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arf.open_file(fn, mode="a") fails with h5py 3.3 #8

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bnavigator opened this issue Jul 1, 2021 · 2 comments · Fixed by #10
Closed

arf.open_file(fn, mode="a") fails with h5py 3.3 #8

bnavigator opened this issue Jul 1, 2021 · 2 comments · Fixed by #10

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@bnavigator
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The internals of h5py have changed, and arf's usage of private _hl fails now:

...
[   16s] python39-h5py-3.3.0-1.1               ########################################
...
[   19s] + PYTHONPATH=/home/abuild/rpmbuild/BUILDROOT/python-arf-2.6.1-1.4.x86_64/usr/lib/python3.9/site-packages
[   19s] + PYTHONDONTWRITEBYTECODE=1
[   19s] + pytest-3.9 --ignore=_build. --ignore=_build.python39 --ignore=_build.python38 -v
...
[   20s] =================================== FAILURES ===================================
[   20s] ____________________ TestArfNavigation.test01_creation_iter ____________________
[   20s] 
[   20s] self = <tests.test_arf.TestArfNavigation testMethod=test01_creation_iter>
[   20s] 
[   20s]     def test01_creation_iter(self):
[   20s] >       self.fp = arf.open_file("test06", mode="a", driver="core", backing_store=False)
[   20s] 
[   20s] tests/test_arf.py:162: 
[   20s] _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
[   20s] arf.py:78: in open_file
[   20s]     fp = files.File(files.make_fid(name, mode, userblock_size, fapl, fcpl))
[   20s] /usr/lib64/python3.9/site-packages/h5py/_hl/files.py:211: in make_fid
[   20s]     fid = h5f.open(name, h5f.ACC_RDWR, fapl=fapl)
[   20s] h5py/_objects.pyx:54: in h5py._objects.with_phil.wrapper
[   20s]     ???
[   20s] h5py/_objects.pyx:55: in h5py._objects.with_phil.wrapper
[   20s]     ???
[   20s] _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
[   20s] 
[   20s] >   ???
[   20s] E   OSError: Unable to open file (unable to open file)
[   20s] 
[   20s] h5py/h5f.pyx:100: OSError
@dmeliza
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dmeliza commented Jul 2, 2021

Thanks for catching this. For now, I'm just going to pin the h5py dependency, but I'll leave the issue open in case you or someone else wants to submit a pull request.

bmwiedemann pushed a commit to bmwiedemann/openSUSE that referenced this issue Jul 8, 2021
https://build.opensuse.org/request/show/904652
by user mcepl + dimstar_suse
- Skip failing test test01_creation_iter (gh#melizalab/arf#8).
@bnavigator
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This was fixed in h5py 3.4

bnavigator added a commit to bnavigator/arf that referenced this issue Apr 3, 2022
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2 participants