Your message dated Wed, 24 Mar 2021 22:48:29 +0000
with message-id <[email protected]>
and subject line Bug#981636: fixed in python-hdf5storage 0.1.17-1
has caused the Debian Bug report #981636,
regarding python3-hdf5storage: fails with h5py 3: ValueError: data type must
provide an itemsize
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
981636: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=981636
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: python3-hdf5storage
Version: 0.1.15+git20200608.09dfc5f-1
Severity: important
Control: forwarded -1 https://github.com/frejanordsiek/hdf5storage/issues/102
After the next stable is released, h5py will be upgraded to v3.
h5py 3 breaks the API, so client packages including python-hdf5storage
will need to be updated (other packages already have already been patched).
The error looks like:
ERROR: test_write_readback.TestPythonMatlabFormat.test_slice
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/python3/dist-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "/tmp/autopkgtest.PRwLn9/autopkgtest_tmp/tests/test_write_readback.py",
line 769, in test_slice
out = self.write_readback(data, random_name(),
File "/tmp/autopkgtest.PRwLn9/autopkgtest_tmp/tests/test_write_readback.py",
line 120, in write_readback
out = hdf5storage.read(path=name_r, filename=filename,
File "/usr/lib/python3/dist-packages/hdf5storage/__init__.py", line 2340, in
read
return f.read(path)
File "/usr/lib/python3/dist-packages/hdf5storage/__init__.py", line 1857, in
read
return self.reads((path, ))[0]
File "/usr/lib/python3/dist-packages/hdf5storage/__init__.py", line 1921, in
reads
datas.append(utilities.read_data(self._file,
File "/usr/lib/python3/dist-packages/hdf5storage/utilities.py", line 212, in
read_data
attributes = collections.defaultdict(defaultfactory,
File "/usr/lib/python3/dist-packages/h5py/_debian_h5py_serial/_hl/base.py",
line 432, in __iter__
yield (key, self._mapping.get(key))
File "/usr/lib/python3.9/_collections_abc.py", line 762, in get
return self[key]
File "h5py/_debian_h5py_serial/_objects.pyx", line 54, in
h5py._debian_h5py_serial._objects.with_phil.wrapper
File "h5py/_debian_h5py_serial/_objects.pyx", line 55, in
h5py._debian_h5py_serial._objects.with_phil.wrapper
File "/usr/lib/python3/dist-packages/h5py/_debian_h5py_serial/_hl/attrs.py",
line 77, in __getitem__
attr.read(arr, mtype=htype)
File "h5py/_debian_h5py_serial/_objects.pyx", line 54, in
h5py._debian_h5py_serial._objects.with_phil.wrapper
File "h5py/_debian_h5py_serial/_objects.pyx", line 55, in
h5py._debian_h5py_serial._objects.with_phil.wrapper
File "h5py/_debian_h5py_serial/h5a.pyx", line 362, in
h5py._debian_h5py_serial.h5a.AttrID.read
File "h5py/_debian_h5py_serial/_proxy.pyx", line 61, in
h5py._debian_h5py_serial._proxy.attr_rw
File "h5py/_debian_h5py_serial/_conv.pyx", line 659, in
h5py._debian_h5py_serial._conv.vlen2ndarray
File "h5py/_debian_h5py_serial/_conv.pyx", line 717, in
h5py._debian_h5py_serial._conv.conv_vlen2ndarray
ValueError: data type must provide an itemsize
Reported upstream:
https://github.com/frejanordsiek/hdf5storage/issues/101
https://github.com/frejanordsiek/hdf5storage/issues/102
-- System Information:
Debian Release: bullseye/sid
APT prefers unstable
APT policy: (500, 'unstable'), (1, 'experimental')
Architecture: amd64 (x86_64)
Foreign Architectures: i386
Kernel: Linux 5.10.0-2-amd64 (SMP w/8 CPU threads)
Kernel taint flags: TAINT_OOT_MODULE
Locale: LANG=en_AU.UTF-8, LC_CTYPE=en_AU.UTF-8 (charmap=UTF-8),
LANGUAGE=en_AU:en
Shell: /bin/sh linked to /usr/bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled
Versions of packages python3-hdf5storage depends on:
ii python3 3.9.1-1
ii python3-h5py 3.1.0-1exp1
ii python3-h5py-serial 3.1.0-1exp1
ii python3-numpy 1:1.19.5-1
ii python3-pkg-resources 51.3.3-1
python3-hdf5storage recommends no packages.
Versions of packages python3-hdf5storage suggests:
pn python-hdf5storage-doc <none>
-- no debconf information
--- End Message ---
--- Begin Message ---
Source: python-hdf5storage
Source-Version: 0.1.17-1
Done: Drew Parsons <[email protected]>
We believe that the bug you reported is fixed in the latest version of
python-hdf5storage, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Drew Parsons <[email protected]> (supplier of updated python-hdf5storage
package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Wed, 24 Mar 2021 23:14:14 +0100
Source: python-hdf5storage
Architecture: source
Version: 0.1.17-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Science Maintainers
<[email protected]>
Changed-By: Drew Parsons <[email protected]>
Closes: 981636
Changes:
python-hdf5storage (0.1.17-1) unstable; urgency=medium
.
* Team upload.
* New upstream release.
- fixes usage with h5py 3. Closes: #981636.
* debian/tests: show test output (verbose -v)
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--- End Message ---
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