Bug 1794277

Summary: python-nibabel fails to build with numpy 1.18
Product: [Fedora] Fedora Reporter: Miro Hrončok <mhroncok>
Component: python-nibabelAssignee: Igor Raits <igor.raits>
Status: CLOSED RAWHIDE QA Contact: Fedora Extras Quality Assurance <extras-qa>
Severity: unspecified Docs Contact:
Priority: unspecified    
Version: rawhideCC: cstratak, igor.raits, mhroncok, neuro-sig, sanjay.ankur
Target Milestone: ---   
Target Release: ---   
Hardware: Unspecified   
OS: Unspecified   
Whiteboard:
Fixed In Version: Doc Type: If docs needed, set a value
Doc Text:
Story Points: ---
Clone Of: Environment:
Last Closed: 2020-02-02 19:40:32 UTC Type: Bug
Regression: --- Mount Type: ---
Documentation: --- CRM:
Verified Versions: Category: ---
oVirt Team: --- RHEL 7.3 requirements from Atomic Host:
Cloudforms Team: --- Target Upstream Version:
Bug Depends On:    
Bug Blocks: 1750908, 1785415    
Attachments:
Description Flags
Build log for py3.9 copr attached. none

Description Miro Hrončok 2020-01-23 07:52:20 UTC
python-nibabel fails to build with Python 3.9.0a2.

Traceback (most recent call last):
  File "/usr/lib/python3.9/site-packages/nose/case.py", line 197, in runTest
    self.test(*self.arg)
  File "/builddir/build/BUILD/nibabel-2.5.1/nibabel/tests/test_minc1.py", line 144, in test_old_namespace
    mf = MincFile(netcdf_file(EG_FNAME))
  File "/builddir/build/BUILD/nibabel-2.5.1/nibabel/externals/netcdf.py", line 238, in __init__
    self._read()
  File "/builddir/build/BUILD/nibabel-2.5.1/nibabel/externals/netcdf.py", line 528, in _read
    self._read_var_array()
  File "/builddir/build/BUILD/nibabel-2.5.1/nibabel/externals/netcdf.py", line 614, in _read_var_array
    data = ndarray.__new__(ndarray, shape, dtype=dtype_,
ValueError: Non-string object detected for the array ordering. Please pass in 'C', 'F', 'A', or 'K' instead

This seems like a numpy problem, rather than Python 3.9

For the build logs, see:
https://copr-be.cloud.fedoraproject.org/results/@python/python3.9/fedora-rawhide-x86_64/01176515-python-nibabel/

For all our attempts to build python-nibabel with Python 3.9, see:
https://copr.fedorainfracloud.org/coprs/g/python/python3.9/package/python-nibabel/

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 3.9:
https://copr.fedorainfracloud.org/coprs/g/python/python3.9/

Let us know here if you have any questions.

Python 3.9 will be included in Fedora 33. To make that update smoother, we're building Fedora packages with early pre-releases of Python 3.9.
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 Ankur Sinha (FranciscoD) 2020-02-02 19:40:11 UTC
Created attachment 1657207 [details]
Build log for py3.9 copr attached.

I updated nibabel to the newest version, and it builds fine with python3.9, and numpy from the COPR too.

Build log attached.