Bug 2345530

Summary:	python-bioread fails to build with Python 3.14: help2man: can't get `--help' info from /builddir/build/BUILD/python-bioread-3.0.1-build/BUILDROOT/usr/bin/acq2hdf5
Product:	[Fedora] Fedora	Reporter:	Karolina Surma <ksurma>
Component:	python-bioread	Assignee:	Ben Beasley <code>
Status:	CLOSED WORKSFORME	QA Contact:
Severity:	unspecified	Docs Contact:
Priority:	unspecified
Version:	rawhide	CC:	code, ksurma, mhroncok, neuro-sig
Target Milestone:	---
Target Release:	---
Hardware:	Unspecified
OS:	Unspecified
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Fixed In Version:		Doc Type:	If docs needed, set a value
Doc Text:		Story Points:	---
Clone Of:		Environment:
Last Closed:	2025-03-14 12:52:10 UTC	Type:	Bug
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Documentation:	---	CRM:
Verified Versions:		Category:	---
oVirt Team:	---	RHEL 7.3 requirements from Atomic Host:
Cloudforms Team:	---	Target Upstream Version:
Embargoed:
Bug Depends On:	2345536
Bug Blocks:	2322407

Description Karolina Surma 2025-02-13 11:50:46 UTC

python-bioread fails to build with Python 3.14.05.

+ for bin in acq2hdf5 acq2mat acq2txt acq_info acq_markers
+ PYTHONPATH=/builddir/build/BUILD/python-bioread-3.0.1-build/BUILDROOT/usr/lib/python3.14/site-packages
+ help2man --no-info --version-string=3.0.1 --output=/builddir/build/BUILD/python-bioread-3.0.1-build/BUILDROOT/usr/share/man/man1/acq2hdf5.1 /builddir/build/BUILD/python-bioread-3.0.1-build/BUILDROOT/usr/bin/acq2hdf5
help2man: can't get `--help' info from /builddir/build/BUILD/python-bioread-3.0.1-build/BUILDROOT/usr/bin/acq2hdf5

https://docs.python.org/3.14/whatsnew/3.14.html

For the build logs, see:
https://copr-be.cloud.fedoraproject.org/results/@python/python3.14/fedora-rawhide-x86_64/08650967-python-bioread/

For all our attempts to build python-bioread with Python 3.14, see:
https://copr.fedorainfracloud.org/coprs/g/python/python3.14/package/python-bioread/

Testing and mass rebuild of packages is happening in copr.
You can follow these instructions to test locally in mock if your package builds with Python 3.14:
https://copr.fedorainfracloud.org/coprs/g/python/python3.14/

Let us know here if you have any questions.

Python 3.14 is planned to be included in Fedora 43.
To make that update smoother, we're building Fedora packages with all pre-releases of Python 3.14.
A build failure prevents us from testing all dependent packages (transitive [Build]Requires),
so if this package is required a lot, it's important for us to get it fixed soon.

We'd appreciate help from the people who know this package best,
but if you don't want to work on this now, let us know so we can try to work around it on our side.

Comment 1 Ben Beasley 2025-02-13 12:32:51 UTC

The root cause is h5py failing to import, which I have reported as bug 2345536.

# PYTHONPATH=/builddir/build/BUILD/python-bioread-3.0.1-build/BUILDROOT/usr/lib/python3.14/site-packages/ /builddir/build/BUILD/python-bioread-3.0.1-build/BUILDROOT/usr/bin/acq2hdf5 --help
Traceback (most recent call last):
  File "/builddir/build/BUILD/python-bioread-3.0.1-build/BUILDROOT/usr/bin/acq2hdf5", line 5, in <module>
    from bioread.runners.acq2hdf5 import main
  File "/builddir/build/BUILD/python-bioread-3.0.1-build/BUILDROOT/usr/lib/python3.14/site-packages/bioread/runners/acq2hdf5.py", line 50, in <module>
    import h5py
  File "/usr/lib64/python3.14/site-packages/h5py/__init__.py", line 45, in <module>
    from ._conv import register_converters as _register_converters, \
                       unregister_converters as _unregister_converters
  File "h5py/_conv.pyx", line 1, in init h5py._conv
  File "h5py/h5r.pyx", line 1, in init h5py.h5r
  File "h5py/h5p.pyx", line 1, in init h5py.h5p
  File "h5py/h5t.pyx", line 289, in init h5py.h5t
  File "h5py/h5t.pyx", line 281, in h5py.h5t._get_available_ftypes
ValueError: chr() arg not in range(0x110000)

Comment 2 Karolina Surma 2025-02-13 13:49:36 UTC

Thank you! I wouldn't have connected the dots and had h5py issue buried somewhere in my backlog.

Comment 3 Ben Beasley 2025-03-14 12:52:10 UTC

I see a successful build in https://copr.fedorainfracloud.org/coprs/g/python/python3.14/build/8750277/, so I guess the h5py issue must have been resolved.