Bug#981636: python3-hdf5storage: fails with h5py 3: ValueError: data type must provide an itemsize

[Drew Parsons]

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