Bug 2345530 - 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
Summary: python-bioread fails to build with Python 3.14: help2man: can't get `--help' ...
Keywords:
Status: CLOSED WORKSFORME
Alias: None
Product: Fedora
Classification: Fedora
Component: python-bioread
Version: rawhide
Hardware: Unspecified
OS: Unspecified
unspecified
unspecified
Target Milestone: ---
Assignee: Ben Beasley
QA Contact:
URL:
Whiteboard:
Depends On: 2345536
Blocks: PYTHON3.14
TreeView+ depends on / blocked
 
Reported: 2025-02-13 11:50 UTC by Karolina Surma
Modified: 2025-03-14 12:52 UTC (History)
4 users (show)

Fixed In Version:
Clone Of:
Environment:
Last Closed: 2025-03-14 12:52:10 UTC
Type: Bug
Embargoed:


Attachments (Terms of Use)

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.


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