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add back patch to fix hardcoded paths in setup.py for libxml2-python 2.12.10 + 2.14.3#25465

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ocaisa merged 1 commit intoeasybuilders:developfrom
boegel:20260228001143_new_pr_libxml2-python21210
Feb 27, 2026
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add back patch to fix hardcoded paths in setup.py for libxml2-python 2.12.10 + 2.14.3#25465
ocaisa merged 1 commit intoeasybuilders:developfrom
boegel:20260228001143_new_pr_libxml2-python21210

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@boegel boegel commented Feb 27, 2026 •
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(created using eb --new-pr)

fix for build problems like this:

libxml.c: In function 'libxml_xmlSAXParseFile':
  libxml.c:1423:12: error: implicit declaration of function 'xmlNewSAXParserCtxt'; did you mean 'xmlNewParserCtxt'? [-Wimplicit-function-declaration]
   1423 |     ctxt = xmlNewSAXParserCtxt(SAX, pyobj_SAX);
        |            ^~~~~~~~~~~~~~~~~~~
        |            xmlNewParserCtxt

This happens because use -I/usr/include/libxml2 is hardcoded, which means trouble if there's a system-wide libxml2 installation.
In my case, there was:

$ rpm -qa | grep libxml2
libxml2-2.9.13-12.el9_6.1.x86_64
libxml2-devel-2.9.13-12.el9_6.1.x86_64
python3-libxml2-2.9.13-12.el9_6.1.x86_64

@github-actions github-actions Bot added 2024a issues & PRs related to 2024a common toolchains 2025b issues & PRs related to 2025b common toolchains change labels Feb 27, 2026
@boegel boegel added bug fix and removed change labels Feb 27, 2026
@boegel boegel added this to the next release (5.2.2?) milestone Feb 27, 2026
@boegel boegel requested a review from ocaisa February 27, 2026 23:14
@boegel boegel mentioned this pull request Feb 27, 2026
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boegel commented Feb 27, 2026

Test report by @boegel
SUCCESS
Build succeeded for 2 out of 2 (total: 2 mins 11 secs) (2 easyconfigs in total)
node4414.skiddo.os - Linux RHEL 9.6, x86_64, AMD EPYC 9755 128-Core Processor (zen5), Python 3.9.21
See https://gist.github.com/boegel/8d08db60f9856eb35b53c5908f9242b7 for a full test report.

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Micket approved these changes Feb 27, 2026
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lgtm

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Micket commented Feb 27, 2026

@boegelbot please test @ jsc-zen3

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Patch still doing the business 7 years later!

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ocaisa commented Feb 27, 2026

@boegelbot please test @ jsc-zen3

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boegel commented Feb 27, 2026

Patch still doing the business 7 years later!

Sure is, not sure why it was omitted...

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boegel commented Feb 27, 2026

@boegelbot please test @ jsc-zen3

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boegelbot commented Feb 27, 2026

@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=25465 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_25465 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

  • exit code: 0
  • output:
Submitted batch job 9900

Test results coming soon (I hope)...

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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 Feb 27, 2026

Test report by @boegelbot
SUCCESS
Build succeeded for 2 out of 2 (total: 2 mins 52 secs) (2 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.7, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.23
See https://gist.github.com/boegelbot/987d29febbf74ac58bae2e081058b9de for a full test report.

@ocaisa ocaisa merged commit c4136b8 into easybuilders:develop Feb 27, 2026
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@boegel boegel deleted the 20260228001143_new_pr_libxml2-python21210 branch February 27, 2026 23:44
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