{bio}[GCC-13.3.0] ShapeMapper2 2.3 by fizwit · Pull Request #22922 · easybuilders/easybuild-easyconfigs

fizwit · 2025-05-20T22:13:32Z

No description provided.

smoors · 2025-05-22T20:29:13Z

+         try:
+             if dms:
+-               if re.search("\.sam", self.filename):
+               if re.search(".sam", self.filename):


this doesn't seem right? without the backslash anything with sam will match, not only the literal .sam.

same for the other cases?

Only '\' needs escapping with Python3.

>>> import re >>> filename = 'sam-filename.sam' >>> re.search("\.sam", filename) <stdin>:1: SyntaxWarning: invalid escape sequence '\.' <re.Match object; span=(12, 16), match='.sam'> >>> re.search(".sam", filename) <re.Match object; span=(12, 16), match='.sam'>

ah, you should use a raw string:

Suggested change

+ if re.search(".sam", self.filename):

+ if re.search(r"\.sam", self.filename):

@smoors Can you apply this suggestion, and then also fix the checksum for the patch file, test & merge?

Thyre · 2025-10-13T13:25:48Z

@boegelbot please test @ jsc-zen3
EB_ARGS="--installpath=/tmp/$USER/ecpr-22922"

Thyre · 2025-10-13T13:27:00Z

Test report by @Thyre
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
ZAM054 - Linux Zorin OS 17, x86_64, 12th Gen Intel(R) Core(TM) i7-1260P, 1 x NVIDIA NVIDIA GeForce MX550, 580.65.06, Python 3.10.12
See https://gist.github.com/Thyre/cee20247aed8c8481238f07e8853e4ef for a full test report.

boegelbot · 2025-10-13T13:30:17Z

@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=22922 EB_ARGS="--installpath=/tmp/$USER/ecpr-22922" EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_22922 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 8328

Test results coming soon (I hope)...

Details

- notification for comment with ID 3397528863 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).

boegelbot · 2025-10-13T13:32:00Z

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 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/2f5aac63afb9877a1239aec17347ae56 for a full test report.

….0.eb Co-authored-by: Sam Moors <[email protected]>

akesandgren · 2025-10-13T13:37:30Z

Test report by @akesandgren
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
b-cn1613.hpc2n.umu.se - Linux Ubuntu 22.04, x86_64, AMD EPYC 7313 16-Core Processor, Python 3.10.12
See https://gist.github.com/akesandgren/74c5856669011eec2bddcbcf712f9367 for a full test report.

boegel · 2025-10-14T06:08:32Z

+]
+
+builddependencies = [
+    ('binutils', '2.42'),


no need for binutils build dependency when using GCC toolchain

Suggested change

('binutils', '2.42'),

('binutils', '2.42'),

boegel · 2025-10-14T06:09:46Z

+         try:
+             if dms:
+-               if re.search("\.sam", self.filename):
+               if re.search(".sam", self.filename):


@smoors Can you apply this suggestion, and then also fix the checksum for the patch file, test & merge?

akesandgren

LGTM

akesandgren · 2025-10-14T08:55:51Z

Test report by @akesandgren
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
b-cn1613.hpc2n.umu.se - Linux Ubuntu 22.04, x86_64, AMD EPYC 7313 16-Core Processor, Python 3.10.12
See https://gist.github.com/akesandgren/20c3aa95cda6624a58af838fa6b111a3 for a full test report.

Changes implemented

akesandgren · 2025-10-14T08:57:27Z

@boegelbot Please test @ jsc-zen3

boegelbot · 2025-10-14T09:00:16Z

@akesandgren: 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=22922 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_22922 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 8349

Test results coming soon (I hope)...

Details

- notification for comment with ID 3400802386 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).

boegelbot · 2025-10-14T09:01:31Z

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/eed68c9758d0e21d3bf486e61d77fccd for a full test report.

akesandgren · 2025-10-14T09:17:30Z

Going in, thanks @fizwit!

{bio}[GCC-13.3.0] ShapeMapper2 2.3

f1b306b

github-actions Bot added the new label May 20, 2025

fizwit mentioned this pull request May 21, 2025

add EasyBuild install method Weeks-UNC/shapemapper2#71

Open

smoors reviewed May 22, 2025

View reviewed changes

Thyre added the 2024a issues & PRs related to 2024a common toolchains label Aug 18, 2025

Thyre added the ready-to-review label Oct 13, 2025

Update easybuild/easyconfigs/s/ShapeMapper2/ShapeMapper2-2.3-GCC-13.3…

624dfd5

….0.eb Co-authored-by: Sam Moors <[email protected]>

akesandgren self-assigned this Oct 13, 2025

boegel previously requested changes Oct 14, 2025

View reviewed changes

updates

650a5e4

akesandgren approved these changes Oct 14, 2025

View reviewed changes

akesandgren added this to the next release (5.2.0?) milestone Oct 14, 2025

akesandgren merged commit df0fdbd into easybuilders:develop Oct 14, 2025
8 checks passed

	+ if re.search(".sam", self.filename):
	+ if re.search(r"\.sam", self.filename):

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fizwit commented May 20, 2025

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fizwit Jul 11, 2025 •

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