'black'
-version = '24.10.0'
+version = '24.1.1'
 
 homepage = 'https://black.readthedocs.io'
 description = """Black is the uncompromising Python code formatter.
@@ -15,15 +15,16 @@ Formatting becomes transparent after a while and you can focus on the content in
 Black makes code review faster by producing the smallest diffs possible.
 """
 
-toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
 
 builddependencies = [
     ('binutils', '2.40'),
     ('hatchling', '1.18.0'),
 ]
 dependencies = [
-    ('Python', '3.11.5'),
-    ('Python-bundle-PyPI', '2023.10'),
+    ('Python', '3.11.3'),
+    ('Python-bundle-PyPI', '2023.06'),
+    ('aiohttp', '3.8.5'),
 ]
 
 exts_list = [
@@ -32,7 +33,7 @@ exts_list = [
         'checksums': ['75dbf8955dc00442a438fc4d0666508a9a97b6bd41aa2f0ffe9d2f2725af0782'],
     }),
     (name, version, {
-        'checksums': ['846ea64c97afe3bc677b761787993be4991810ecc7a4a937816dd6bddedc4875'],
+        'checksums': ['48b5760dcbfe5cf97fd4fba23946681f3a81514c6ab8a45b50da67ac8fbc6c7b'],
     }),
 ]

Updated software python-docx-1.0.1-GCCcore-12.3.0.eb

Diff against python-docx-0.8.11-GCCcore-12.2.0.eb

easybuild/easyconfigs/p/python-docx/python-docx-0.8.11-GCCcore-12.2.0.eb

diff --git a/easybuild/easyconfigs/p/python-docx/python-docx-0.8.11-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/python-docx/python-docx-1.0.1-GCCcore-12.3.0.eb
index bdf831729d..48964defac 100644
--- a/easybuild/easyconfigs/p/python-docx/python-docx-0.8.11-GCCcore-12.2.0.eb
+++ b/easybuild/easyconfigs/p/python-docx/python-docx-1.0.1-GCCcore-12.3.0.eb
@@ -1,23 +1,23 @@
 easyblock = 'PythonPackage'
 
 name = 'python-docx'
-version = '0.8.11'
+version = '1.0.1'
 
 homepage = 'https://python-docx.readthedocs.io/en/latest/'
 description = 'python-docx is a Python library for creating and updating Microsoft Word (.docx) files'
 
-toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
 
 source_urls = [PYPI_LOWER_SOURCE]
 sources = [SOURCELOWER_TAR_GZ]
-checksums = ['1105d233a0956dd8dd1e710d20b159e2d72ac3c301041b95f4d4ceb3e0ebebc4']
+checksums = ['255148e15a4414244ec75f50e92d19864e52a7416768c65491707a7414659524']
 
 builddependencies = [
-    ('binutils', '2.39'),
+    ('binutils', '2.40'),
 ]
 
 dependencies = [
-    ('Python', '3.10.8'),
+    ('Python', '3.11.3'),
     ('lxml', '4.9.2'),
 ]

Updated software samclip-0.4.0-GCCcore-12.3.0.eb

Diff against samclip-0.4.0-GCCcore-13.3.0.eb

easybuild/easyconfigs/s/samclip/samclip-0.4.0-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/s/samclip/samclip-0.4.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/s/samclip/samclip-0.4.0-GCCcore-12.3.0.eb
index 3fe141168d..65de144750 100644
--- a/easybuild/easyconfigs/s/samclip/samclip-0.4.0-GCCcore-13.3.0.eb
+++ b/easybuild/easyconfigs/s/samclip/samclip-0.4.0-GCCcore-12.3.0.eb
@@ -10,14 +10,14 @@ version = '0.4.0'
 homepage = 'https://github.com/tseemann/samclip'
 description = """Filter SAM file for soft and hard clipped alignments."""
 
-toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
 
 github_account = 'tseemann'
 source_urls = [GITHUB_SOURCE]
 sources = ['v%(version)s.tar.gz']
 checksums = ['8196b705b0319b168949f42818eb3a6bcf96119a24daa950fa0d908d3111d127']
 
-dependencies = [('Perl', '5.38.2')]
+dependencies = [('Perl', '5.36.1')]
 
 sanity_check_paths = {
     'files': [name],
Diff against samclip-0.4.0-GCCcore-11.2.0.eb

easybuild/easyconfigs/s/samclip/samclip-0.4.0-GCCcore-11.2.0.eb

diff --git a/easybuild/easyconfigs/s/samclip/samclip-0.4.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/s/samclip/samclip-0.4.0-GCCcore-12.3.0.eb
index ff7f93d50b..65de144750 100644
--- a/easybuild/easyconfigs/s/samclip/samclip-0.4.0-GCCcore-11.2.0.eb
+++ b/easybuild/easyconfigs/s/samclip/samclip-0.4.0-GCCcore-12.3.0.eb
@@ -1,5 +1,6 @@
 # Author: Denis Kristak (INUITS)
 # License: GPLv2
+# Update: Petr Král (INUITS)
 
 easyblock = 'Tarball'
 
@@ -9,14 +10,14 @@ version = '0.4.0'
 homepage = 'https://github.com/tseemann/samclip'
 description = """Filter SAM file for soft and hard clipped alignments."""
 
-toolchain = {'name': 'GCCcore', 'version': '11.2.0'}
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
 
 github_account = 'tseemann'
 source_urls = [GITHUB_SOURCE]
 sources = ['v%(version)s.tar.gz']
 checksums = ['8196b705b0319b168949f42818eb3a6bcf96119a24daa950fa0d908d3111d127']
 
-dependencies = [('Perl', '5.34.0')]
+dependencies = [('Perl', '5.36.1')]
 
 sanity_check_paths = {
     'files': [name],

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verdurin commented Jun 3, 2025

Test report by @verdurin
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in total)
easybuild-el8.cloud.in.bmrc.ox.ac.uk - Linux Rocky Linux 8.10 (Green Obsidian), x86_64, Intel Xeon Processor (Skylake, IBRS), Python 3.11.11
See https://gist.github.com/verdurin/71eddc7016bb3fc8f6a3045563d08677 for a full test report.

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verdurin commented Jun 3, 2025

@boegelbot please test @ jsc-zen3

@verdurin verdurin changed the title {bio,devel}[GCCcore/12.3.0,gfbf/2023a] TBProfiler v6.6.3, black v24.1.1 w/ R 4.3.2 {bio,devel}[GCCcore/12.3.0,gfbf/2023a] TBProfiler v6.6.3 and deps - black, python-docx, and samclip Jun 3, 2025
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verdurin commented Jun 3, 2025

Test report by @verdurin
SUCCESS
Build succeeded for 4 out of 4 (4 easyconfigs in total)
easybuild-el8.cloud.in.bmrc.ox.ac.uk - Linux Rocky Linux 8.10 (Green Obsidian), x86_64, Intel Xeon Processor (Skylake, IBRS), Python 3.11.11
See https://gist.github.com/verdurin/3dce3b4a7764e688439bd9f1df8c45c1 for a full test report.

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boegelbot commented Jun 3, 2025

@verdurin: 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=23014 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_23014 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

  • exit code: 0
  • output:
Submitted batch job 6593

Test results coming soon (I hope)...

Details

- notification for comment with ID 2935889375 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 3, 2025

Test report by @boegelbot
SUCCESS
Build succeeded for 18 out of 18 (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/f22e9379a9b954a1ef7676027e49bb37 for a full test report.

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bedroge commented Jul 1, 2025

Test report by @bedroge
SUCCESS
Build succeeded for 4 out of 4 (4 easyconfigs in total)
bob-Latitude-5300 - Linux Ubuntu 24.04.2 LTS (Noble Numbat), x86_64, Intel(R) Core(TM) i7-8665U CPU @ 1.90GHz, Python 3.12.3
See https://gist.github.com/bedroge/dfb38869b8e9256494290def4499e284 for a full test report.

@boegel boegel added this to the 5.1.1 milestone Jul 2, 2025
boegel
boegel approved these changes Jul 2, 2025
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lgtm

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boegel commented Jul 2, 2025

Test report by @boegel
SUCCESS
Build succeeded for 4 out of 4 (4 easyconfigs in total)
node3512.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/7d5cda940c1e4ff853395ec0286c205b for a full test report.

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smoors commented Jul 2, 2025

Going in, thanks @verdurin!

@smoors smoors merged commit 1da3f4d into easybuilders:develop Jul 2, 2025
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